Commit a7a3476c1d675c695e792541d685809feb059775 - bio-tradis

New upstream version 1.4.5+dfsg2 Michael R. Crusoe 4 years ago

48 changed file(s) with 4068 addition(s) and 637 deletion(s). Raw diff Collapse all Expand all

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~~.gitattributes~~ less more

0		.bam filter=lfs diff=lfs merge=lfs -text
1		samples/sample_lg_tr.bam filter=lfs diff=lfs merge=lfs -text
2		sample_lg_tr.bam filter=lfs diff=lfs merge=lfs -text

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~~.gitignore~~ less more

0		blib/
1		.build/
2		_build/
3		build/
4		cover_db/
5		inc/
6		Build
7		!Build/
8		Build.bat
9		.last_cover_stats
10		Makefile
11		Makefile.old
12		MANIFEST.bak
13		META.yml
14		MYMETA.yml
15		nytprof.out
16		pm_to_blib
17		Bio-Tradis-*
18		.DS_Store
19		*.tar.gz
20		*.swp

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~~.travis.yml~~ less more

0		sudo: required
1		services:
2		- docker
3		install:
4		- docker pull sangerpathogens/bio-tradis
5		script:
6		- docker run --rm -it sangerpathogens/bio-tradis /bin/bash -c "git clone https://github.com/sanger-pathogens/Bio-Tradis.git && cd Bio-Tradis && dzil test"

+680

-0

LICENSE less more

	0	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
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	2	This is free software, licensed under:
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	4	The GNU General Public License, Version 3, June 2007
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	615	SUCH DAMAGES.
	616
	617	17. Interpretation of Sections 15 and 16.
	618
	619	If the disclaimer of warranty and limitation of liability provided
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	623	Program, unless a warranty or assumption of liability accompanies a
	624	copy of the Program in return for a fee.
	625
	626	END OF TERMS AND CONDITIONS
	627
	628	How to Apply These Terms to Your New Programs
	629
	630	If you develop a new program, and you want it to be of the greatest
	631	possible use to the public, the best way to achieve this is to make it
	632	free software which everyone can redistribute and change under these terms.
	633
	634	To do so, attach the following notices to the program. It is safest
	635	to attach them to the start of each source file to most effectively
	636	state the exclusion of warranty; and each file should have at least
	637	the "copyright" line and a pointer to where the full notice is found.
	638
	639	<one line to give the program's name and a brief idea of what it does.>
	640	Copyright (C) <year> <name of author>
	641
	642	This program is free software: you can redistribute it and/or modify
	643	it under the terms of the GNU General Public License as published by
	644	the Free Software Foundation, either version 3 of the License, or
	645	(at your option) any later version.
	646
	647	This program is distributed in the hope that it will be useful,
	648	but WITHOUT ANY WARRANTY; without even the implied warranty of
	649	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	650	GNU General Public License for more details.
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	652	You should have received a copy of the GNU General Public License
	653	along with this program. If not, see <http://www.gnu.org/licenses/>.
	654
	655	Also add information on how to contact you by electronic and paper mail.
	656
	657	If the program does terminal interaction, make it output a short
	658	notice like this when it starts in an interactive mode:
	659
	660	<program> Copyright (C) <year> <name of author>
	661	This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
	662	This is free software, and you are welcome to redistribute it
	663	under certain conditions; type `show c' for details.
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	665	The hypothetical commands `show w' and `show c' should show the appropriate
	666	parts of the General Public License. Of course, your program's commands
	667	might be different; for a GUI interface, you would use an "about box".
	668
	669	You should also get your employer (if you work as a programmer) or school,
	670	if any, to sign a "copyright disclaimer" for the program, if necessary.
	671	For more information on this, and how to apply and follow the GNU GPL, see
	672	<http://www.gnu.org/licenses/>.
	673
	674	The GNU General Public License does not permit incorporating your program
	675	into proprietary programs. If your program is a subroutine library, you
	676	may consider it more useful to permit linking proprietary applications with
	677	the library. If this is what you want to do, use the GNU Lesser General
	678	Public License instead of this License. But first, please read
	679	<http://www.gnu.org/philosophy/why-not-lgpl.html>.

+194

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MANIFEST less more

	0	# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.012.
	1	AUTHORS
	2	BioTraDISTutorial.pdf
	3	CHANGELOG.md
	4	Dockerfile
	5	LICENSE
	6	MANIFEST
	7	META.json
	8	META.yml
	9	Makefile.PL
	10	README
	11	README.md
	12	_config.yml
	13	bcinstall.log
	14	bin/add_tradis_tags
	15	bin/bacteria_tradis
	16	bin/check_tradis_tags
	17	bin/combine_tradis_plots
	18	bin/filter_tradis_tags
	19	bin/remove_tradis_tags
	20	bin/tradis_comparison.R
	21	bin/tradis_essentiality.R
	22	bin/tradis_gene_insert_sites
	23	bin/tradis_merge_plots
	24	bin/tradis_plot
	25	build/bwa-0.7.17.tbz
	26	build/samtools-1.3.tbz
	27	build/smalt-0.7.6.tgz
	28	build/tabix-master.tgz
	29	dist.ini
	30	install_dependencies.sh
	31	lib/Bio/Tradis.pm
	32	lib/Bio/Tradis/AddTagsToSeq.pm
	33	lib/Bio/Tradis/Analysis/Exceptions.pm
	34	lib/Bio/Tradis/Analysis/InsertSite.pm
	35	lib/Bio/Tradis/CombinePlots.pm
	36	lib/Bio/Tradis/CommandLine/AddTags.pm
	37	lib/Bio/Tradis/CommandLine/CheckTags.pm
	38	lib/Bio/Tradis/CommandLine/FilterFastqTags.pm
	39	lib/Bio/Tradis/CommandLine/PlotCombine.pm
	40	lib/Bio/Tradis/CommandLine/PlotTradis.pm
	41	lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm
	42	lib/Bio/Tradis/CommandLine/RunMapping.pm
	43	lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
	44	lib/Bio/Tradis/CommandLine/TradisBam.pm
	45	lib/Bio/Tradis/DetectTags.pm
	46	lib/Bio/Tradis/Exception.pm
	47	lib/Bio/Tradis/FilterTags.pm
	48	lib/Bio/Tradis/Map.pm
	49	lib/Bio/Tradis/Parser/Bam.pm
	50	lib/Bio/Tradis/Parser/Cigar.pm
	51	lib/Bio/Tradis/Parser/Fastq.pm
	52	lib/Bio/Tradis/RemoveTags.pm
	53	lib/Bio/Tradis/RunTradis.pm
	54	lib/Bio/Tradis/Samtools.pm
	55	lib/Bio/Tradis/TradisPlot.pm
	56	recipes/Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml
	57	recipes/Tradis_adapter_primers.xlsx
	58	recipes/Transposon10/Chemistry/Chemistry.xml
	59	recipes/Transposon10/Exposures/Sony.xml
	60	recipes/Transposon10/Exposures/SonyV2.xml
	61	recipes/Transposon10/Protocol/1Read1Index.xml
	62	recipes/Transposon10/Protocol/1Read2Index.xml
	63	recipes/Transposon10/Protocol/2Read1Index.xml
	64	recipes/Transposon10/Protocol/2Read2Index.xml
	65	recipes/Transposon10/Reads/Reads.xml
	66	recipes/Transposon10/Reagents/MaintenanceWash.xml
	67	recipes/Transposon10/Reagents/PostRunWash.xml
	68	recipes/Transposon10/Reagents/Sequencing.xml
	69	recipes/Transposon10/Wash/LineWash.xml
	70	recipes/Transposon10/Wash/MaintenanceWash.xml
	71	recipes/Transposon10/Wash/PostRunWash.xml
	72	recipes/Transposon10/Wash/PostRunWashOriginal.xml
	73	recipes/Transposon10/Wash/StandbyWash.xml
	74	recipes/Transposon12/Chemistry/Chemistry.xml
	75	recipes/Transposon12/Exposures/Sony.xml
	76	recipes/Transposon12/Exposures/SonyV2.xml
	77	recipes/Transposon12/Protocol/1Read1Index.xml
	78	recipes/Transposon12/Protocol/1Read2Index.xml
	79	recipes/Transposon12/Protocol/2Read1Index.xml
	80	recipes/Transposon12/Protocol/2Read2Index.xml
	81	recipes/Transposon12/Reads/Reads.xml
	82	recipes/Transposon12/Reagents/MaintenanceWash.xml
	83	recipes/Transposon12/Reagents/PostRunWash.xml
	84	recipes/Transposon12/Reagents/Sequencing.xml
	85	recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx
	86	recipes/Transposon12/Wash/LineWash.xml
	87	recipes/Transposon12/Wash/MaintenanceWash.xml
	88	recipes/Transposon12/Wash/PostRunWash.xml
	89	recipes/Transposon12/Wash/PostRunWashOriginal.xml
	90	recipes/Transposon12/Wash/StandbyWash.xml
	91	software_license
	92	source_path
	93	t/00-report-prereqs.dd
	94	t/00-report-prereqs.t
	95	t/Bio/Tradis/AddTagsToSeq.t
	96	t/Bio/Tradis/Analysis/InsertSite.t
	97	t/Bio/Tradis/CombinePlots.t
	98	t/Bio/Tradis/CommandLine/TradisAnalysis.t
	99	t/Bio/Tradis/DetectTags.t
	100	t/Bio/Tradis/FilterTags.t
	101	t/Bio/Tradis/Map.t
	102	t/Bio/Tradis/Parser/Bam.t
	103	t/Bio/Tradis/Parser/Cigar.t
	104	t/Bio/Tradis/Parser/Fastq.t
	105	t/Bio/Tradis/RemoveTags.t
	106	t/Bio/Tradis/RunTradisBWA.t
	107	t/Bio/Tradis/RunTradisSmalt.t
	108	t/Bio/Tradis/RunTradisTaglessBwa.t
	109	t/Bio/Tradis/RunTradisTaglessSmalt.t
	110	t/Bio/Tradis/TradisPlot.t
	111	t/data/AddTags/expected_tradis.bam
	112	t/data/AddTags/expected_tradis.cram
	113	t/data/AddTags/sample_sm_no_tr.bam
	114	t/data/AddTags/sample_sm_tr.bam
	115	t/data/AddTags/sample_sm_tr.cram
	116	t/data/CombinePlots/comb_expected.stats
	117	t/data/CombinePlots/comb_sample.txt
	118	t/data/CombinePlots/first.expected.plot
	119	t/data/CombinePlots/sample1.sm.plot.gz
	120	t/data/CombinePlots/sample2.sm.plot.gz
	121	t/data/CombinePlots/second.expected.plot
	122	t/data/CombinePlots/tabix_sorted.insert_site_plot.gz
	123	t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi
	124	t/data/CombinePlots/test1.plot
	125	t/data/CombinePlots/test2.plot
	126	t/data/CombinePlots/test3.plot
	127	t/data/CombinePlots/test4.plot
	128	t/data/CombinePlots/zip_comb_exp.plot
	129	t/data/CombinePlots/zip_comb_exp.stats
	130	t/data/CombinePlots/zip_comb_list.txt
	131	t/data/CommandLine/fastq.list
	132	t/data/CommandLine/test_1.fastq
	133	t/data/CommandLine/test_2.fastq
	134	t/data/DetectTags/AE004091.fasta
	135	t/data/DetectTags/AE004091.fasta.fai
	136	t/data/DetectTags/sample_sm_no_tr.bam
	137	t/data/DetectTags/sample_sm_tr.bam
	138	t/data/DetectTags/sample_sm_tr.cram
	139	t/data/FilterTags/expected.1mm.caa.fastq
	140	t/data/FilterTags/expected.caa.fastq
	141	t/data/FilterTags/expected.tna.fastq
	142	t/data/FilterTags/sample.fastq
	143	t/data/FilterTags/sample.fastq.gz
	144	t/data/InsertSite/2_reads.bam
	145	t/data/InsertSite/small_multi_sequence.bam
	146	t/data/Map/expected.bwa.mapped
	147	t/data/Map/expected.smalt.mapped
	148	t/data/Map/smallref.fa
	149	t/data/Map/test.fastq
	150	t/data/Parsers/test.bam
	151	t/data/Parsers/test.fastq
	152	t/data/RemoveTags/expected.rm.1mm.caa.fastq
	153	t/data/RemoveTags/expected.rm.caa.fastq
	154	t/data/RemoveTags/expected.rm.tna.fastq
	155	t/data/RemoveTags/sample.caa.fastq
	156	t/data/RemoveTags/sample.tna.fastq
	157	t/data/RunTradisBWA/expected.1mm.plot.gz
	158	t/data/RunTradisBWA/expected.plot.gz
	159	t/data/RunTradisBWA/filelist.txt
	160	t/data/RunTradisBWA/filtered.fastq
	161	t/data/RunTradisBWA/mapped.sam
	162	t/data/RunTradisBWA/notags.fastq
	163	t/data/RunTradisBWA/smallref.fa
	164	t/data/RunTradisBWA/test.tagged.fastq
	165	t/data/RunTradisBWA/test.tagged.fastq.gz
	166	t/data/RunTradisBWA/test2.tagged.fastq
	167	t/data/RunTradisBWA/test2.tagged.fastq.gz
	168	t/data/RunTradisSmalt/expected.1mm.plot.gz
	169	t/data/RunTradisSmalt/expected.plot.gz
	170	t/data/RunTradisSmalt/filelist.txt
	171	t/data/RunTradisSmalt/filtered.fastq
	172	t/data/RunTradisSmalt/mapped.sam
	173	t/data/RunTradisSmalt/notags.fastq
	174	t/data/RunTradisSmalt/smallref.fa
	175	t/data/RunTradisSmalt/test.tagged.fastq
	176	t/data/RunTradisSmalt/test.tagged.fastq.gz
	177	t/data/RunTradisSmalt/test2.tagged.fastq
	178	t/data/RunTradisSmalt/test2.tagged.fastq.gz
	179	t/data/RunTradisTaglessBWA/expected.plot.gz
	180	t/data/RunTradisTaglessBWA/filelist.txt
	181	t/data/RunTradisTaglessBWA/mapped.sam
	182	t/data/RunTradisTaglessBWA/notags.fastq
	183	t/data/RunTradisTaglessBWA/smallref.fa
	184	t/data/RunTradisTaglessSmalt/expected.plot.gz
	185	t/data/RunTradisTaglessSmalt/mapped.sam
	186	t/data/RunTradisTaglessSmalt/notags.fastq
	187	t/data/RunTradisTaglessSmalt/smallref.fa
	188	t/data/TradisPlot/expected.plot.gz
	189	t/data/TradisPlot/sample.fastq
	190	t/data/TradisPlot/test.mapped.bam
	191	t/requires_external.t
	192	xt/author/00-compile.t
	193	xt/author/pod-syntax.t

