testdata/filter_nh_file01.gff3 - genometools (HEAD)

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example_1.bam
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filter_luafilter_filtered_LTR.gff3
filter_luafilter_filtered_orf_frame.gff3
filter_luafilter_filtered_orf_pos.gff3
filter_luafilter_filtered_orfs.gff3
filter_luafilter_test.gff3
filter_luafilter_test_no_frame_attribute.gff3
filter_nh_file01.gff3
filter_nh_file02.gff3
filter_nh_file03.gff3
filter_nh_file04.gff3
filter_targetbest_complex_test.gff3
filter_targetbest_complex_test.out
filter_targetbest_multiple_test.gff3
filter_targetbest_simple_test.gff3
filter_targetbest_simple_test.out
foo.32.des
foo.32.esq
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foo.32.info_nomap
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foobar.fas
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foorcfoo.fas
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frompos.fas
gap_fail1.gff3
gap_fail2.gff3
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gap_fail4.gff3
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gap_fail7.gff3
genbank_test.gbk
genbank_test1.gbk
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genbank_test7.gbk
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genome_stream_stdin.gff3
gff3_file_1_short.txt
gff3_file_1_short_sorted.txt
gff3_numeric_a.gff
gff3_numeric_mixed.gff3
gff3_numeric_mixed.out
gff3_numeric_only.gff3
gff3_numeric_only.out
gmap2gff3_prob.gmap
gmap2gff3_prob.out
graphics_curve_test_coords.txt
graphics_test.out
gt.supp
gt_bioseq_fail_1.fas
gt_bioseq_fail_2.fas
gt_bioseq_fail_3.fas
gt_bioseq_fail_4.fas
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gt_bioseq_seqlengthdistri.out
gt_bioseq_succ_1.fas
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gt_bioseq_succ_3.fas
gt_bioseq_succ_3.gc
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gt_bioseq_succ_3.out3
gt_cds_descrange_multi.fas
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gt_cds_descrange_wrong_range.fas
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gt_cds_test_1.in
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gt_chseqids_test_2.gff3
gt_chseqids_test_2.out
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gt_chseqids_test_3.gff3
gt_chseqids_test_4.chseqids
gt_chseqids_test_4.gff3
gt_chseqids_test_4.out
gt_chseqids_test_5.chseqids
gt_chseqids_test_5.gff3
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gt_csa_prob_1.debug
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gt_encseq_col_test1.fasta
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gt_extractfeat_mappings.gff3
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gt_extractfeat_mappings_seprm.lua
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gt_extractfeat_retainids.gff3
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gt_extractfeat_seqid.fas
gt_extractfeat_seqid_target.fas
gt_extractfeat_seqid_target.gff3
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gt_extractfeat_succ_3.gff3
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gt_fingerprint_extract.out
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gt_gff3_addintrons_overlapping_exons_with_introns.gff3
