Codebase list cd-hit / 5ba8578
Merge pull request #86 from tseemann/fix_perl_hashbangs Set all hashbangs to /usr/bin/env perl Weizhong Li authored 4 years ago GitHub committed 4 years ago
59 changed file(s) with 61 addition(s) and 61 deletion(s). Raw diff Collapse all Expand all
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FET.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Storable;
33 use strict;
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cd-hit-2d-para.pl less more
0 #!/usr/bin/perl -w
0 #!/usr/bin/env perl
11 # =============================================================================
22 # CD-HIT
33 # http://cd-hit.org/
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cd-hit-auxtools/cd-hit-dup-PE-out.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my $script_name = $0;
33 my $script_dir = $0;
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cd-hit-clstr_2_blm8.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 #
22
33 my $rep;
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cd-hit-div.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #not like cd-hit-div, this script do not sort input
33 #or throw away seq
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cd-hit-para.pl less more
0 #!/usr/bin/perl -w
0 #!/usr/bin/env perl
11 # =============================================================================
22 # CD-HIT
33 # http://cd-hit.org/
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clstr2tree.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 $clstr = shift;
33 $fr = shift; # for nr80.clstr $fr = 0.8
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clstr2txt.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my $no = 0;
33 my $clstr_no = "";
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clstr2xml.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...]
33 #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results
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clstr_cut.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #keep only top $no proteins in cluster
33
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clstr_list.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Storable;
33 use strict;
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clstr_list_sort.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Storable;
33 use strict;
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clstr_merge.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 # the order of clusters need to be identical
33 my ($master_clstr, @clstr) = @ARGV;
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clstr_merge_noorder.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 # order of clusters don't need to be the same
33 # but then I have to read everything into memory
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clstr_quality_eval.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 ## calculate the sensitivity and specificity of clusters
33 ## if the input fasta file has pre-defined classification term
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clstr_quality_eval_by_link.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 ## calculate the sensitivity and specificity of clusters
33 ## if the input fasta file has pre-defined classification term
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clstr_reduce.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22
33 $file90 = shift;
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clstr_renumber.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 $no = 0;
22 while($ll=<>){
33 if ($ll =~ /^>Cluster (\d+)/) {
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clstr_rep.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 $rep = "";
33 $no = 0;
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clstr_reps_faa_rev.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 # output single fasta file
22 # for each cluster output at least $cutoff seqs
33
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clstr_rev.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 # if nr90 from nr100 and
22 # nr80 from nr90, so I have nr90.clstr and nr80.clstr
33 # but, in nr80.clstr, some gi numbers whose from nr100 are there
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clstr_select.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #my $by = shift;
33 my $min;
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clstr_select_rep.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #my $by = shift;
33 my $min;
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clstr_size_histogram.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 if(@ARGV==0){
33 print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n";
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clstr_size_stat.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 if(@ARGV==0){
33 print "Usage:\n\tclstr_size_stat.pl clstr_file\n";
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clstr_sort_by.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my $sort_by_what = shift;
33 $sort_by_what = "no" unless $sort_by_what;
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clstr_sort_prot_by.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my $sort_by = shift;
33 $sort_by = "len" unless ($sort_by);
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clstr_sql_tbl.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 if(@ARGV==0){
33 print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n";
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clstr_sql_tbl_sort.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 if(@ARGV==0){
33 print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n";
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make_multi_seq.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #note you have to use "-d 0" in the cd-hit run
33 #note you better to use "-g 1" in the cd-hit run
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plot_2d.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Image::Magick;
33
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plot_len1.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 $file90 = shift;
33 $segs = shift;
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psi-cd-hit/cd-hit-div.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 #not like cd-hit-div, this script do not sort input
33 #or throw away seq
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psi-cd-hit/clstr_select_rep.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my $by = shift;
33 my $min;
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psi-cd-hit/clstr_select_seq.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my $by = shift;