+654

-0

META.json less more

	0	{
	1	"abstract" : "Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308",
	2	"author" : [
	3	"Carla Cummins <path-help@sanger.ac.uk>"
	4	],
	5	"dynamic_config" : 0,
	6	"generated_by" : "Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010",
	7	"license" : [
	8	"gpl_3"
	9	],
	10	"meta-spec" : {
	11	"url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
	12	"version" : 2
	13	},
	14	"name" : "Bio-Tradis",
	15	"no_index" : {
	16	"directory" : [
	17	"eg",
	18	"examples",
	19	"inc",
	20	"share",
	21	"t",
	22	"xt"
	23	]
	24	},
	25	"prereqs" : {
	26	"configure" : {
	27	"requires" : {
	28	"ExtUtils::MakeMaker" : "0"
	29	}
	30	},
	31	"develop" : {
	32	"requires" : {
	33	"File::Spec" : "0",
	34	"IO::Handle" : "0",
	35	"IPC::Open3" : "0",
	36	"Test::More" : "0",
	37	"Test::Pod" : "1.41",
	38	"perl" : "5.006"
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	40	},
	41	"runtime" : {
	42	"requires" : {
	43	"Bio::Seq" : "0",
	44	"Bio::SeqIO" : "0",
	45	"Cwd" : "0",
	46	"Data::Dumper" : "0",
	47	"Exception::Class" : "0",
	48	"File::Basename" : "0",
	49	"File::Path" : "0",
	50	"File::Spec" : "0",
	51	"File::Temp" : "0",
	52	"FindBin" : "0",
	53	"Getopt::Long" : "0",
	54	"Moose" : "0",
	55	"Text::CSV" : "0",
	56	"Try::Tiny" : "0",
	57	"strict" : "0",
	58	"warnings" : "0"
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	61	"test" : {
	62	"recommends" : {
	63	"CPAN::Meta" : "2.120900"
	64	},
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	67	"ExtUtils::MakeMaker" : "0",
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	69	"Test::Exception" : "0",
	70	"Test::Files" : "0",
	71	"Test::More" : "0",
	72	"Test::Most" : "0"
	73	}
	74	}
	75	},
	76	"provides" : {
	77	"Bio::Tradis" : {
	78	"file" : "lib/Bio/Tradis.pm",
	79	"version" : "v1.4.5"
	80	},
	81	"Bio::Tradis::AddTagsToSeq" : {
	82	"file" : "lib/Bio/Tradis/AddTagsToSeq.pm",
	83	"version" : "v1.4.5"
	84	},
	85	"Bio::Tradis::Analysis::Exceptions" : {
	86	"file" : "lib/Bio/Tradis/Analysis/Exceptions.pm",
	87	"version" : "v1.4.5"
	88	},
	89	"Bio::Tradis::Analysis::InsertSite" : {
	90	"file" : "lib/Bio/Tradis/Analysis/InsertSite.pm",
	91	"version" : "v1.4.5"
	92	},
	93	"Bio::Tradis::CombinePlots" : {
	94	"file" : "lib/Bio/Tradis/CombinePlots.pm",
	95	"version" : "v1.4.5"
	96	},
	97	"Bio::Tradis::CommandLine::AddTags" : {
	98	"file" : "lib/Bio/Tradis/CommandLine/AddTags.pm",
	99	"version" : "v1.4.5"
	100	},
	101	"Bio::Tradis::CommandLine::CheckTags" : {
	102	"file" : "lib/Bio/Tradis/CommandLine/CheckTags.pm",
	103	"version" : "v1.4.5"
	104	},
	105	"Bio::Tradis::CommandLine::FilterFastqTags" : {
	106	"file" : "lib/Bio/Tradis/CommandLine/FilterFastqTags.pm",
	107	"version" : "v1.4.5"
	108	},
	109	"Bio::Tradis::CommandLine::PlotCombine" : {
	110	"file" : "lib/Bio/Tradis/CommandLine/PlotCombine.pm",
	111	"version" : "v1.4.5"
	112	},
	113	"Bio::Tradis::CommandLine::PlotTradis" : {
	114	"file" : "lib/Bio/Tradis/CommandLine/PlotTradis.pm",
	115	"version" : "v1.4.5"
	116	},
	117	"Bio::Tradis::CommandLine::RemoveFastqTags" : {
	118	"file" : "lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm",
	119	"version" : "v1.4.5"
	120	},
	121	"Bio::Tradis::CommandLine::RunMapping" : {
	122	"file" : "lib/Bio/Tradis/CommandLine/RunMapping.pm",
	123	"version" : "v1.4.5"
	124	},
	125	"Bio::Tradis::CommandLine::TradisAnalysis" : {
	126	"file" : "lib/Bio/Tradis/CommandLine/TradisAnalysis.pm",
	127	"version" : "v1.4.5"
	128	},
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	132	},
	133	"Bio::Tradis::DetectTags" : {
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+482

-0

META.yml less more

	0	---
	1	abstract: 'Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308'
	2	author:
	3	- 'Carla Cummins <path-help@sanger.ac.uk>'
	4	build_requires:
	5	Env::Path: '0.18'
	6	ExtUtils::MakeMaker: '0'
	7	File::Spec: '0'
	8	Test::Exception: '0'
	9	Test::Files: '0'
	10	Test::More: '0'
	11	Test::Most: '0'
	12	configure_requires:
	13	ExtUtils::MakeMaker: '0'
	14	dynamic_config: 0
	15	generated_by: 'Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010'
	16	license: gpl
	17	meta-spec:
	18	url: http://module-build.sourceforge.net/META-spec-v1.4.html
	19	version: '1.4'
	20	name: Bio-Tradis
	21	no_index:
	22	directory:
	23	- eg
	24	- examples
	25	- inc
	26	- share
	27	- t
	28	- xt
	29	provides:
	30	Bio::Tradis:
	31	file: lib/Bio/Tradis.pm
	32	version: v1.4.5
	33	Bio::Tradis::AddTagsToSeq:
	34	file: lib/Bio/Tradis/AddTagsToSeq.pm
	35	version: v1.4.5
	36	Bio::Tradis::Analysis::Exceptions:
	37	file: lib/Bio/Tradis/Analysis/Exceptions.pm
	38	version: v1.4.5
	39	Bio::Tradis::Analysis::InsertSite:
	40	file: lib/Bio/Tradis/Analysis/InsertSite.pm
	41	version: v1.4.5
	42	Bio::Tradis::CombinePlots:
	43	file: lib/Bio/Tradis/CombinePlots.pm
	44	version: v1.4.5
	45	Bio::Tradis::CommandLine::AddTags:
	46	file: lib/Bio/Tradis/CommandLine/AddTags.pm
	47	version: v1.4.5
	48	Bio::Tradis::CommandLine::CheckTags:
	49	file: lib/Bio/Tradis/CommandLine/CheckTags.pm
	50	version: v1.4.5
	51	Bio::Tradis::CommandLine::FilterFastqTags:
	52	file: lib/Bio/Tradis/CommandLine/FilterFastqTags.pm
	53	version: v1.4.5
	54	Bio::Tradis::CommandLine::PlotCombine:
	55	file: lib/Bio/Tradis/CommandLine/PlotCombine.pm
	56	version: v1.4.5
	57	Bio::Tradis::CommandLine::PlotTradis:
	58	file: lib/Bio/Tradis/CommandLine/PlotTradis.pm
	59	version: v1.4.5
	60	Bio::Tradis::CommandLine::RemoveFastqTags:
	61	file: lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm
	62	version: v1.4.5
	63	Bio::Tradis::CommandLine::RunMapping:
	64	file: lib/Bio/Tradis/CommandLine/RunMapping.pm
	65	version: v1.4.5
	66	Bio::Tradis::CommandLine::TradisAnalysis:
	67	file: lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
	68	version: v1.4.5
	69	Bio::Tradis::CommandLine::TradisBam:
	70	file: lib/Bio/Tradis/CommandLine/TradisBam.pm
	71	version: v1.4.5
	72	Bio::Tradis::DetectTags:
	73	file: lib/Bio/Tradis/DetectTags.pm
	74	version: v1.4.5
	75	Bio::Tradis::Exception:
	76	file: lib/Bio/Tradis/Exception.pm
	77	version: v1.4.5
	78	Bio::Tradis::FilterTags:
	79	file: lib/Bio/Tradis/FilterTags.pm
	80	version: v1.4.5
	81	Bio::Tradis::Map:
	82	file: lib/Bio/Tradis/Map.pm
	83	version: v1.4.5
	84	Bio::Tradis::Parser::Bam:
	85	file: lib/Bio/Tradis/Parser/Bam.pm
	86	version: v1.4.5
	87	Bio::Tradis::Parser::Cigar:
	88	file: lib/Bio/Tradis/Parser/Cigar.pm
	89	version: v1.4.5
	90	Bio::Tradis::Parser::Fastq:
	91	file: lib/Bio/Tradis/Parser/Fastq.pm
	92	version: v1.4.5
	93	Bio::Tradis::RemoveTags:
	94	file: lib/Bio/Tradis/RemoveTags.pm
	95	version: v1.4.5
	96	Bio::Tradis::RunTradis:
	97	file: lib/Bio/Tradis/RunTradis.pm
	98	version: v1.4.5
	99	Bio::Tradis::Samtools:
	100	file: lib/Bio/Tradis/Samtools.pm
	101	version: v1.4.5
	102	Bio::Tradis::TradisPlot:
	103	file: lib/Bio/Tradis/TradisPlot.pm
	104	version: v1.4.5
	105	requires:
	106	Bio::Seq: '0'
	107	Bio::SeqIO: '0'
	108	Cwd: '0'
	109	Data::Dumper: '0'
	110	Exception::Class: '0'
	111	File::Basename: '0'
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	115	FindBin: '0'
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	117	Moose: '0'
	118	Text::CSV: '0'
	119	Try::Tiny: '0'
	120	strict: '0'
	121	warnings: '0'
	122	resources:
	123	homepage: http://www.sanger.ac.uk/
	124	repository: https://github.com/sanger-pathogens/Bio-Tradis.git
	125	version: 1.4.5
	126	x_Dist_Zilla:
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+100

-0

Makefile.PL less more

	0	# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.012.
	1	use strict;
	2	use warnings;
	3
	4
	5
	6	use ExtUtils::MakeMaker;
	7
	8	my %WriteMakefileArgs = (
	9	"ABSTRACT" => "Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308",
	10	"AUTHOR" => "Carla Cummins <path-help\@sanger.ac.uk>",
	11	"CONFIGURE_REQUIRES" => {
	12	"ExtUtils::MakeMaker" => 0
	13	},
	14	"DISTNAME" => "Bio-Tradis",
	15	"EXE_FILES" => [
	16	"bin/add_tradis_tags",
	17	"bin/bacteria_tradis",
	18	"bin/check_tradis_tags",
	19	"bin/combine_tradis_plots",
	20	"bin/filter_tradis_tags",
	21	"bin/remove_tradis_tags",
	22	"bin/tradis_comparison.R",
	23	"bin/tradis_essentiality.R",
	24	"bin/tradis_gene_insert_sites",
	25	"bin/tradis_merge_plots",
	26	"bin/tradis_plot"
	27	],
	28	"LICENSE" => "gpl",
	29	"NAME" => "Bio::Tradis",
	30	"PREREQ_PM" => {
	31	"Bio::Seq" => 0,
	32	"Bio::SeqIO" => 0,
	33	"Cwd" => 0,
	34	"Data::Dumper" => 0,
	35	"Exception::Class" => 0,
	36	"File::Basename" => 0,
	37	"File::Path" => 0,
	38	"File::Spec" => 0,
	39	"File::Temp" => 0,
	40	"FindBin" => 0,
	41	"Getopt::Long" => 0,
	42	"Moose" => 0,
	43	"Text::CSV" => 0,
	44	"Try::Tiny" => 0,
	45	"strict" => 0,
	46	"warnings" => 0
	47	},
	48	"TEST_REQUIRES" => {
	49	"Env::Path" => "0.18",
	50	"ExtUtils::MakeMaker" => 0,
	51	"File::Spec" => 0,
	52	"Test::Exception" => 0,
	53	"Test::Files" => 0,
	54	"Test::More" => 0,
	55	"Test::Most" => 0
	56	},
	57	"VERSION" => "1.4.5",
	58	"test" => {
	59	"TESTS" => "t/.t t/Bio/Tradis/.t t/Bio/Tradis/Analysis/.t t/Bio/Tradis/CommandLine/.t t/Bio/Tradis/Parser/*.t"
	60	}
	61	);
	62
	63
	64	my %FallbackPrereqs = (
	65	"Bio::Seq" => 0,
	66	"Bio::SeqIO" => 0,
	67	"Cwd" => 0,
	68	"Data::Dumper" => 0,
	69	"Env::Path" => "0.18",
	70	"Exception::Class" => 0,
	71	"ExtUtils::MakeMaker" => 0,
	72	"File::Basename" => 0,
	73	"File::Path" => 0,
	74	"File::Spec" => 0,
	75	"File::Temp" => 0,
	76	"FindBin" => 0,
	77	"Getopt::Long" => 0,
	78	"Moose" => 0,
	79	"Test::Exception" => 0,
	80	"Test::Files" => 0,
	81	"Test::More" => 0,
	82	"Test::Most" => 0,
	83	"Text::CSV" => 0,
	84	"Try::Tiny" => 0,
	85	"strict" => 0,
	86	"warnings" => 0
	87	);
	88
	89
	90	unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) {
	91	delete $WriteMakefileArgs{TEST_REQUIRES};
	92	delete $WriteMakefileArgs{BUILD_REQUIRES};
	93	$WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs;
	94	}
	95
	96	delete $WriteMakefileArgs{CONFIGURE_REQUIRES}
	97	unless eval { ExtUtils::MakeMaker->VERSION(6.52) };
	98
	99	WriteMakefile(%WriteMakefileArgs);