gt_gff3_fail_1.gff3
gt_gff3_illegal_feature_start.gff3
gt_gff3_illegal_region_start.gff3
gt_gff3_linesort.in.gff3
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gt_gff3_offset_test.gff3
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gt_gtf_to_gff3_test.gff3
gt_gtf_to_gff3_test.gtf
gt_gtf_to_gff3_test_fail_no_flank.gtf
gt_gtf_to_gff3_test_inconsistent_strand1.gtf
gt_gtf_to_gff3_test_inconsistent_strand2.gtf
gt_gtf_to_gff3_test_stop_codon_in_cds.gff3
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gt_seqorder_test.fas
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gt_sketch_multiline_without_parent.gff3
gt_sketch_textwidth.gff3
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gt_splicesiteinfo_test_1.out
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gt_splicesiteinfo_test_6.gff3
gt_splicesiteinfo_test_6.mapping
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gt_translate.in
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gt_uniq_test_2.gff3
gt_uniq_test_2.out
gt_uniq_test_3.gff3
gt_uniq_test_3.out
gt_uniq_test_4.gff3
gt_uniq_test_4.out
gt_uniq_test_5.gff3
gt_uniq_test_5.out
gt_uniq_test_6.gff3
gt_uniq_test_6.out
gt_view.sh
gt_view_prob_1.gff3
gt_view_prob_2.gff3
header.gff3
header_3_1_21.gff3
identity_score_matrix
illegal_is_circular_value.gff3
illegal_uppercase_attribute.gff3
inconsistent_sequence_ids.gff3
interfeat_pseudo.gff3
interfeat_pseudo.out
invalidregex.XRF_abbr
invalidtag.XRF_abbr
is_circular_example.gff3
is_circular_example_with_sequence_region.gff3
linesort_test_1.gff3
linesort_test_1.out
linesort_test_2.gff3
linesort_test_2.out
linesort_test_3.gff3
linesort_test_3.out
lua_aaseq.fas
lua_dnaseq.fas
marker.fas
marker.out
match_part_gap.gff3
matchtool_blast.db
matchtool_blast.match
matchtool_blast.match.bz2
matchtool_blast.match.gz
matchtool_blast.out
matchtool_blast_corrupt.match
matchtool_blast_empty.match
matchtool_blast_empty.out
matchtool_blast_neg.match
matchtool_blast_too_few.match
matchtool_blast_too_many.match
matchtool_blastalln.out
matchtool_blastallp.out
matchtool_blastn.db
matchtool_blastn.out
matchtool_blastn.query
matchtool_blastp.db
matchtool_blastp.out
matchtool_blastp.query
matchtool_open.match
matchtool_open.match.bz2
matchtool_open.match.gz
matchtool_open.out
matchtool_open_corrupt.match
matchtool_open_empty.match
matchtool_open_empty.out
matchtool_open_neg.match
matchtool_open_too_few.match
matchtool_open_too_many.match
matchtool_see-ext.match
md5_seqid_missing_seqid.gff3
md5_seqid_too_short.gff3
md5_seqid_wrong_separator.gff3
merge_with_seq.gff3
mergefeat.gff3
mergefeat.out
mergefeat_no_merge.gff3
meta_directives.gff3
mini_peptide_repeats.fas
minimal_fasta.gff3
minimal_fasta_without_directive.gff3
missing_gff3_header.gff3
missingabbr.XRF_abbr
multi_feature_different_sequence_id.gff3
multi_feature_multi.gff3
multi_feature_orphan_fail.gff3
multi_feature_orphan_succ.gff3
multi_feature_simple.gff3
multi_feature_simple_reverted.gff3
multi_feature_undefined_parent.gff3
multi_feature_with_different_parent_1.gff3
multi_feature_with_different_parent_1_tidy.gff3
multi_feature_with_different_parent_2.gff3
multi_feature_with_different_parent_2_tidy.gff3