33 my $min;
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psi-cd-hit/fetch_fasta_by_ids.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my ($gi_file, $seq_file) = @ARGV;
33
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psi-cd-hit/fetch_fasta_exclude_ids.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 my ($gi_file, $seq_file) = @ARGV;
33
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psi-cd-hit/psi-2d.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22
33 my $script_name = $0;
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psi-cd-hit/psi-cd-hit-local-old.pl less more
0 #!/usr/bin/perl -w
0 #!/usr/bin/env perl
11 ################################################################################
22 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
33 ################################################################################
11371137
11381138 open(REPERL, "> $remote_perl_script") || die;
11391139 print REPERL <<EOD;
1140 #!/usr/bin/perl
1140 #!/usr/bin/env perl
11411141 \$host = shift;
11421142 \$arg = shift;
11431143
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psi-cd-hit/psi-cd-hit-local.pl less more
0 #!/usr/bin/perl -w
0 #!/usr/bin/env perl
11 ################################################################################
22 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
33 ################################################################################
13711371
13721372 open(REPERL, "> $remote_perl_script") || die;
13731373 print REPERL <<EOD;
1374 #!/usr/bin/perl
1374 #!/usr/bin/env perl
13751375 \$host = shift;
13761376 \$instance = shift;
13771377 \$arg = shift;
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psi-cd-hit/psi-cd-hit-old.pl less more
0 #!/usr/bin/perl -w
0 #!/usr/bin/env perl
11 ################################################################################
22 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
33 ################################################################################
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psi-cd-hit/psi-cd-hit.pl less more
0 #!/usr/bin/perl -w
0 #!/usr/bin/env perl
11 ################################################################################
22 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
33 ################################################################################
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usecases/Miseq-16S/16S-ref-db-PE-splice.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ## =========================== NGS tools ==========================================
22 ## NGS tools for metagenomic sequence analysis
33 ## May also be used for other type NGS data analysis
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usecases/Miseq-16S/NG-Omics-Miseq-16S.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ################################################################################
22 # NGS workflow by Weizhong Li, http://weizhongli-lab.org
33 ################################################################################
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usecases/Miseq-16S/NG-Omics-WF.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 # =============================== NG-Omics-WF ==================================
22 # _ _ _____ ____ _ __ ________
33 # | \ | |/ ____| / __ \ (_) \ \ / / ____|
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usecases/Miseq-16S/OTU_2_taxon_table.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ## =========================== NGS tools ==========================================
22 ## NGS tools for metagenomic sequence analysis
33 ## May also be used for other type NGS data analysis
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usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Getopt::Std;
33 my $script_name = $0;
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usecases/Miseq-16S/clstr_2_OTU_table.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 #
22 use Getopt::Std;
33 getopts("i:s:S:o:f:j:b:h:",\%opts);
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usecases/Miseq-16S/filter-chimeric-and-small.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Getopt::Std;
33 my $script_name = $0;
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usecases/Miseq-16S/filter-chimeric-by-ref.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Getopt::Std;
33 my $script_name = $0;
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usecases/Miseq-16S/filter-nontop-ref.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Getopt::Std;
33 my $script_name = $0;
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usecases/Miseq-16S/filter-refonly-cluster.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Getopt::Std;
33 my $script_name = $0;
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usecases/Miseq-16S/greengene-ann1.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ## =========================== NGS tools ==========================================
22 ## NGS tools for metagenomic sequence analysis
33 ## May also be used for other type NGS data analysis
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usecases/Miseq-16S/pool_samples.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 #
22 use Getopt::Std;
33 getopts("s:S:o:f:j:",\%opts);
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usecases/Miseq-16S/silva-ann1.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ## =========================== NGS tools ==========================================
22 ## NGS tools for metagenomic sequence analysis
33 ## May also be used for other type NGS data analysis
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usecases/Miseq-16S/silva-qiime-format-ann1.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ## =========================== NGS tools ==========================================
22 ## NGS tools for metagenomic sequence analysis
33 ## May also be used for other type NGS data analysis
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usecases/miRNA-seq/NG-Omics-miRNA-seq.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 ################################################################################
22 # NGS workflow by Weizhong Li, http://weizhongli-lab.org
33 ################################################################################
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usecases/miRNA-seq/clstr_2_miRNA-table.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11 #
22 use Getopt::Std;
33 getopts("i:s:S:o:f:j:",\%opts);
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usecases/miRNA-seq/filter-small-cluster.pl less more
0 #!/usr/bin/perl
0 #!/usr/bin/env perl
11
22 use Getopt::Std;
33 my $script_name = $0;