+42

-0

README less more

	0	NAME
	1
	2	Bio::Tradis - Bio-Tradis contains a set of tools to analyse the output
	3	from TraDIS analyses. For more information on the TraDIS method, see
	4	http://genome.cshlp.org/content/19/12/2308
	5
	6	VERSION
	7
	8	version 1.4.5
	9
	10	SYNOPSIS
	11
	12	Bio-Tradis provides functionality to:
	13
	14	* detect TraDIS tags in a BAM file - Bio::Tradis::DetectTags
	15
	16	* add the tags to the reads - Bio::Tradis::AddTagsToSeq
	17
	18	* filter reads in a FastQ file containing a user defined tag -
	19	Bio::Tradis::FilterTags
	20
	21	* remove tags - Bio::Tradis::RemoveTags
	22
	23	* map to a reference genome - Bio::Tradis::Map
	24
	25	* create an insertion site plot file - Bio::Tradis::TradisPlot
	26
	27	Most of these functions are available as standalone scripts or as perl
	28	modules.
	29
	30	AUTHOR
	31
	32	Carla Cummins <path-help@sanger.ac.uk>
	33
	34	COPYRIGHT AND LICENSE
	35
	36	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	37
	38	This is free software, licensed under:
	39
	40	The GNU General Public License, Version 3, June 2007
	41

+33

-5

bin/add_tradis_tags less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::DetectTags;
	3	$Bio::Tradis::Bin::DetectTags::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: check if tr tag is present
6	7	# PODNAME: check_tags
7	8
8		=head1 SYNOPSIS
9
10		Checks the presence of tr/tq tags in a given BAM file
11
12		=cut
13	9
14	10	BEGIN { unshift( @INC, '../lib' ) }
15	11	BEGIN { unshift( @INC, './lib' ) }

19	15	use Bio::Tradis::CommandLine::AddTags;
20	16
21	17	Bio::Tradis::CommandLine::AddTags->new(args => \@ARGV, script_name => $0)->run;
	18
	19	__END__
	20
	21	=pod
	22
	23	=encoding UTF-8
	24
	25	=head1 NAME
	26
	27	check_tags - check if tr tag is present
	28
	29	=head1 VERSION
	30
	31	version 1.4.5
	32
	33	=head1 SYNOPSIS
	34
	35	Checks the presence of tr/tq tags in a given BAM file
	36
	37	=head1 AUTHOR
	38
	39	Carla Cummins <path-help@sanger.ac.uk>
	40
	41	=head1 COPYRIGHT AND LICENSE
	42
	43	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	44
	45	This is free software, licensed under:
	46
	47	The GNU General Public License, Version 3, June 2007
	48
	49	=cut

+34

-7

bin/bacteria_tradis less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::RunTradis;
3
	3	$Bio::Tradis::Bin::RunTradis::VERSION = '1.4.5';
4	4	use FindBin qw($Bin);
5	5
6	6
7	7	# ABSTRACT: Perform full tradis analysis
8	8	# PODNAME: run_tradis
9	9
10		=head1 SYNOPSIS
11
12		Take a fastq, reference and a tag and generates insertion
13		site plots for use in Artemis
14
15		=cut
16	10
17	11	BEGIN { unshift( @INC, '../lib' ) }
18	12	BEGIN { unshift( @INC, './lib' ) }

22	16	use Bio::Tradis::CommandLine::TradisAnalysis;
23	17
24	18	Bio::Tradis::CommandLine::TradisAnalysis->new(args => \@ARGV, script_name => $0)->run;
	19
	20	__END__
	21
	22	=pod
	23
	24	=encoding UTF-8
	25
	26	=head1 NAME
	27
	28	run_tradis - Perform full tradis analysis
	29
	30	=head1 VERSION
	31
	32	version 1.4.5
	33
	34	=head1 SYNOPSIS
	35
	36	Take a fastq, reference and a tag and generates insertion
	37	site plots for use in Artemis
	38
	39	=head1 AUTHOR
	40
	41	Carla Cummins <path-help@sanger.ac.uk>
	42
	43	=head1 COPYRIGHT AND LICENSE
	44
	45	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	46
	47	This is free software, licensed under:
	48
	49	The GNU General Public License, Version 3, June 2007
	50
	51	=cut

+33

-5

bin/check_tradis_tags less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::DetectTags;
	3	$Bio::Tradis::Bin::DetectTags::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: check if tr tag is present
6	7	# PODNAME: check_tags
7	8
8		=head1 SYNOPSIS
9
10		Checks the presence of tr/tq tags in a given BAM file
11
12		=cut
13	9
14	10	BEGIN { unshift( @INC, '../lib' ) }
15	11	BEGIN { unshift( @INC, './lib' ) }

19	15	use Bio::Tradis::CommandLine::CheckTags;
20	16
21	17	Bio::Tradis::CommandLine::CheckTags->new(args => \@ARGV, script_name => $0)->run;
	18
	19	__END__
	20
	21	=pod
	22
	23	=encoding UTF-8
	24
	25	=head1 NAME
	26
	27	check_tags - check if tr tag is present
	28
	29	=head1 VERSION
	30
	31	version 1.4.5
	32
	33	=head1 SYNOPSIS
	34
	35	Checks the presence of tr/tq tags in a given BAM file
	36
	37	=head1 AUTHOR
	38
	39	Carla Cummins <path-help@sanger.ac.uk>
	40
	41	=head1 COPYRIGHT AND LICENSE
	42
	43	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	44
	45	This is free software, licensed under:
	46
	47	The GNU General Public License, Version 3, June 2007
	48
	49	=cut

+35

-7

bin/combine_tradis_plots less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::CombineTradisPlots;
	3	$Bio::Tradis::Bin::CombineTradisPlots::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files
6	7
7	8	# PODNAME: combine_tradis_plot
8	9
9		=head1 SYNOPSIS
10
11		Takes a tab-delimited file with an ID as the first column followed by
12		a list of plotfiles to combine per row. The ID will be used to name the new
13		plotfile and as an identifier in the stats file, so ensure these are unique.
14
15		=cut
16	10
17	11	BEGIN { unshift( @INC, '../lib' ) }
18	12	BEGIN { unshift( @INC, './lib' ) }

22	16	use Bio::Tradis::CommandLine::PlotCombine;
23	17
24	18	Bio::Tradis::CommandLine::PlotCombine->new(args => \@ARGV, script_name => $0)->run;
	19
	20	__END__
	21
	22	=pod
	23
	24	=encoding UTF-8
	25
	26	=head1 NAME
	27
	28	combine_tradis_plot - Combine multiple plotfiles and generate updated statistics for the combined files
	29
	30	=head1 VERSION
	31
	32	version 1.4.5
	33
	34	=head1 SYNOPSIS
	35
	36	Takes a tab-delimited file with an ID as the first column followed by
	37	a list of plotfiles to combine per row. The ID will be used to name the new
	38	plotfile and as an identifier in the stats file, so ensure these are unique.
	39
	40	=head1 AUTHOR
	41
	42	Carla Cummins <path-help@sanger.ac.uk>
	43
	44	=head1 COPYRIGHT AND LICENSE
	45
	46	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	47
	48	This is free software, licensed under:
	49
	50	The GNU General Public License, Version 3, June 2007
	51
	52	=cut

+34

-6

bin/filter_tradis_tags less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::FilterTags;
	3	$Bio::Tradis::Bin::FilterTags::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: filter tags at start of fastq sequences
6	7	# PODNAME: filter_tags
7	8
8		=head1 SYNOPSIS
9
10		Checks tags at the start of the fastq sequence and returns a file containing those that
11		match the tag provided
12
13		=cut
14	9
15	10	BEGIN { unshift( @INC, '../lib' ) }
16	11	BEGIN { unshift( @INC, './lib' ) }

20	15	use Bio::Tradis::CommandLine::FilterFastqTags;
21	16
22	17	Bio::Tradis::CommandLine::FilterFastqTags->new(args => \@ARGV, script_name => $0)->run;
	18
	19	__END__
	20
	21	=pod
	22
	23	=encoding UTF-8
	24
	25	=head1 NAME
	26
	27	filter_tags - filter tags at start of fastq sequences
	28
	29	=head1 VERSION
	30
	31	version 1.4.5
	32
	33	=head1 SYNOPSIS
	34
	35	Checks tags at the start of the fastq sequence and returns a file containing those that
	36	match the tag provided
	37
	38	=head1 AUTHOR
	39
	40	Carla Cummins <path-help@sanger.ac.uk>
	41
	42	=head1 COPYRIGHT AND LICENSE
	43
	44	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	45
	46	This is free software, licensed under:
	47
	48	The GNU General Public License, Version 3, June 2007
	49
	50	=cut

+33

-5

bin/remove_tradis_tags less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::RemoveTags;
	3	$Bio::Tradis::Bin::RemoveTags::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: remove user specified tags from start of fastq sequences
6	7	# PODNAME: remove_tags
7	8
8		=head1 SYNOPSIS
9
10		Removes tags from the sequence and quality strings based on user input
11
12		=cut
13	9
14	10	BEGIN { unshift( @INC, '../lib' ) }
15	11	BEGIN { unshift( @INC, './lib' ) }

19	15	use Bio::Tradis::CommandLine::RemoveFastqTags;
20	16
21	17	Bio::Tradis::CommandLine::RemoveFastqTags->new(args => \@ARGV, script_name => $0)->run;
	18
	19	__END__
	20
	21	=pod
	22
	23	=encoding UTF-8
	24
	25	=head1 NAME
	26
	27	remove_tags - remove user specified tags from start of fastq sequences
	28
	29	=head1 VERSION
	30
	31	version 1.4.5
	32
	33	=head1 SYNOPSIS
	34
	35	Removes tags from the sequence and quality strings based on user input
	36
	37	=head1 AUTHOR
	38
	39	Carla Cummins <path-help@sanger.ac.uk>
	40
	41	=head1 COPYRIGHT AND LICENSE
	42
	43	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	44
	45	This is free software, licensed under:
	46
	47	The GNU General Public License, Version 3, June 2007
	48
	49	=cut

+49

-21

bin/tradis_gene_insert_sites less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::GeneInsertSites;
	3	$Bio::Tradis::Bin::GeneInsertSites::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: Generate insertion site details from TraDIS pipeline plots
6	7
7	8	# PODNAME: tradis_gene_insert_sites
8	9
9		=head1 NAME
10
11		tradis_gene_insert_sites.pl
12
13		=head1 SYNOPSIS
14
15		=head1 DESCRIPTION
16
17		This script is for TRADIS analysis. It takes in a plot file created by the TRADIS pathogen informatics pipeline, and an embl file of
18		annotation.
19		It then outputs a tab delimited file with the insert site details. This is then used as input to an R script to calculate essentialit
20		y.
21
22		=head1 CONTACT
23
24		path-help@sanger.ac.uk
25		Original author: Lars Barquist
26
27		=head1 METHODS
28
29		=cut
30	10
31	11	use strict;
32	12	use warnings;

327	307	{
328	308	['locus_tag','gene_name','ncrna','start','end','strand','read_count','ins_index','gene_length','ins_count','fcn'];
329	309	}
	310
	311	__END__
	312
	313	=pod
	314
	315	=encoding UTF-8
	316
	317	=head1 NAME
	318
	319	tradis_gene_insert_sites - Generate insertion site details from TraDIS pipeline plots
	320
	321	=head1 VERSION
	322
	323	version 1.4.5
	324
	325	=head1 SYNOPSIS
	326
	327	=head1 DESCRIPTION
	328
	329	This script is for TRADIS analysis. It takes in a plot file created by the TRADIS pathogen informatics pipeline, and an embl file of
	330	annotation.
	331	It then outputs a tab delimited file with the insert site details. This is then used as input to an R script to calculate essentialit
	332	y.
	333
	334	=head1 NAME
	335
	336	tradis_gene_insert_sites.pl
	337
	338	=head1 CONTACT
	339
	340	path-help@sanger.ac.uk
	341	Original author: Lars Barquist
	342
	343	=head1 METHODS
	344
	345	=head1 AUTHOR
	346
	347	Carla Cummins <path-help@sanger.ac.uk>
	348
	349	=head1 COPYRIGHT AND LICENSE
	350
	351	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	352
	353	This is free software, licensed under:
	354
	355	The GNU General Public License, Version 3, June 2007
	356
	357	=cut

+48

-20

bin/tradis_merge_plots less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::MergePlots;
	3	$Bio::Tradis::Bin::MergePlots::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT:
6	7
7	8	# PODNAME: tradis_merge_plots
8	9
9		=head1 NAME
10
11		tradis_merge_plots
12
13		=head1 SYNOPSIS
14
15		tradis_merge_plots - Given a study name or ID, group by sample and tag, and generate tab files for input to R.
16
17		=head1 DESCRIPTION
18
19		Given a study name or ID, group by sample and tag, and generate tab files for input to R.
20
21		=head1 CONTACT
22
23		path-help@sanger.ac.uk
24
25		=head1 METHODS
26
27		=cut
28	10
29	11	package TraDISMergePlots::Main;
30
	12	$TraDISMergePlots::Main::VERSION = '1.4.5';
31	13	use Moose;
32	14	use Getopt::Long;
33	15	use File::Basename;

96	78	}
97	79	}
98	80	}
	81
	82	__END__
	83
	84	=pod
	85
	86	=encoding UTF-8
	87
	88	=head1 NAME
	89
	90	tradis_merge_plots -
	91
	92	=head1 VERSION
	93
	94	version 1.4.5
	95
	96	=head1 SYNOPSIS
	97
	98	tradis_merge_plots - Given a study name or ID, group by sample and tag, and generate tab files for input to R.
	99
	100	=head1 DESCRIPTION
	101
	102	Given a study name or ID, group by sample and tag, and generate tab files for input to R.
	103
	104	=head1 NAME
	105
	106	tradis_merge_plots
	107
	108	=head1 CONTACT
	109
	110	path-help@sanger.ac.uk
	111
	112	=head1 METHODS
	113
	114	=head1 AUTHOR
	115
	116	Carla Cummins <path-help@sanger.ac.uk>
	117
	118	=head1 COPYRIGHT AND LICENSE
	119
	120	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	121
	122	This is free software, licensed under:
	123
	124	The GNU General Public License, Version 3, June 2007
	125
	126	=cut