multiple_header_lines.gff3
multiple_top_level_parents.gff3
not_sorted.gff3
nowildcardatend.fna
nowildcardatend_rev.fna
order_sketch_out.txt
orphaned_parent.gff3
png_devel_1.gff3
png_devel_10.gff3
png_devel_11.gff3
png_devel_12.gff3
png_devel_2.gff3
png_devel_3.gff3
png_devel_4.gff3
png_devel_5.gff3
png_devel_6.gff3
png_devel_7.gff3
png_devel_8.gff3
png_devel_9.gff3
png_prob_1.gff3
png_prob_2.gff3
png_prob_3.gff3
png_prob_4.gff3
png_prob_5.gff3
png_test_1.gff3
png_test_3.gff3
problematic.fas
pseudo_feature_minimal.gff3
Q1.gz
query-fwd.match
query-rev.match
Query1
Query2
Query3
Random-Small.embl
Random-Small.fna
Random-Small.gbk
Random.embl
Random.fna
Random.gbk
Random.magicmatch
Random159.embl
Random159.fna
Random159.gbk
Random160.embl
Random160.fna
Random160.gbk
Random80.fna
RandomN.embl
RandomN.fna
RandomN.gbk
RandomN.magicmatch
rcr_testreads.fq
rcr_testreads_on_seq.bam
rcr_testreads_on_seq.bam.bai
rcr_testreads_on_seq.sam
rcr_testseq.fa
rcr_testseq.fa.fai
Reads1.fna
Reads2-spmitv.txt
Reads2.fna
Reads3.fna
Reference1
Reference2
regionmapping_1.lua
regionmapping_2.lua
regionmapping_3.lua
regionmapping_4.lua
regionmapping_5.lua
regionmapping_6.lua
Repfind-example.fna
resetsource.gff3
resetsource.out
retain_1.gff3
retain_2.gff3
retain_both.gff3
retainids.gff3
reverse_feature_order.gff3
reverse_feature_order.out
reverse_feature_order_multiple_parents.gff3
reverse_feature_order_multiple_parents.out
reverse_standard_gene_as_tree.gff3
revision_numbers.gff3
revision_numbers.out
sain.fna
Scaffold_102.fa
Scaffold_102.gff3
Scaffold_102.joined.out
Scaffold_102.out
script_example.out
script_filter_output.txt
see-ext-ani-at1MB-U8.txt
see-ext-at1MB-400-al-from-dtrace.matches
see-ext-at1MB-400-cigar.matches
see-ext-at1MB-400-cigarX.matches
see-ext-at1MB-400-dtrace.matches
see-ext-at1MB-400-evalue-bitscore.matches
see-ext-at1MB-400-seqdesc.matches
see-ext-at1MB-400-seqlength.matches
see-ext-at1MB-400-trace.matches
see-ext-at1MB-500-al.matches
see-ext-at1MB-500-alignment-seed_in_algn.matches
see-ext-at1MB-500-failed_seed.matches
see-ext-at1MB-Atinsert100-evalue-bitscore-cigar-seqlength.matches
see-ext-at1MB-Atinsert100-evalue-bitscore-cigarX-seqlength.matches
see-ext-at1MB-maxmat250.matches
see-ext-at1MB-mincoverage200-tabsep.matches
see-ext-at1MB-U8-200-al-from-dtrace.matches
see-ext-at1MB-u8-failed_seed-evalue.matches
see-ext-at1MB-u8-maxmat30.matches
see-ext-at1MB-u8.matches
see-ext-at1MB.matches
see-ext-fastq_long-u8.matches
see-ext-fastq_long.matches
see-ext-paired-u8.matches
see-ext-paired.matches
see-ext-U8-evalue-bitscore.matches
seedextend1.out.gz
seedextend2.out.gz
seedextend3.out
self_referential.gff3
seqfilter_prot_wildcard.fas
seqfilter_prot_wildcard_no_wildcards.fas
sequence_region_1.gff3
sequence_region_2.gff3
sequence_region_joined.gff3
sequence_region_negative_end.gff3
sequence_region_negative_start.gff3
shorten_desc.clipped.fas
shorten_desc.embl
shorten_desc.fas
shorten_desc.gbk
shorthand.XRF_abbr
simple_orphan.gff3
Small.embl
Small.fna
Small.gbk
small_poly.fas
Smalldup.fna
solid_color_reads.fastq
splice_site_prob.gff3
splice_site_prob.out
Splintoptions
standard_fasta_example.fas
standard_fasta_example.gff3