+34

-6

bin/tradis_plot less more

0	0	#!/usr/bin/env perl
1	1
2	2	package Bio::Tradis::Bin::TradisPlot;
	3	$Bio::Tradis::Bin::TradisPlot::VERSION = '1.4.5';
3	4	use FindBin qw($Bin);
4	5
5	6	# ABSTRACT: Generate plots as part of a tradis analysis
6	7	# PODNAME: tradis_plot
7	8
8		=head1 SYNOPSIS
9
10		Generate insertion plots for Artemis from a mapped fastq file and
11		a reference in GFF format
12
13		=cut
14	9
15	10	BEGIN { unshift( @INC, '../lib' ) }
16	11	BEGIN { unshift( @INC, './lib' ) }

20	15	use Bio::Tradis::CommandLine::PlotTradis;
21	16
22	17	Bio::Tradis::CommandLine::PlotTradis->new(args => \@ARGV, script_name => $0)->run;
	18
	19	__END__
	20
	21	=pod
	22
	23	=encoding UTF-8
	24
	25	=head1 NAME
	26
	27	tradis_plot - Generate plots as part of a tradis analysis
	28
	29	=head1 VERSION
	30
	31	version 1.4.5
	32
	33	=head1 SYNOPSIS
	34
	35	Generate insertion plots for Artemis from a mapped fastq file and
	36	a reference in GFF format
	37
	38	=head1 AUTHOR
	39
	40	Carla Cummins <path-help@sanger.ac.uk>
	41
	42	=head1 COPYRIGHT AND LICENSE
	43
	44	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	45
	46	This is free software, licensed under:
	47
	48	The GNU General Public License, Version 3, June 2007
	49
	50	=cut

+66

-39

lib/Bio/Tradis/AddTagsToSeq.pm less more

0	0	package Bio::Tradis::AddTagsToSeq;
1
	1	$Bio::Tradis::AddTagsToSeq::VERSION = '1.4.5';
2	2	# ABSTRACT: Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.
3	3
4		=head1 NAME
5
6		Bio::Tradis::AddTagsToSeq
7
8		=head1 SYNOPSIS
9
10		Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence and creates temporary SAM file,
11		which is then converted to BAM
12
13		use Bio::Tradis::AddTagsToSeq;
14
15		my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc');
16		$pipeline->add_tags_to_seq();
17
18		=head1 PARAMETERS
19
20		=head2 Required
21
22		C<bamfile> - path to/name of file containing reads and tags
23
24		=head2 Optional
25
26		C<outfile> - name to assign to output BAM. Defaults to C<file.tr.bam> for an input file named C<file.bam>
27
28		=head1 METHODS
29
30		C<add_tags_to_seq> - add TraDIS tags to reads. For unmapped reads, the tag
31		is added to the start of the read sequence and quality
32		strings. For reads where the flag indicates that it is
33		mapped and reverse complemented, the reverse complemented
34		tags are added to the end of the read strings.
35		This is because many conversion tools (e.g. picard) takes
36		the read orientation into account and will re-reverse the
37		mapped/rev comp reads during conversion, leaving all tags
38		in the correct orientation at the start of the sequences
39		in the resulting FastQ file.
40
41		=cut
42	4
43	5	use Moose;
44	6	use Bio::Seq;

205	167	__PACKAGE__->meta->make_immutable;
206	168	no Moose;
207	169	1;
	170
	171	__END__
	172
	173	=pod
	174
	175	=encoding UTF-8
	176
	177	=head1 NAME
	178
	179	Bio::Tradis::AddTagsToSeq - Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.
	180
	181	=head1 VERSION
	182
	183	version 1.4.5
	184
	185	=head1 SYNOPSIS
	186
	187	Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence and creates temporary SAM file,
	188	which is then converted to BAM
	189
	190	use Bio::Tradis::AddTagsToSeq;
	191
	192	my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc');
	193	$pipeline->add_tags_to_seq();
	194
	195	=head1 NAME
	196
	197	Bio::Tradis::AddTagsToSeq
	198
	199	=head1 PARAMETERS
	200
	201	=head2 Required
	202
	203	C<bamfile> - path to/name of file containing reads and tags
	204
	205	=head2 Optional
	206
	207	C<outfile> - name to assign to output BAM. Defaults to C<file.tr.bam> for an input file named C<file.bam>
	208
	209	=head1 METHODS
	210
	211	C<add_tags_to_seq> - add TraDIS tags to reads. For unmapped reads, the tag
	212	is added to the start of the read sequence and quality
	213	strings. For reads where the flag indicates that it is
	214	mapped and reverse complemented, the reverse complemented
	215	tags are added to the end of the read strings.
	216	This is because many conversion tools (e.g. picard) takes
	217	the read orientation into account and will re-reverse the
	218	mapped/rev comp reads during conversion, leaving all tags
	219	in the correct orientation at the start of the sequences
	220	in the resulting FastQ file.
	221
	222	=head1 AUTHOR
	223
	224	Carla Cummins <path-help@sanger.ac.uk>
	225
	226	=head1 COPYRIGHT AND LICENSE
	227
	228	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	229
	230	This is free software, licensed under:
	231
	232	The GNU General Public License, Version 3, June 2007
	233
	234	=cut

+33

-6

lib/Bio/Tradis/Analysis/Exceptions.pm less more

0	0	package Bio::Tradis::Analysis::Exceptions;
1	1	# ABSTRACT: Custom exceptions
2
3		=head1 SYNOPSIS
4
5		Basic exception catcher
6
7		=cut
	2	$Bio::Tradis::Analysis::Exceptions::VERSION = '1.4.5';
8	3
9	4	use Exception::Class (
10	5	Bio::Tradis::Analysis::Exceptions::FailedToOpenAlignmentSlice => { description => 'Couldnt get reads from alignment slice. Error with Samtools or BAM' },

17	12	);
18	13
19	14	1;
	15
	16	__END__
	17
	18	=pod
	19
	20	=encoding UTF-8
	21
	22	=head1 NAME
	23
	24	Bio::Tradis::Analysis::Exceptions - Custom exceptions
	25
	26	=head1 VERSION
	27
	28	version 1.4.5
	29
	30	=head1 SYNOPSIS
	31
	32	Basic exception catcher
	33
	34	=head1 AUTHOR
	35
	36	Carla Cummins <path-help@sanger.ac.uk>
	37
	38	=head1 COPYRIGHT AND LICENSE
	39
	40	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	41
	42	This is free software, licensed under:
	43
	44	The GNU General Public License, Version 3, June 2007
	45
	46	=cut

+44

-18

lib/Bio/Tradis/Analysis/InsertSite.pm less more

0	0	package Bio::Tradis::Analysis::InsertSite;
1	1	# ABSTRACT: Take in a bam file and plot the start position of each read
2
3		=head1 NAME
4
5		InsertSite.pm - Take in a bam file and plot the start position of each read
6
7		=head1 SYNOPSIS
8
9		Takes in a mapped BAM file and plot the start position of each read
10
11		use Bio::Tradis::Analysis::InsertSite;
12		my $insertsite_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new(
13		filename => 'my_file.bam',
14		output_base_filename => 'my_output_file'
15		);
16		$insertsite_plots_from_bam->create_plots();
17
18
19		=cut
	2	$Bio::Tradis::Analysis::InsertSite::VERSION = '1.4.5';
20	3
21	4
22	5	use Moose;

204	187	}
205	188
206	189	1;
	190
	191	__END__
	192
	193	=pod
	194
	195	=encoding UTF-8
	196
	197	=head1 NAME
	198
	199	Bio::Tradis::Analysis::InsertSite - Take in a bam file and plot the start position of each read
	200
	201	=head1 VERSION
	202
	203	version 1.4.5
	204
	205	=head1 SYNOPSIS
	206
	207	Takes in a mapped BAM file and plot the start position of each read
	208
	209	use Bio::Tradis::Analysis::InsertSite;
	210	my $insertsite_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new(
	211	filename => 'my_file.bam',
	212	output_base_filename => 'my_output_file'
	213	);
	214	$insertsite_plots_from_bam->create_plots();
	215
	216	=head1 NAME
	217
	218	InsertSite.pm - Take in a bam file and plot the start position of each read
	219
	220	=head1 AUTHOR
	221
	222	Carla Cummins <path-help@sanger.ac.uk>
	223
	224	=head1 COPYRIGHT AND LICENSE
	225
	226	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	227
	228	This is free software, licensed under:
	229
	230	The GNU General Public License, Version 3, June 2007
	231
	232	=cut

+58

-31

lib/Bio/Tradis/CombinePlots.pm less more

0	0	package Bio::Tradis::CombinePlots;
1
	1	$Bio::Tradis::CombinePlots::VERSION = '1.4.5';
2	2	# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files
3	3
4		=head1 SYNOPSIS
5
6		Takes a tab-delimited file with an ID as the first column followed by
7		a list of plotfiles to combine per row. The ID will be used to name the new
8		plotfile and as an identifier in the stats file, so ensure these are unique.
9
10		For example, an input file named plots_to_combine.txt:
11
12		tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
13		tradis2 plot2.1.gz plot2.2.gz
14		tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
15
16		will produce
17
18		=over
19
20		1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
21		tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
22		2. a stats file named plots_to_combine.stats
23
24		=back
25
26		=head1 USAGE
27
28		use Bio::Tradis::CombinePlots;
29
30		my $pipeline = Bio::Tradis::CombinePlots->new(plotfile => 'abc');
31		$pipeline->combine;
32
33		=cut
34	4
35	5	use Moose;
36	6	use strict;

325	295	__PACKAGE__->meta->make_immutable;
326	296	no Moose;
327	297	1;
	298
	299	__END__
	300
	301	=pod
	302
	303	=encoding UTF-8
	304
	305	=head1 NAME
	306
	307	Bio::Tradis::CombinePlots - Combine multiple plotfiles and generate updated statistics for the combined files
	308
	309	=head1 VERSION
	310
	311	version 1.4.5
	312
	313	=head1 SYNOPSIS
	314
	315	Takes a tab-delimited file with an ID as the first column followed by
	316	a list of plotfiles to combine per row. The ID will be used to name the new
	317	plotfile and as an identifier in the stats file, so ensure these are unique.
	318
	319	For example, an input file named plots_to_combine.txt:
	320
	321	tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
	322	tradis2 plot2.1.gz plot2.2.gz
	323	tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
	324
	325	will produce
	326
	327	=over
	328
	329	1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
	330	tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
	331	2. a stats file named plots_to_combine.stats
	332
	333	=back
	334
	335	=head1 USAGE
	336
	337	use Bio::Tradis::CombinePlots;
	338
	339	my $pipeline = Bio::Tradis::CombinePlots->new(plotfile => 'abc');
	340	$pipeline->combine;
	341
	342	=head1 AUTHOR
	343
	344	Carla Cummins <path-help@sanger.ac.uk>
	345
	346	=head1 COPYRIGHT AND LICENSE
	347
	348	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	349
	350	This is free software, licensed under:
	351
	352	The GNU General Public License, Version 3, June 2007
	353
	354	=cut

+33

-6

lib/Bio/Tradis/CommandLine/AddTags.pm less more

0	0	package Bio::Tradis::CommandLine::AddTags;
1
	1	$Bio::Tradis::CommandLine::AddTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Add given tags to the start of the sequence
3	3
4		=head1 SYNOPSIS
5
6		Adds given tags to the start of the sequence
7
8		=cut
9	4
10	5	use Moose;
11	6	use Getopt::Long qw(GetOptionsFromArray);

81	76	__PACKAGE__->meta->make_immutable;
82	77	no Moose;
83	78	1;
	79
	80	__END__
	81
	82	=pod
	83
	84	=encoding UTF-8
	85
	86	=head1 NAME
	87
	88	Bio::Tradis::CommandLine::AddTags - Add given tags to the start of the sequence
	89
	90	=head1 VERSION
	91
	92	version 1.4.5
	93
	94	=head1 SYNOPSIS
	95
	96	Adds given tags to the start of the sequence
	97
	98	=head1 AUTHOR
	99
	100	Carla Cummins <path-help@sanger.ac.uk>
	101
	102	=head1 COPYRIGHT AND LICENSE
	103
	104	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	105
	106	This is free software, licensed under:
	107
	108	The GNU General Public License, Version 3, June 2007
	109
	110	=cut

+34

-7

lib/Bio/Tradis/CommandLine/CheckTags.pm less more

0	0	package Bio::Tradis::CommandLine::CheckTags;
1
	1	$Bio::Tradis::CommandLine::CheckTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Check for presence of tr tag in BAM file
3	3
4		=head1 SYNOPSIS
5
6		Check for presence of tr tag in BAM file
7
8		=cut
9	4
10	5	use Moose;
11	6	use Getopt::Long qw(GetOptionsFromArray);

66	61
67	62	__PACKAGE__->meta->make_immutable;
68	63	no Moose;
69		1;⏎
	64	1;
	65
	66	__END__
	67
	68	=pod
	69
	70	=encoding UTF-8
	71
	72	=head1 NAME
	73
	74	Bio::Tradis::CommandLine::CheckTags - Check for presence of tr tag in BAM file
	75
	76	=head1 VERSION
	77
	78	version 1.4.5
	79
	80	=head1 SYNOPSIS
	81
	82	Check for presence of tr tag in BAM file
	83
	84	=head1 AUTHOR
	85
	86	Carla Cummins <path-help@sanger.ac.uk>
	87
	88	=head1 COPYRIGHT AND LICENSE
	89
	90	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	91
	92	This is free software, licensed under:
	93
	94	The GNU General Public License, Version 3, June 2007
	95
	96	=cut

+33

-6

lib/Bio/Tradis/CommandLine/FilterFastqTags.pm less more

0	0	package Bio::Tradis::CommandLine::FilterFastqTags;
1
	1	$Bio::Tradis::CommandLine::FilterFastqTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Remove given tags from the start of the sequence
3	3
4		=head1 SYNOPSIS
5
6		Removes tags from the sequence and quality strings
7
8		=cut
9	4
10	5	use Moose;
11	6	use Getopt::Long qw(GetOptionsFromArray);

81	76	__PACKAGE__->meta->make_immutable;
82	77	no Moose;
83	78	1;
	79
	80	__END__
	81
	82	=pod
	83
	84	=encoding UTF-8
	85
	86	=head1 NAME
	87
	88	Bio::Tradis::CommandLine::FilterFastqTags - Remove given tags from the start of the sequence
	89
	90	=head1 VERSION
	91
	92	version 1.4.5
	93
	94	=head1 SYNOPSIS
	95
	96	Removes tags from the sequence and quality strings
	97
	98	=head1 AUTHOR
	99
	100	Carla Cummins <path-help@sanger.ac.uk>
	101
	102	=head1 COPYRIGHT AND LICENSE
	103
	104	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	105
	106	This is free software, licensed under:
	107
	108	The GNU General Public License, Version 3, June 2007
	109
	110	=cut

+52

-25

lib/Bio/Tradis/CommandLine/PlotCombine.pm less more

0	0	package Bio::Tradis::CommandLine::PlotCombine;
1
	1	$Bio::Tradis::CommandLine::PlotCombine::VERSION = '1.4.5';
2	2	# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files
3	3
4		=head1 SYNOPSIS
5
6		Takes a tab-delimited file with an ID as the first column followed by
7		a list of plotfiles to combine per row. The ID will be used to name the new
8		plotfile and as an identifier in the stats file, so ensure these are unique.
9
10		For example, an input file named plots_to_combine.txt:
11
12		tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
13		tradis2 plot2.1.gz plot2.2.gz
14		tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
15
16		will produce:
17
18		=over
19
20		=item 1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
21		tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
22
23		=item 2. a stats file named plots_to_combine.stats
24
25		=back
26
27		=cut
28	4
29	5	use Moose;
30	6	use Getopt::Long qw(GetOptionsFromArray);

98	74	__PACKAGE__->meta->make_immutable;
99	75	no Moose;
100	76	1;
	77
	78	__END__
	79
	80	=pod
	81
	82	=encoding UTF-8
	83
	84	=head1 NAME
	85
	86	Bio::Tradis::CommandLine::PlotCombine - Combine multiple plotfiles and generate updated statistics for the combined files
	87
	88	=head1 VERSION
	89
	90	version 1.4.5
	91
	92	=head1 SYNOPSIS
	93
	94	Takes a tab-delimited file with an ID as the first column followed by
	95	a list of plotfiles to combine per row. The ID will be used to name the new
	96	plotfile and as an identifier in the stats file, so ensure these are unique.
	97
	98	For example, an input file named plots_to_combine.txt:
	99
	100	tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
	101	tradis2 plot2.1.gz plot2.2.gz
	102	tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
	103
	104	will produce:
	105
	106	=over
	107
	108	=item 1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz,
	109	tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
	110
	111	=item 2. a stats file named plots_to_combine.stats
	112
	113	=back
	114
	115	=head1 AUTHOR
	116
	117	Carla Cummins <path-help@sanger.ac.uk>
	118
	119	=head1 COPYRIGHT AND LICENSE
	120
	121	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	122
	123	This is free software, licensed under:
	124
	125	The GNU General Public License, Version 3, June 2007
	126
	127	=cut

+34

-7

lib/Bio/Tradis/CommandLine/PlotTradis.pm less more

0	0	package Bio::Tradis::CommandLine::PlotTradis;
1
	1	$Bio::Tradis::CommandLine::PlotTradis::VERSION = '1.4.5';
2	2	# ABSTRACT: Generate plots as part of a tradis analysis
3	3
4		=head1 SYNOPSIS
5
6		Generate insertion plots for Artemis from a mapped fastq file and
7		a reference in GFF format
8
9		=cut
10	4
11	5	use Moose;
12	6	use Getopt::Long qw(GetOptionsFromArray);

76	70	__PACKAGE__->meta->make_immutable;
77	71	no Moose;
78	72	1;
	73
	74	__END__
	75
	76	=pod
	77
	78	=encoding UTF-8
	79
	80	=head1 NAME
	81
	82	Bio::Tradis::CommandLine::PlotTradis - Generate plots as part of a tradis analysis
	83
	84	=head1 VERSION
	85
	86	version 1.4.5
	87
	88	=head1 SYNOPSIS
	89
	90	Generate insertion plots for Artemis from a mapped fastq file and
	91	a reference in GFF format
	92
	93	=head1 AUTHOR
	94
	95	Carla Cummins <path-help@sanger.ac.uk>
	96
	97	=head1 COPYRIGHT AND LICENSE
	98
	99	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	100
	101	This is free software, licensed under:
	102
	103	The GNU General Public License, Version 3, June 2007
	104
	105	=cut

+33

-6

lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm less more

0	0	package Bio::Tradis::CommandLine::RemoveFastqTags;
1
	1	$Bio::Tradis::CommandLine::RemoveFastqTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Remove given tags from the start of the sequence
3	3
4		=head1 SYNOPSIS
5
6		Removes tags from the sequence and quality strings
7
8		=cut
9	4
10	5	use Moose;
11	6	use Getopt::Long qw(GetOptionsFromArray);

81	76	__PACKAGE__->meta->make_immutable;
82	77	no Moose;
83	78	1;
	79
	80	__END__
	81
	82	=pod
	83
	84	=encoding UTF-8
	85
	86	=head1 NAME
	87
	88	Bio::Tradis::CommandLine::RemoveFastqTags - Remove given tags from the start of the sequence
	89
	90	=head1 VERSION
	91
	92	version 1.4.5
	93
	94	=head1 SYNOPSIS
	95
	96	Removes tags from the sequence and quality strings
	97
	98	=head1 AUTHOR
	99
	100	Carla Cummins <path-help@sanger.ac.uk>
	101
	102	=head1 COPYRIGHT AND LICENSE
	103
	104	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	105
	106	This is free software, licensed under:
	107
	108	The GNU General Public License, Version 3, June 2007
	109
	110	=cut

+34

-7

lib/Bio/Tradis/CommandLine/RunMapping.pm less more

0	0	package Bio::Tradis::CommandLine::RunMapping;
1
	1	$Bio::Tradis::CommandLine::RunMapping::VERSION = '1.4.5';
2	2	# ABSTRACT: Perform mapping
3	3
4		=head1 SYNOPSIS
5
6		Takes a reference genome and indexes it.
7		Maps given fastq files to ref.
8
9		=cut
10	4
11	5	use Moose;
12	6	use Getopt::Long qw(GetOptionsFromArray);

122	116	__PACKAGE__->meta->make_immutable;
123	117	no Moose;
124	118	1;
	119
	120	__END__
	121
	122	=pod
	123
	124	=encoding UTF-8
	125
	126	=head1 NAME
	127
	128	Bio::Tradis::CommandLine::RunMapping - Perform mapping
	129
	130	=head1 VERSION
	131
	132	version 1.4.5
	133
	134	=head1 SYNOPSIS
	135
	136	Takes a reference genome and indexes it.
	137	Maps given fastq files to ref.
	138
	139	=head1 AUTHOR
	140
	141	Carla Cummins <path-help@sanger.ac.uk>
	142
	143	=head1 COPYRIGHT AND LICENSE
	144
	145	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	146
	147	This is free software, licensed under:
	148
	149	The GNU General Public License, Version 3, June 2007
	150
	151	=cut

+34

-7

lib/Bio/Tradis/CommandLine/TradisAnalysis.pm less more

0	0	package Bio::Tradis::CommandLine::TradisAnalysis;
1
	1	$Bio::Tradis::CommandLine::TradisAnalysis::VERSION = '1.4.5';
2	2	# ABSTRACT: Perform full tradis analysis
3	3
4		=head1 SYNOPSIS
5
6		Takes a fastq, reference and a tag and generates insertion
7		site plots for use in Artemis
8
9		=cut
10	4
11	5	use Moose;
12	6	use Getopt::Long qw(GetOptionsFromArray);

281	275	__PACKAGE__->meta->make_immutable;
282	276	no Moose;
283	277	1;
	278
	279	__END__
	280
	281	=pod
	282
	283	=encoding UTF-8
	284
	285	=head1 NAME
	286
	287	Bio::Tradis::CommandLine::TradisAnalysis - Perform full tradis analysis
	288
	289	=head1 VERSION
	290
	291	version 1.4.5
	292
	293	=head1 SYNOPSIS
	294
	295	Takes a fastq, reference and a tag and generates insertion
	296	site plots for use in Artemis
	297
	298	=head1 AUTHOR
	299
	300	Carla Cummins <path-help@sanger.ac.uk>
	301
	302	=head1 COPYRIGHT AND LICENSE
	303
	304	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	305
	306	This is free software, licensed under:
	307
	308	The GNU General Public License, Version 3, June 2007
	309
	310	=cut

+34

-7

lib/Bio/Tradis/CommandLine/TradisBam.pm less more

0	0	package Bio::Tradis::CommandLine::TradisBam;
1
	1	$Bio::Tradis::CommandLine::TradisBam::VERSION = '1.4.5';
2	2	# ABSTRACT: Adds tags to sequences if tags are present
3	3
4		=head1 SYNOPSIS
5
6		Checks for tradis tags in the BAM and outputs processed TraDIS BAM file
7		with tags attached
8
9		=cut
10	4
11	5	use Moose;
12	6	use Getopt::Long qw(GetOptionsFromArray);

99	93	__PACKAGE__->meta->make_immutable;
100	94	no Moose;
101	95	1;
	96
	97	__END__
	98
	99	=pod
	100
	101	=encoding UTF-8
	102
	103	=head1 NAME
	104
	105	Bio::Tradis::CommandLine::TradisBam - Adds tags to sequences if tags are present
	106
	107	=head1 VERSION
	108
	109	version 1.4.5
	110
	111	=head1 SYNOPSIS
	112
	113	Checks for tradis tags in the BAM and outputs processed TraDIS BAM file
	114	with tags attached
	115
	116	=head1 AUTHOR
	117
	118	Carla Cummins <path-help@sanger.ac.uk>
	119
	120	=head1 COPYRIGHT AND LICENSE
	121
	122	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	123
	124	This is free software, licensed under:
	125
	126	The GNU General Public License, Version 3, June 2007
	127
	128	=cut

+51

-24

lib/Bio/Tradis/DetectTags.pm less more

0	0	package Bio::Tradis::DetectTags;
1
	1	$Bio::Tradis::DetectTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Detect tr tags in BAM file
3	3
4		=head1 NAME
5
6		Bio::Tradis::DetectTags
7
8		=head1 SYNOPSIS
9
10		Detects presence of tr/tq tags in BAM files from Tradis analyses
11		use Bio::Tradis::DetectTags;
12
13		my $pipeline = Bio::Tradis::DetectTags->new(bamfile => 'abc');
14		$pipeline->tags_present();
15
16		=head1 PARAMETERS
17
18		=head2 Required
19
20		C<bamfile> - path to/name of file to check
21
22		=head1 METHODS
23
24		C<tags_present> - returns true if TraDIS tags are detected in C<bamfile>
25
26		=cut
27	4
28	5	use Moose;
29	6	use Bio::Tradis::Parser::Bam

51	28	__PACKAGE__->meta->make_immutable;
52	29	no Moose;
53	30	1;
	31
	32	__END__
	33
	34	=pod
	35
	36	=encoding UTF-8
	37
	38	=head1 NAME
	39
	40	Bio::Tradis::DetectTags - Detect tr tags in BAM file
	41
	42	=head1 VERSION
	43
	44	version 1.4.5
	45
	46	=head1 SYNOPSIS
	47
	48	Detects presence of tr/tq tags in BAM files from Tradis analyses
	49	use Bio::Tradis::DetectTags;
	50
	51	my $pipeline = Bio::Tradis::DetectTags->new(bamfile => 'abc');
	52	$pipeline->tags_present();
	53
	54	=head1 NAME
	55
	56	Bio::Tradis::DetectTags
	57
	58	=head1 PARAMETERS
	59
	60	=head2 Required
	61
	62	C<bamfile> - path to/name of file to check
	63
	64	=head1 METHODS
	65
	66	C<tags_present> - returns true if TraDIS tags are detected in C<bamfile>
	67
	68	=head1 AUTHOR
	69
	70	Carla Cummins <path-help@sanger.ac.uk>
	71
	72	=head1 COPYRIGHT AND LICENSE
	73
	74	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	75
	76	This is free software, licensed under:
	77
	78	The GNU General Public License, Version 3, June 2007
	79
	80	=cut

+33

-6

lib/Bio/Tradis/Exception.pm less more

0	0	package Bio::Tradis::Exception;
1	1	# ABSTRACT: Exceptions for input data
2
3		=head1 SYNOPSIS
4
5		Exceptions for input data
6
7		=cut
	2	$Bio::Tradis::Exception::VERSION = '1.4.5';
8	3
9	4
10	5	use Exception::Class (

13	8	);
14	9
15	10	1;
	11
	12	__END__
	13
	14	=pod
	15
	16	=encoding UTF-8
	17
	18	=head1 NAME
	19
	20	Bio::Tradis::Exception - Exceptions for input data
	21
	22	=head1 VERSION
	23
	24	version 1.4.5
	25
	26	=head1 SYNOPSIS
	27
	28	Exceptions for input data
	29
	30	=head1 AUTHOR
	31
	32	Carla Cummins <path-help@sanger.ac.uk>
	33
	34	=head1 COPYRIGHT AND LICENSE
	35
	36	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	37
	38	This is free software, licensed under:
	39
	40	The GNU General Public License, Version 3, June 2007
	41
	42	=cut

+66

-39

lib/Bio/Tradis/FilterTags.pm less more

0	0	package Bio::Tradis::FilterTags;
1
	1	$Bio::Tradis::FilterTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Filter tags in a fastq file
3	3
4		=head1 SYNOPSIS
5
6		Reads in a fastq file with tradis tags already attached to the start of the sequence
7		Filters reads that contain the provided tag
8		Outputs a file *.tag.fastq unless an alternative outfile name is specified
9
10		use Bio::Tradis::FilterTags;
11
12		my $pipeline = Bio::Tradis::FilterTags->new(fastqfile => 'abc', tag => 'abc');
13		$pipeline->filter_tags();
14
15		=head1 PARAMETERS
16
17		=head2 Required
18
19		=over
20
21		=item * C<fastqfile> - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.
22
23		=item * C<tag> - TraDIS tag to match
24
25		=back
26
27		=head2 Optional
28
29		=over
30
31		=item * C<mismatch> - number of mismatches to allow when matching the tag. Default = 0
32
33		=item * C<outfile> - output file name. Defaults to C<file.tag.fastq> for an input file named C<file.fastq>
34
35		=back
36
37		=head1 METHODS
38
39		C<filter_tags> - outputs all reads containing the provided tag to C<outfile>
40
41		=cut
42	4
43	5	use Moose;
44	6	use Bio::Tradis::Parser::Fastq;