standard_fasta_example_only_annotation.gff3
standard_fasta_example_rejoined.gff3
standard_fasta_example_with_id.gff3
standard_fasta_example_with_id.out
standard_gene_as_dag.gff3
standard_gene_as_dag_sorted.gff3
standard_gene_as_tree.blocks
standard_gene_as_tree.gff3
standard_gene_as_tree.header
standard_gene_as_tree.hotspots
standard_gene_as_tree.recmaps
standard_gene_as_tree.types
standard_gene_simple.gff3
standard_gene_with_introns_as_tree.gff3
sw100K1.fsa
sw100K1.magicmatch
sw100K2.fsa
sw100K2.magicmatch
target_attribute_swapped_range.gff3
target_attribute_without_strand.gff3
terminator_separation.gff3
test.XRF_abbr
test1.fasta
test1.fastq
test10_multiline.fastq
test2_wrong_begin.fastq
test3_different_seqnames.fastq
test4_different_seqlengths.fastq
test5_tricky.fastq
test6_premature_end.fastq
test7_empty_seq.fastq
test9_uneven_length.fastq
test_1_multiset.txt
test_1_result.txt
test_1_text.txt
test_2_multiset.txt
test_2_result.txt
test_2_text.txt
test_3_multiset.txt
test_3_result.txt
test_3_text.txt
testspec.lua
testspec_fi.lua
trackname1.out
trackname1.style
transcript.gff3
transcript.png
transcript.style
transient_edges_bug.gff3
trembl-difflenkey.faa
trembl-emptykey.faa
trembl-eqlen.faa
trembl-keys.txt
trembl-wrongkey.txt
trembl.faa
trkeys-result.txt
trkeys.txt
tRNA.dos.fas
trna_glutamine.embl
trna_glutamine.fna
trna_glutamine.gbk
trna_glutamine.out
TTT-small-wrongchar.embl
TTT-small-wrongchar.fna
TTT-small-wrongchar.gbk
TTT-small.embl
TTT-small.fna
TTT-small.gbk
TTTN.fna
two_fasta_seqs.gff3
two_fasta_seqs_without_sequence_regions.gff3
U89959_cds.fas
U89959_cds.gff3
U89959_cds_1.fas
U89959_cds_10.fas
U89959_cds_11.fas
U89959_cds_12.fas
U89959_cds_13.fas
U89959_cds_14.fas
U89959_cds_16.fas
U89959_cds_2.fas
U89959_cds_21.fas
U89959_cds_22.fas
U89959_cds_23.fas
U89959_cds_24.fas
U89959_cds_25.fas
U89959_cds_3.fas
U89959_cds_4.fas
U89959_cds_5.fas
U89959_cds_6.fas
U89959_cds_9.fas
U89959_csas.gff3
U89959_csas.gff3md5
U89959_csas.gff3md5old
U89959_ests.checklist
U89959_ests.checklist_uniq
U89959_ests.fas
U89959_ests.magicmatch
U89959_ests_gi_8690080_soft_masked.fas
U89959_ests_gi_8690080_unmasked.checklist
U89959_ests_no_wildcards.fas
U89959_ests_unique.fas
U89959_genomic.fas
U89959_genomic.magicmatch
U89959_ginums.corrupt
U89959_ginums.out
U89959_ginums.txt
U89959_sas.gff3
U89959_sas.gff3md5
U89959_sas.gff3md5old
U89959_sas.minus_targets
undefined_parent.gff3
unknown_meta_directive.gff3
unknown_meta_directive_without_argument.gff3
unsorted_gff3_file.txt
uppercase_attributes.gff3
Verysmall.embl
Verysmall.fna
Verysmall.gbk
wildcardatend.fna
wildcardatend_rev.fna

filter_nh_file01.gff3 @HEAD — raw · history · blame

##gff-version 3
seq0	LTRharvest	repeat_region	473776	477112	.	?	.	ID=repeat_region1
seq0	LTRharvest	target_site_duplication	473776	473779	.	?	.	Parent=repeat_region1
seq0	LTRharvest	LTR_retrotransposon	473780	477108	.	?	.	ID=LTR_retrotransposon1;Parent=repeat_region1
seq0	ORFfinder	reading_frame	473826	474046	.	+	.	Parent=LTR_retrotransposon1;frame=1
seq0	ORFfinder	reading_frame	473936	474007	.	-	.	Parent=LTR_retrotransposon1;frame=2
seq0	LTRharvest	target_site_duplication	477109	477112	.	?	.	Parent=repeat_region1
###