159	121	__PACKAGE__->meta->make_immutable;
160	122	no Moose;
161	123	1;
	124
	125	__END__
	126
	127	=pod
	128
	129	=encoding UTF-8
	130
	131	=head1 NAME
	132
	133	Bio::Tradis::FilterTags - Filter tags in a fastq file
	134
	135	=head1 VERSION
	136
	137	version 1.4.5
	138
	139	=head1 SYNOPSIS
	140
	141	Reads in a fastq file with tradis tags already attached to the start of the sequence
	142	Filters reads that contain the provided tag
	143	Outputs a file *.tag.fastq unless an alternative outfile name is specified
	144
	145	use Bio::Tradis::FilterTags;
	146
	147	my $pipeline = Bio::Tradis::FilterTags->new(fastqfile => 'abc', tag => 'abc');
	148	$pipeline->filter_tags();
	149
	150	=head1 PARAMETERS
	151
	152	=head2 Required
	153
	154	=over
	155
	156	=item * C<fastqfile> - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.
	157
	158	=item * C<tag> - TraDIS tag to match
	159
	160	=back
	161
	162	=head2 Optional
	163
	164	=over
	165
	166	=item * C<mismatch> - number of mismatches to allow when matching the tag. Default = 0
	167
	168	=item * C<outfile> - output file name. Defaults to C<file.tag.fastq> for an input file named C<file.fastq>
	169
	170	=back
	171
	172	=head1 METHODS
	173
	174	C<filter_tags> - outputs all reads containing the provided tag to C<outfile>
	175
	176	=head1 AUTHOR
	177
	178	Carla Cummins <path-help@sanger.ac.uk>
	179
	180	=head1 COPYRIGHT AND LICENSE
	181
	182	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	183
	184	This is free software, licensed under:
	185
	186	The GNU General Public License, Version 3, June 2007
	187
	188	=cut

+84

-61

lib/Bio/Tradis/Map.pm less more

0	0	package Bio::Tradis::Map;
1
	1	$Bio::Tradis::Map::VERSION = '1.4.5';
2	2	# ABSTRACT: Perform mapping
3	3
4		=head1 SYNOPSIS
5
6		Takes a reference genome and indexes it.
7		Maps given fastq files to ref.
8
9		use Bio::Tradis::Map;
10
11		my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc');
12		$pipeline->index_ref();
13		$pipeline->do_mapping();
14
15		=head1 PARAMETERS
16
17		=head2 Required
18
19		=over
20
21		=item * C<fastqfile> - path to/name of file containing reads to map to the reference
22
23		=item * C<reference> - path to/name of reference genome in fasta format (.fa)
24
25		=back
26
27		=head2 Optional
28
29		=over
30
31		=item * C<refname> - name to assign to the reference index files. Default = ref.index
32
33		=item * C<outfile> - name to assign to the mapped SAM file. Default = mapped.sam
34
35		=back
36
37		=head1 METHODS
38
39		=over
40
41		=item * C<index_ref> - create index files of the reference genome. These are required
42		for the mapping step. Only skip this step if index files already
43		exist. -k and -s options for referencing are calculated based
44		on the length of the reads being mapped as per table:
45
46		=begin html
47
48		<table>
49		<tr><th>Read length</th><th>k</th><th>s</th></tr>
50		<tr><td><70</td><td>13</td><td>4<td></tr>
51		<tr><td>>70 and <100</td><td>13</td><td>6<td></tr>
52		<tr><td>>100</td><td>20</td><td>6<td></tr>
53		</table>
54
55		=end html
56
57		=item * C<do_mapping> - map C<fastqfile> to C<reference>. Options used for mapping are: C<-r -1 -x -y 0.96>
58
59		=back
60
61		For more information on the mapping and indexing options discussed here, see the L<SMALT manual\|ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf>
62
63		=cut
64	4
65	5	use Moose;
66	6	use Bio::Tradis::Parser::Fastq;

168	108	__PACKAGE__->meta->make_immutable;
169	109	no Moose;
170	110	1;
	111
	112	__END__
	113
	114	=pod
	115
	116	=encoding UTF-8
	117
	118	=head1 NAME
	119
	120	Bio::Tradis::Map - Perform mapping
	121
	122	=head1 VERSION
	123
	124	version 1.4.5
	125
	126	=head1 SYNOPSIS
	127
	128	Takes a reference genome and indexes it.
	129	Maps given fastq files to ref.
	130
	131	use Bio::Tradis::Map;
	132
	133	my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc');
	134	$pipeline->index_ref();
	135	$pipeline->do_mapping();
	136
	137	=head1 PARAMETERS
	138
	139	=head2 Required
	140
	141	=over
	142
	143	=item * C<fastqfile> - path to/name of file containing reads to map to the reference
	144
	145	=item * C<reference> - path to/name of reference genome in fasta format (.fa)
	146
	147	=back
	148
	149	=head2 Optional
	150
	151	=over
	152
	153	=item * C<refname> - name to assign to the reference index files. Default = ref.index
	154
	155	=item * C<outfile> - name to assign to the mapped SAM file. Default = mapped.sam
	156
	157	=back
	158
	159	=head1 METHODS
	160
	161	=over
	162
	163	=item * C<index_ref> - create index files of the reference genome. These are required
	164	for the mapping step. Only skip this step if index files already
	165	exist. -k and -s options for referencing are calculated based
	166	on the length of the reads being mapped as per table:
	167
	168	=for html <table>
	169	<tr><th>Read length</th><th>k</th><th>s</th></tr>
	170	<tr><td><70</td><td>13</td><td>4<td></tr>
	171	<tr><td>>70 and <100</td><td>13</td><td>6<td></tr>
	172	<tr><td>>100</td><td>20</td><td>6<td></tr>
	173	</table>
	174
	175	=item * C<do_mapping> - map C<fastqfile> to C<reference>. Options used for mapping are: C<-r -1 -x -y 0.96>
	176
	177	=back
	178
	179	For more information on the mapping and indexing options discussed here, see the L<SMALT manual\|ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf>
	180
	181	=head1 AUTHOR
	182
	183	Carla Cummins <path-help@sanger.ac.uk>
	184
	185	=head1 COPYRIGHT AND LICENSE
	186
	187	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	188
	189	This is free software, licensed under:
	190
	191	The GNU General Public License, Version 3, June 2007
	192
	193	=cut

+84

-57

lib/Bio/Tradis/Parser/Bam.pm less more

0	0	package Bio::Tradis::Parser::Bam;
1
	1	$Bio::Tradis::Parser::Bam::VERSION = '1.4.5';
2	2	# ABSTRACT: Very basic BAM parser. Limited functionality.
3	3
4		=head1 SYNOPSIS
5
6		Parses BAM files and gives access to basic info in them.
7
8		use Bio::Tradis::Parser::Bam;
9
10		my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc');
11		$pipeline->read_info;
12		$pipeline->next_read;
13		$pipeline->seq_info;
14		$pipeline->is_mapped;
15		$pipeline->is_reverse;
16
17		=cut
18	4
19	5	use Moose;
20	6

81	67
82	68	### Public methods ###
83	69
84		=seq_info
85		Reads BAM header and returns a hash (keys are sequence ids, values are hash
86		refs with keys as tags (like LN and M5))
87		=cut
88	70
89	71	sub seq_info {
90	72	my ($self) = @_;

110	92	return %all_seq_info;
111	93	}
112	94
113		=next_read
114		Moves _currentread to the next entry in the BAM. Returns 0 if EOF.
115		=cut
116	95
117	96	sub next_read {
118	97	my ($self) = @_;

134	113	close $self->_bam_handle;
135	114	}
136	115
137		=read_info
	116
	117	sub read_info {
	118	my ($self) = @_;
	119	return $self->_currentread;
	120	}
	121
	122
	123	sub is_mapped {
	124	my ($self) = @_;
	125	my $flag = ${ $self->_currentread }{BINARY_FLAG};
	126	my @flag_array = split( '', $flag );
	127	my $resl;
	128	if ( $flag_array[-3] ) { $resl = 0; }
	129	else { $resl = 1; }
	130	return $resl;
	131	}
	132
	133
	134	sub is_reverse {
	135	my ($self) = @_;
	136	my $flag = ${ $self->_currentread }{BINARY_FLAG};
	137	my @flag_array = split( '', $flag );
	138
	139	#print @flag_array;
	140	return $flag_array[-5];
	141	}
	142
	143	__PACKAGE__->meta->make_immutable;
	144	no Moose;
	145	1;
	146
	147	__END__
	148
	149	=pod
	150
	151	=encoding UTF-8
	152
	153	=head1 NAME
	154
	155	Bio::Tradis::Parser::Bam - Very basic BAM parser. Limited functionality.
	156
	157	=head1 VERSION
	158
	159	version 1.4.5
	160
	161	=head1 SYNOPSIS
	162
	163	Parses BAM files and gives access to basic info in them.
	164
	165	use Bio::Tradis::Parser::Bam;
	166
	167	my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc');
	168	$pipeline->read_info;
	169	$pipeline->next_read;
	170	$pipeline->seq_info;
	171	$pipeline->is_mapped;
	172	$pipeline->is_reverse;
	173
	174	=seq_info
	175	Reads BAM header and returns a hash (keys are sequence ids, values are hash
	176	refs with keys as tags (like LN and M5))
	177
	178	=next_read
	179	Moves _currentread to the next entry in the BAM. Returns 0 if EOF.
	180
	181	=read_info
138	182	Returns info from _currentread = hash reference with field name as key.
139	183	Standard fields are named as per the SAM format specification:
140	184	1 : QNAME

150	194	11 : QUAL
151	195	Additional fields will use their tag names.
152	196	Complete line is returned with key READ
153		=cut
154
155		sub read_info {
156		my ($self) = @_;
157		return $self->_currentread;
158		}
159
160		=is_mapped
	197
	198	=is_mapped
161	199	Parses the flag for the current read and determines if mapped.
162	200	Returns 0 or 1.
163		=cut
164
165		sub is_mapped {
166		my ($self) = @_;
167		my $flag = ${ $self->_currentread }{BINARY_FLAG};
168		my @flag_array = split( '', $flag );
169		my $resl;
170		if ( $flag_array[-3] ) { $resl = 0; }
171		else { $resl = 1; }
172		return $resl;
173		}
174
175		=is_reverse
	201
	202	=is_reverse
176	203	Parses the flag for the current read and determines if reverse
177	204	complemented. Returns 0 or 1.
	205
	206	=head1 AUTHOR
	207
	208	Carla Cummins <path-help@sanger.ac.uk>
	209
	210	=head1 COPYRIGHT AND LICENSE
	211
	212	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	213
	214	This is free software, licensed under:
	215
	216	The GNU General Public License, Version 3, June 2007
	217
178	218	=cut
179
180		sub is_reverse {
181		my ($self) = @_;
182		my $flag = ${ $self->_currentread }{BINARY_FLAG};
183		my @flag_array = split( '', $flag );
184
185		#print @flag_array;
186		return $flag_array[-5];
187		}
188
189		__PACKAGE__->meta->make_immutable;
190		no Moose;
191		1;

+39

-12

lib/Bio/Tradis/Parser/Cigar.pm less more

0	0	package Bio::Tradis::Parser::Cigar;
1
	1	$Bio::Tradis::Parser::Cigar::VERSION = '1.4.5';
2	2	# ABSTRACT: Take in a cigar string and output start and end relative to the reference sequence
3	3
4		=head1 SYNOPSIS
5
6		Take in a cigar string and output start and end relative to the reference sequence
7
8		use Bio::Tradis::Parser::Cigar;
9
10		my $cigar = Bio::Tradis::Parser::Cigar->new(coordinate => 123, cigar => '10S90M');
11		$cigar->start;
12		$cigar->end;
13
14		=cut
15	4
16	5	use Moose;
17	6

68	57	__PACKAGE__->meta->make_immutable;
69	58	no Moose;
70	59	1;
	60
	61	__END__
	62
	63	=pod
	64
	65	=encoding UTF-8
	66
	67	=head1 NAME
	68
	69	Bio::Tradis::Parser::Cigar - Take in a cigar string and output start and end relative to the reference sequence
	70
	71	=head1 VERSION
	72
	73	version 1.4.5
	74
	75	=head1 SYNOPSIS
	76
	77	Take in a cigar string and output start and end relative to the reference sequence
	78
	79	use Bio::Tradis::Parser::Cigar;
	80
	81	my $cigar = Bio::Tradis::Parser::Cigar->new(coordinate => 123, cigar => '10S90M');
	82	$cigar->start;
	83	$cigar->end;
	84
	85	=head1 AUTHOR
	86
	87	Carla Cummins <path-help@sanger.ac.uk>
	88
	89	=head1 COPYRIGHT AND LICENSE
	90
	91	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	92
	93	This is free software, licensed under:
	94
	95	The GNU General Public License, Version 3, June 2007
	96
	97	=cut

+49

-22

lib/Bio/Tradis/Parser/Fastq.pm less more

0	0	package Bio::Tradis::Parser::Fastq;
1
	1	$Bio::Tradis::Parser::Fastq::VERSION = '1.4.5';
2	2	# ABSTRACT: Basic FastQ parser.
3	3
4		=head1 SYNOPSIS
5
6		Parses fastq files.
7
8		use Bio::Tradis::Parser::Fastq;
9
10		my $pipeline = Bio::Tradis::Parser::Fastq->new(file => 'abc');
11		$pipeline->next_read;
12		$pipeline->read_info;
13
14		=cut
15	4
16	5	use Moose;
17	6

41	30
42	31	### Public methods ###
43	32
44		=next_read
45		Moves to the next read. Returns 1 if read exists, returns 0
46		if EOF
47		=cut
48	33
49	34	sub next_read {
50	35	my ($self) = @_;

60	45	}
61	46	}
62	47
63		=read_info
64		Returns an array of info for the read in an array.
65		0 = id
66		1 = sequence
67		2 = quality string
68		=cut
69	48	sub read_info {
70	49	my ($self) = @_;
71	50	my $fqh = $self->_fastq_handle;

98	77	__PACKAGE__->meta->make_immutable;
99	78	no Moose;
100	79	1;
	80
	81	__END__
	82
	83	=pod
	84
	85	=encoding UTF-8
	86
	87	=head1 NAME
	88
	89	Bio::Tradis::Parser::Fastq - Basic FastQ parser.
	90
	91	=head1 VERSION
	92
	93	version 1.4.5
	94
	95	=head1 SYNOPSIS
	96
	97	Parses fastq files.
	98
	99	use Bio::Tradis::Parser::Fastq;
	100
	101	my $pipeline = Bio::Tradis::Parser::Fastq->new(file => 'abc');
	102	$pipeline->next_read;
	103	$pipeline->read_info;
	104
	105	=next_read
	106	Moves to the next read. Returns 1 if read exists, returns 0
	107	if EOF
	108
	109	=read_info
	110	Returns an array of info for the read in an array.
	111	0 = id
	112	1 = sequence
	113	2 = quality string
	114
	115	=head1 AUTHOR
	116
	117	Carla Cummins <path-help@sanger.ac.uk>
	118
	119	=head1 COPYRIGHT AND LICENSE
	120
	121	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	122
	123	This is free software, licensed under:
	124
	125	The GNU General Public License, Version 3, June 2007
	126
	127	=cut

+66

-39

lib/Bio/Tradis/RemoveTags.pm less more

0	0	package Bio::Tradis::RemoveTags;
1
	1	$Bio::Tradis::RemoveTags::VERSION = '1.4.5';
2	2	# ABSTRACT: Remove tags from seqs a fastq file
3	3
4		=head1 SYNOPSIS
5
6		Reads in a fastq file with tradis tags already attached to the start of the sequence
7		Removes tags from the sequence and quality strings
8		Outputs a file *.rmtag.fastq unless an out file is specified
9
10		use Bio::Tradis::RemoveTags;
11
12		my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc');
13		$pipeline->remove_tags();
14
15		=head1 PARAMETERS
16
17		=head2 Required
18
19		=over
20
21		=item * C<fastqfile> - path to/name of file to filter
22
23		=item * C<tag> - TraDIS tag to remove
24
25		=back
26
27		=head2 Optional
28
29		=over
30
31		=item * C<mismatch> - number of mismatches to allow when removing the tag. Default = 0
32
33		=item * C<outfile> - defaults to C<file.rmtag.fastq> for and input file named C<file.fastq>
34
35		=back
36
37		=head1 METHODS
38
39		C<remove_tags> - output all reads with the tags removed to C<outfile>
40
41		=cut
42	4
43	5	use Moose;
44	6	use Bio::Tradis::Parser::Fastq;

119	81	__PACKAGE__->meta->make_immutable;
120	82	no Moose;
121	83	1;
	84
	85	__END__
	86
	87	=pod
	88
	89	=encoding UTF-8
	90
	91	=head1 NAME
	92
	93	Bio::Tradis::RemoveTags - Remove tags from seqs a fastq file
	94
	95	=head1 VERSION
	96
	97	version 1.4.5
	98
	99	=head1 SYNOPSIS
	100
	101	Reads in a fastq file with tradis tags already attached to the start of the sequence
	102	Removes tags from the sequence and quality strings
	103	Outputs a file *.rmtag.fastq unless an out file is specified
	104
	105	use Bio::Tradis::RemoveTags;
	106
	107	my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc');
	108	$pipeline->remove_tags();
	109
	110	=head1 PARAMETERS
	111
	112	=head2 Required
	113
	114	=over
	115
	116	=item * C<fastqfile> - path to/name of file to filter
	117
	118	=item * C<tag> - TraDIS tag to remove
	119
	120	=back
	121
	122	=head2 Optional
	123
	124	=over
	125
	126	=item * C<mismatch> - number of mismatches to allow when removing the tag. Default = 0
	127
	128	=item * C<outfile> - defaults to C<file.rmtag.fastq> for and input file named C<file.fastq>
	129
	130	=back
	131
	132	=head1 METHODS
	133
	134	C<remove_tags> - output all reads with the tags removed to C<outfile>
	135
	136	=head1 AUTHOR
	137
	138	Carla Cummins <path-help@sanger.ac.uk>
	139
	140	=head1 COPYRIGHT AND LICENSE
	141
	142	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	143
	144	This is free software, licensed under:
	145
	146	The GNU General Public License, Version 3, June 2007
	147
	148	=cut

+78

-51

lib/Bio/Tradis/RunTradis.pm less more

0	0	package Bio::Tradis::RunTradis;
1
	1	$Bio::Tradis::RunTradis::VERSION = '1.4.5';
2	2	# ABSTRACT: Perform all steps required for a tradis analysis
3	3
4		=head1 SYNOPSIS
5
6		Takes a fastq file with tags already attached, filters the tags matching user input,
7		removes the tags, maps to a reference (.fa) and generates insertion site plots for use in
8		Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis.
9
10		use Bio::Tradis::RunTradis;
11
12		my $pipeline = Bio::Tradis::RunTradis->new(
13		fastqfile => 'abc',
14		reference => 'abc',
15		tag => 'abc',
16		tagdirection => '5'\|'3'
17		);
18		$pipeline->run_tradis();
19
20		=head1 PARAMETERS
21
22		=head2 Required
23
24		=over
25
26		=item * C<fastqfile> - file containing a list of fastqs (gzipped or raw) to run the
27		complete analysis on. This includes all (including
28		intermediary format conversion and sorting) steps starting from
29		filtering.
30
31		=item * C<reference> - path to/name of reference genome in fasta format (.fa)
32
33		=back
34
35		=head2 Optional
36
37		=over
38
39		=item * C<mismatch> - number of mismatches to allow when filtering/removing the tag. Default = 0
40
41		=item * C<tagdirection> - direction of the tag, 5' or 3'. Default = 3
42
43		=item * C<mapping_score> - cutoff value for mapping score when creating insertion site plots. Default = 30
44
45		=item * C<tag> - TraDIS tag to filter and then remove
46
47		=back
48
49		=head1 METHODS
50
51		C<run_tradis> - run complete analysis with given parameters
52
53		=cut
54	4
55	5	use Cwd;
56	6	use Moose;

519	469	__PACKAGE__->meta->make_immutable;
520	470	no Moose;
521	471	1;
	472
	473	__END__
	474
	475	=pod
	476
	477	=encoding UTF-8
	478
	479	=head1 NAME
	480
	481	Bio::Tradis::RunTradis - Perform all steps required for a tradis analysis
	482
	483	=head1 VERSION
	484
	485	version 1.4.5
	486
	487	=head1 SYNOPSIS
	488
	489	Takes a fastq file with tags already attached, filters the tags matching user input,
	490	removes the tags, maps to a reference (.fa) and generates insertion site plots for use in
	491	Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis.
	492
	493	use Bio::Tradis::RunTradis;
	494
	495	my $pipeline = Bio::Tradis::RunTradis->new(
	496	fastqfile => 'abc',
	497	reference => 'abc',
	498	tag => 'abc',
	499	tagdirection => '5'\|'3'
	500	);
	501	$pipeline->run_tradis();
	502
	503	=head1 PARAMETERS
	504
	505	=head2 Required
	506
	507	=over
	508
	509	=item * C<fastqfile> - file containing a list of fastqs (gzipped or raw) to run the
	510	complete analysis on. This includes all (including
	511	intermediary format conversion and sorting) steps starting from
	512	filtering.
	513
	514	=item * C<reference> - path to/name of reference genome in fasta format (.fa)
	515
	516	=back
	517
	518	=head2 Optional
	519
	520	=over
	521
	522	=item * C<mismatch> - number of mismatches to allow when filtering/removing the tag. Default = 0
	523
	524	=item * C<tagdirection> - direction of the tag, 5' or 3'. Default = 3
	525
	526	=item * C<mapping_score> - cutoff value for mapping score when creating insertion site plots. Default = 30
	527
	528	=item * C<tag> - TraDIS tag to filter and then remove
	529
	530	=back
	531
	532	=head1 METHODS
	533
	534	C<run_tradis> - run complete analysis with given parameters
	535
	536	=head1 AUTHOR
	537
	538	Carla Cummins <path-help@sanger.ac.uk>
	539
	540	=head1 COPYRIGHT AND LICENSE
	541
	542	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	543
	544	This is free software, licensed under:
	545
	546	The GNU General Public License, Version 3, June 2007
	547
	548	=cut

+39

-13

lib/Bio/Tradis/Samtools.pm less more

0	0	package Bio::Tradis::Samtools;
1
	1	$Bio::Tradis::Samtools::VERSION = '1.4.5';
2	2	# ABSTRACT: Change samtools syntax depending on version found
3	3
4		=head1 SYNOPSIS
5
6		Change samtools syntax depending on version found
7		use Bio::Tradis::Samtools;
8
9		my $obj = Bio::Tradis::Samtools->new(
10		exec => 'samtools'
11		);
12
13		$obj->run_sort();
14
15		=cut
16	4
17	5	use Moose;
18	6	use File::Spec;

99	87
100	88	1;
101	89
	90	__END__
	91
	92	=pod
	93
	94	=encoding UTF-8
	95
	96	=head1 NAME
	97
	98	Bio::Tradis::Samtools - Change samtools syntax depending on version found
	99
	100	=head1 VERSION
	101
	102	version 1.4.5
	103
	104	=head1 SYNOPSIS
	105
	106	Change samtools syntax depending on version found
	107	use Bio::Tradis::Samtools;
	108
	109	my $obj = Bio::Tradis::Samtools->new(
	110	exec => 'samtools'
	111	);
	112
	113	$obj->run_sort();
	114
	115	=head1 AUTHOR
	116
	117	Carla Cummins <path-help@sanger.ac.uk>
	118
	119	=head1 COPYRIGHT AND LICENSE
	120
	121	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	122
	123	This is free software, licensed under:
	124
	125	The GNU General Public License, Version 3, June 2007
	126
	127	=cut

+53

-26

lib/Bio/Tradis/TradisPlot.pm less more

0	0	package Bio::Tradis::TradisPlot;
	1	$Bio::Tradis::TradisPlot::VERSION = '1.4.5';
	2	# ABSTRACT: Generate plots as part of a tradis analysis
1	3
2		# ABSTRACT: Generate plots as part of a tradis analysis
	4
	5	use Moose;
	6	use Bio::Tradis::Analysis::InsertSite;
	7
	8	has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 );
	9	has 'outfile' =>
	10	( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' );
	11	has 'mapping_score' =>
	12	( is => 'rw', isa => 'Int', required => 1, default => 30 );
	13
	14	sub plot {
	15	my ($self) = @_;
	16
	17	Bio::Tradis::Analysis::InsertSite->new(
	18	filename => $self->mappedfile,
	19	output_base_filename => $self->outfile,
	20	mapping_score => $self->mapping_score
	21	)->create_plots;
	22
	23	return 1;
	24	}
	25
	26	__PACKAGE__->meta->make_immutable;
	27	no Moose;
	28	1;
	29
	30	__END__
	31
	32	=pod
	33
	34	=encoding UTF-8
	35
	36	=head1 NAME
	37
	38	Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis
	39
	40	=head1 VERSION
	41
	42	version 1.4.5
3	43
4	44	=head1 SYNOPSIS
5	45

31	71
32	72	C<plot> - create insertion site plots for reads in `mappedfile`. This file will be readable by the L<Artemis genome browser\|http://www.sanger.ac.uk/resources/software/artemis/>
33	73
	74	=head1 AUTHOR
	75
	76	Carla Cummins <path-help@sanger.ac.uk>
	77
	78	=head1 COPYRIGHT AND LICENSE
	79
	80	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	81
	82	This is free software, licensed under:
	83
	84	The GNU General Public License, Version 3, June 2007
	85
34	86	=cut
35
36		use Moose;
37		use Bio::Tradis::Analysis::InsertSite;
38
39		has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 );
40		has 'outfile' =>
41		( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' );
42		has 'mapping_score' =>
43		( is => 'rw', isa => 'Int', required => 1, default => 30 );
44
45		sub plot {
46		my ($self) = @_;
47
48		Bio::Tradis::Analysis::InsertSite->new(
49		filename => $self->mappedfile,
50		output_base_filename => $self->outfile,
51		mapping_score => $self->mapping_score
52		)->create_plots;
53
54		return 1;
55		}
56
57		__PACKAGE__->meta->make_immutable;
58		no Moose;
59		1;

+28

-2

lib/Bio/Tradis.pm less more

0	0	use strict;
1	1	use warnings;
2	2	package Bio::Tradis;
	3	$Bio::Tradis::VERSION = '1.4.5';
	4	# ABSTRACT: Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308
3	5
4		# ABSTRACT: Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308
	6	1;
	7
	8	__END__
	9
	10	=pod
	11
	12	=encoding UTF-8
	13
	14	=head1 NAME
	15
	16	Bio::Tradis - Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308
	17
	18	=head1 VERSION
	19
	20	version 1.4.5
5	21
6	22	=head1 SYNOPSIS
7	23

25	41
26	42	Most of these functions are available as standalone scripts or as perl modules.
27	43
	44	=head1 AUTHOR
	45
	46	Carla Cummins <path-help@sanger.ac.uk>
	47
	48	=head1 COPYRIGHT AND LICENSE
	49
	50	This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
	51
	52	This is free software, licensed under:
	53
	54	The GNU General Public License, Version 3, June 2007
28	55
29	56	=cut
30		1;

+53

-0

t/00-report-prereqs.dd less more

	0	do { my $x = {
	1	'configure' => {
	2	'requires' => {
	3	'ExtUtils::MakeMaker' => '0'
	4	}
	5	},
	6	'develop' => {
	7	'requires' => {
	8	'File::Spec' => '0',
	9	'IO::Handle' => '0',
	10	'IPC::Open3' => '0',
	11	'Test::More' => '0',
	12	'Test::Pod' => '1.41',
	13	'perl' => '5.006'
	14	}
	15	},
	16	'runtime' => {
	17	'requires' => {
	18	'Bio::Seq' => '0',
	19	'Bio::SeqIO' => '0',
	20	'Cwd' => '0',
	21	'Data::Dumper' => '0',
	22	'Exception::Class' => '0',
	23	'File::Basename' => '0',
	24	'File::Path' => '0',
	25	'File::Spec' => '0',
	26	'File::Temp' => '0',
	27	'FindBin' => '0',
	28	'Getopt::Long' => '0',
	29	'Moose' => '0',
	30	'Text::CSV' => '0',
	31	'Try::Tiny' => '0',
	32	'strict' => '0',
	33	'warnings' => '0'
	34	}
	35	},
	36	'test' => {
	37	'recommends' => {
	38	'CPAN::Meta' => '2.120900'
	39	},
	40	'requires' => {
	41	'Env::Path' => '0.18',
	42	'ExtUtils::MakeMaker' => '0',
	43	'File::Spec' => '0',
	44	'Test::Exception' => '0',
	45	'Test::Files' => '0',
	46	'Test::More' => '0',
	47	'Test::Most' => '0'
	48	}
	49	}
	50	};
	51	$x;
	52	}⏎

+193

-0

t/00-report-prereqs.t less more

	0	#!perl
	1
	2	use strict;
	3	use warnings;
	4
	5	# This test was generated by Dist::Zilla::Plugin::Test::ReportPrereqs 0.027
	6
	7	use Test::More tests => 1;
	8
	9	use ExtUtils::MakeMaker;
	10	use File::Spec;
	11
	12	# from $version::LAX
	13	my $lax_version_re =
	14	qr/(?: undef \| (?: (?:[0-9]+) (?: \. \| (?:\.[0-9]+) (?:_[0-9]+)? )?
	15	\|
	16	(?:\.[0-9]+) (?:_[0-9]+)?
	17	) \| (?:
	18	v (?:[0-9]+) (?: (?:\.[0-9]+)+ (?:_[0-9]+)? )?
	19	\|
	20	(?:[0-9]+)? (?:\.[0-9]+){2,} (?:_[0-9]+)?
	21	)
	22	)/x;
	23
	24	# hide optional CPAN::Meta modules from prereq scanner
	25	# and check if they are available
	26	my $cpan_meta = "CPAN::Meta";
	27	my $cpan_meta_pre = "CPAN::Meta::Prereqs";
	28	my $HAS_CPAN_META = eval "require $cpan_meta; $cpan_meta->VERSION('2.120900')" && eval "require $cpan_meta_pre"; ## no critic
	29
	30	# Verify requirements?
	31	my $DO_VERIFY_PREREQS = 1;
	32
	33	sub _max {
	34	my $max = shift;
	35	$max = ( $_ > $max ) ? $_ : $max for @_;
	36	return $max;
	37	}
	38
	39	sub _merge_prereqs {
	40	my ($collector, $prereqs) = @_;
	41
	42	# CPAN::Meta::Prereqs object
	43	if (ref $collector eq $cpan_meta_pre) {
	44	return $collector->with_merged_prereqs(
	45	CPAN::Meta::Prereqs->new( $prereqs )
	46	);
	47	}
	48
	49	# Raw hashrefs
	50	for my $phase ( keys %$prereqs ) {
	51	for my $type ( keys %{ $prereqs->{$phase} } ) {
	52	for my $module ( keys %{ $prereqs->{$phase}{$type} } ) {
	53	$collector->{$phase}{$type}{$module} = $prereqs->{$phase}{$type}{$module};
	54	}
	55	}
	56	}
	57
	58	return $collector;
	59	}
	60
	61	my @include = qw(
	62
	63	);
	64
	65	my @exclude = qw(
	66
	67	);
	68
	69	# Add static prereqs to the included modules list
	70	my $static_prereqs = do './t/00-report-prereqs.dd';
	71
	72	# Merge all prereqs (either with ::Prereqs or a hashref)
	73	my $full_prereqs = _merge_prereqs(
	74	( $HAS_CPAN_META ? $cpan_meta_pre->new : {} ),
	75	$static_prereqs
	76	);
	77
	78	# Add dynamic prereqs to the included modules list (if we can)
	79	my ($source) = grep { -f } 'MYMETA.json', 'MYMETA.yml';
	80	my $cpan_meta_error;
	81	if ( $source && $HAS_CPAN_META
	82	&& (my $meta = eval { CPAN::Meta->load_file($source) } )
	83	) {
	84	$full_prereqs = _merge_prereqs($full_prereqs, $meta->prereqs);
	85	}
	86	else {
	87	$cpan_meta_error = $@; # capture error from CPAN::Meta->load_file($source)
	88	$source = 'static metadata';
	89	}
	90
	91	my @full_reports;
	92	my @dep_errors;
	93	my $req_hash = $HAS_CPAN_META ? $full_prereqs->as_string_hash : $full_prereqs;
	94
	95	# Add static includes into a fake section
	96	for my $mod (@include) {
	97	$req_hash->{other}{modules}{$mod} = 0;
	98	}
	99
	100	for my $phase ( qw(configure build test runtime develop other) ) {
	101	next unless $req_hash->{$phase};
	102	next if ($phase eq 'develop' and not $ENV{AUTHOR_TESTING});
	103
	104	for my $type ( qw(requires recommends suggests conflicts modules) ) {
	105	next unless $req_hash->{$phase}{$type};
	106
	107	my $title = ucfirst($phase).' '.ucfirst($type);
	108	my @reports = [qw/Module Want Have/];
	109
	110	for my $mod ( sort keys %{ $req_hash->{$phase}{$type} } ) {
	111	next if $mod eq 'perl';
	112	next if grep { $_ eq $mod } @exclude;
	113
	114	my $file = $mod;
	115	$file =~ s{::}{/}g;
	116	$file .= ".pm";
	117	my ($prefix) = grep { -e File::Spec->catfile($_, $file) } @INC;
	118
	119	my $want = $req_hash->{$phase}{$type}{$mod};
	120	$want = "undef" unless defined $want;
	121	$want = "any" if !$want && $want == 0;
	122
	123	my $req_string = $want eq 'any' ? 'any version required' : "version '$want' required";
	124
	125	if ($prefix) {
	126	my $have = MM->parse_version( File::Spec->catfile($prefix, $file) );
	127	$have = "undef" unless defined $have;
	128	push @reports, [$mod, $want, $have];
	129
	130	if ( $DO_VERIFY_PREREQS && $HAS_CPAN_META && $type eq 'requires' ) {
	131	if ( $have !~ /\A$lax_version_re\z/ ) {
	132	push @dep_errors, "$mod version '$have' cannot be parsed ($req_string)";
	133	}
	134	elsif ( ! $full_prereqs->requirements_for( $phase, $type )->accepts_module( $mod => $have ) ) {
	135	push @dep_errors, "$mod version '$have' is not in required range '$want'";
	136	}
	137	}
	138	}
	139	else {
	140	push @reports, [$mod, $want, "missing"];
	141
	142	if ( $DO_VERIFY_PREREQS && $type eq 'requires' ) {
	143	push @dep_errors, "$mod is not installed ($req_string)";
	144	}
	145	}
	146	}
	147
	148	if ( @reports ) {
	149	push @full_reports, "=== $title ===\n\n";
	150
	151	my $ml = _max( map { length $_->[0] } @reports );
	152	my $wl = _max( map { length $_->[1] } @reports );
	153	my $hl = _max( map { length $_->[2] } @reports );
	154
	155	if ($type eq 'modules') {
	156	splice @reports, 1, 0, ["-" x $ml, "", "-" x $hl];
	157	push @full_reports, map { sprintf(" %s %s\n", -$ml, $_->[0], $hl, $_->[2]) } @reports;
	158	}
	159	else {
	160	splice @reports, 1, 0, ["-" x $ml, "-" x $wl, "-" x $hl];
	161	push @full_reports, map { sprintf(" %s %s %*s\n", -$ml, $_->[0], $wl, $_->[1], $hl, $_->[2]) } @reports;
	162	}
	163
	164	push @full_reports, "\n";
	165	}
	166	}
	167	}
	168
	169	if ( @full_reports ) {
	170	diag "\nVersions for all modules listed in $source (including optional ones):\n\n", @full_reports;
	171	}
	172
	173	if ( $cpan_meta_error \|\| @dep_errors ) {
	174	diag "\n* WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING *\n";
	175	}
	176
	177	if ( $cpan_meta_error ) {
	178	my ($orig_source) = grep { -f } 'MYMETA.json', 'MYMETA.yml';
	179	diag "\nCPAN::Meta->load_file('$orig_source') failed with: $cpan_meta_error\n";
	180	}
	181
	182	if ( @dep_errors ) {
	183	diag join("\n",
	184	"\nThe following REQUIRED prerequisites were not satisfied:\n",
	185	@dep_errors,
	186	"\n"
	187	);
	188	}
	189
	190	pass;
	191
	192	# vim: ts=4 sts=4 sw=4 et:

-0

t/requires_external.t less more

	0	#!/usr/bin/env perl
	1
	2	use Test::Most;
	3	plan tests => 6;
	4	bail_on_fail if 0;
	5	use Env::Path 0.18 'PATH';
	6
	7	ok(scalar PATH->Whence($_), "$_ in PATH") for qw(awk samtools gunzip gzip smalt tabix);
	8

+129

-0

xt/author/00-compile.t less more

	0	use 5.006;
	1	use strict;
	2	use warnings;
	3
	4	# this test was generated with Dist::Zilla::Plugin::Test::Compile 2.058
	5
	6	use Test::More;
	7
	8	plan tests => 35;
	9
	10	my @module_files = (
	11	'Bio/Tradis.pm',
	12	'Bio/Tradis/AddTagsToSeq.pm',
	13	'Bio/Tradis/Analysis/Exceptions.pm',
	14	'Bio/Tradis/Analysis/InsertSite.pm',
	15	'Bio/Tradis/CombinePlots.pm',
	16	'Bio/Tradis/CommandLine/AddTags.pm',
	17	'Bio/Tradis/CommandLine/CheckTags.pm',
	18	'Bio/Tradis/CommandLine/FilterFastqTags.pm',
	19	'Bio/Tradis/CommandLine/PlotCombine.pm',
	20	'Bio/Tradis/CommandLine/PlotTradis.pm',
	21	'Bio/Tradis/CommandLine/RemoveFastqTags.pm',
	22	'Bio/Tradis/CommandLine/RunMapping.pm',
	23	'Bio/Tradis/CommandLine/TradisAnalysis.pm',
	24	'Bio/Tradis/CommandLine/TradisBam.pm',
	25	'Bio/Tradis/DetectTags.pm',
	26	'Bio/Tradis/Exception.pm',
	27	'Bio/Tradis/FilterTags.pm',
	28	'Bio/Tradis/Map.pm',
	29	'Bio/Tradis/Parser/Bam.pm',
	30	'Bio/Tradis/Parser/Cigar.pm',
	31	'Bio/Tradis/Parser/Fastq.pm',
	32	'Bio/Tradis/RemoveTags.pm',
	33	'Bio/Tradis/RunTradis.pm',
	34	'Bio/Tradis/Samtools.pm',
	35	'Bio/Tradis/TradisPlot.pm'
	36	);
	37
	38	my @scripts = (
	39	'bin/add_tradis_tags',
	40	'bin/bacteria_tradis',
	41	'bin/check_tradis_tags',
	42	'bin/combine_tradis_plots',
	43	'bin/filter_tradis_tags',
	44	'bin/remove_tradis_tags',
	45	'bin/tradis_gene_insert_sites',
	46	'bin/tradis_merge_plots',
	47	'bin/tradis_plot'
	48	);
	49
	50	# no fake home requested
	51
	52	my @switches = (
	53	-d 'blib' ? '-Mblib' : '-Ilib',
	54	);
	55
	56	use File::Spec;
	57	use IPC::Open3;
	58	use IO::Handle;
	59
	60	open my $stdin, '<', File::Spec->devnull or die "can't open devnull: $!";
	61
	62	my @warnings;
	63	for my $lib (@module_files)
	64	{
	65	# see L<perlfaq8/How can I capture STDERR from an external command?>
	66	my $stderr = IO::Handle->new;
	67
	68	diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} }
	69	$^X, @switches, '-e', "require q[$lib]"))
	70	if $ENV{PERL_COMPILE_TEST_DEBUG};
	71
	72	my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-e', "require q[$lib]");
	73	binmode $stderr, ':crlf' if $^O eq 'MSWin32';
	74	my @_warnings = <$stderr>;
	75	waitpid($pid, 0);
	76	is($?, 0, "$lib loaded ok");
	77
	78	shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/
	79	and not eval { +require blib; blib->VERSION('1.01') };
	80
	81	if (@_warnings)
	82	{
	83	warn @_warnings;
	84	push @warnings, @_warnings;
	85	}
	86	}
	87
	88	foreach my $file (@scripts)
	89	{ SKIP: {
	90	open my $fh, '<', $file or warn("Unable to open $file: $!"), next;
	91	my $line = <$fh>;
	92
	93	close $fh and skip("$file isn't perl", 1) unless $line =~ /^#!\s(?:\Sperl\S)((?:\s+-\w))(?:\s#.*)?$/;
	94	@switches = (@switches, split(' ', $1)) if $1;
	95
	96	close $fh and skip("$file uses -T; not testable with PERL5LIB", 1)
	97	if grep { $_ eq '-T' } @switches and $ENV{PERL5LIB};
	98
	99	my $stderr = IO::Handle->new;
	100
	101	diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} }
	102	$^X, @switches, '-c', $file))
	103	if $ENV{PERL_COMPILE_TEST_DEBUG};
	104
	105	my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-c', $file);
	106	binmode $stderr, ':crlf' if $^O eq 'MSWin32';
	107	my @_warnings = <$stderr>;
	108	waitpid($pid, 0);
	109	is($?, 0, "$file compiled ok");
	110
	111	shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/
	112	and not eval { +require blib; blib->VERSION('1.01') };
	113
	114	# in older perls, -c output is simply the file portion of the path being tested
	115	if (@_warnings = grep { !/\bsyntax OK$/ }
	116	grep { chomp; $_ ne (File::Spec->splitpath($file))[2] } @_warnings)
	117	{
	118	warn @_warnings;
	119	push @warnings, @_warnings;
	120	}
	121	} }
	122
	123
	124
	125	is(scalar(@warnings), 0, 'no warnings found')
	126	or diag 'got warnings: ', ( Test::More->can('explain') ? Test::More::explain(\@warnings) : join("\n", '', @warnings) );
	127
	128

-0

xt/author/pod-syntax.t less more

	0	#!perl
	1	# This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests.
	2	use strict; use warnings;
	3	use Test::More;
	4	use Test::Pod 1.41;
	5
	6	all_pod_files_ok();