| Previous changeset 5:69e0806b63a4 (2019-10-01) Next changeset 7:4dea02886337 (2019-11-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" |
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modified:
gffread.xml test-data/Homo_sapiens.GRCh37_19.71.gff3 test-data/ecoli-k12.processed.gff3 |
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removed:
cuff_macros.xml |
| b |
| diff -r 69e0806b63a4 -r 6ea09f60dee9 cuff_macros.xml --- a/cuff_macros.xml Tue Oct 01 12:20:13 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,85 +0,0 @@ -<macros> - <token name="@VERSION@">2.2.1</token> - - <xml name="requirements"> - <requirements> - <requirement type="package" version="2.2.1">cufflinks</requirement> - <yield /> - </requirements> - </xml> - - <xml name="condition_inputs"> - <!-- DEFAULT : use BAM/SAM files --> - <conditional name="in_type"> - <param name="set_in_type" type="select" label="Input data type" - help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> - <option value="BAM">SAM/BAM</option> - <option value="CXB">Cuffquant (CXB)</option> - <option value="CONDITION_LIST">List of single replicate conditions</option> - <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> - </param> - <when value="BAM"> - <repeat name="conditions" title="Condition" min="2"> - <param name="name" label="Condition name" type="text"/> - <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> - </repeat> - </when> - <when value="CXB"> - <repeat name="conditions" title="Condition" min="2"> - <param name="name" label="Condition name" type="text"/> - <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> - </repeat> - </when> - <when value="CONDITION_LIST"> - <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> - </when> - <when value="CONDITION_REPLICATE_LIST"> - <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> - </when> - </conditional> - </xml> - <token name="@CONDITION_SAMPLES@"> - #if $in_type.set_in_type in ['BAM', 'CXB'] - #for $condition in $in_type.conditions: - #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) - '$samples' - #end for - #elif $in_type.set_in_type == 'CONDITION_LIST' - #for $sample in $in_type.conditions: - '$sample' - #end for - #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' - #for $condition_list in $in_type.conditions: - #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) - '$samples' - #end for - #end if - </token> - <token name="@CONDITION_LABELS@"> - #import re - #if $in_type.set_in_type in ['BAM', 'CXB'] - #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' - #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] - #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' - #end if - --labels $labels - </token> - <xml name="cufflinks_gtf_inputs"> - <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> - <repeat name="additional_inputs" title="Additional GTF Inputs (type Dataset Collection Lists)"> - <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> - </repeat> - </xml> - <token name="@CUFFLINKS_GTF_INPUTS@"> - ## Inputs. - #for $input_file in $inputs: - '${input_file}' - #end for - #for $additional_input in $additional_inputs: - #for $input_file in $additional_input.additional_inputs: - '${input_file}' - #end for - #end for - </token> - <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> -</macros> |
| b |
| diff -r 69e0806b63a4 -r 6ea09f60dee9 gffread.xml --- a/gffread.xml Tue Oct 01 12:20:13 2019 -0400 +++ b/gffread.xml Fri Nov 01 12:54:52 2019 -0400 |
| [ |
| b'@@ -1,7 +1,7 @@\n-<tool id="gffread" name="gffread" version="@VERSION@.2">\n+<tool id="gffread" name="gffread" version="@VERSION@.1">\n <description>Filters and/or converts GFF3/GTF2 records</description>\n <macros>\n- <import>cuff_macros.xml</import>\n+ <token name="@VERSION@">0.11.4</token>\n <xml name="fasta_output_select">\n <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">\n <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>\n@@ -47,7 +47,9 @@\n </param>\n </xml>\n </macros>\n- <expand macro="requirements" />\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">gffread</requirement>\n+ </requirements>\n <command detect_errors="aggressive">\n <![CDATA[\n #if $reference_genome.source == \'history\':\n@@ -124,7 +126,9 @@\n <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>\n <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>\n <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>\n- <option value="--no-pseudo">filter out records matching the \'pseudo\' keyword (--no-pseudo)</option>\n+ <!-- The no-pseudo option is broken in 0.11.4 of gffread.\n+ See https://github.com/gpertea/gffread/issues/43 -->\n+ <!-- <option value="\\-\\-no-pseudo">filter out records matching the \'pseudo\' keyword (\\-\\-no-pseudo)</option> -->\n </param>\n <conditional name="region">\n <param name="region_filter" type="select" label="Filter by genome region">\n@@ -272,10 +276,13 @@\n <param name="full_gff_attribute_preservation" value="-F"/>\n <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />\n </test>\n-\n+ \n+<!-- The no-pseudo option is broken in 0.11.4 of gffread.\n+ See https://github.com/gpertea/gffread/issues/43 -->\n+<!-- \n <test>\n <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>\n- <param name="filtering" value="--no-pseudo"/>\n+ <param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting\n <param name="gff_fmt" value="gtf"/>\n <output name="output_gtf">\n <assert_contents>\n@@ -283,6 +290,7 @@\n </assert_contents>\n </output>\n </test>\n+-->\n \n <test>\n <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>\n@@ -335,25 +343,25 @@\n <param name="gff_fmt" value="gtf"/>\n <output name="output_gtf">\n <assert_contents>\n- <not_has_text text="ENST00000587541" />\n+ <has_text text="ENST00000587541" />\n <has_text text="ENST00000382683" />\n </assert_contents>\n </output>\n <output name="output_exons">\n <assert_contents>\n- <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />\n+ <has_text text="ENST00000346144 CDS=47-934" />\n <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />\n </assert_contents>\n </output>\n <output name="output_cds">\n <assert_contents>\n- <has_text text="ENST00000346144 gene=MADCAM1" />\n+ <has_text text="ENST00000346144" />\n <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />\n </assert_contents>\n </output>\n <output name="output_pep">\n <asse'..b' without exon/CDS\n+ features (see --tlf option below); automatic if the input\n+ filename ends with .tlf)\n+ \n+ Clustering:\n+ -M/--merge : cluster the input transcripts into loci, discarding\n+ "duplicated" transcripts (those with the same exact introns\n+ and fully contained or equal boundaries)\n+ -d <dupinfo> : for -M option, write duplication info to file <dupinfo>\n+ --cluster-only: same as -M/--merge but without discarding any of the\n+ "duplicate" transcripts, only create "locus" features\n+ -K for -M option: also discard as redundant the shorter, fully contained\n+ transcripts (intron chains matching a part of the container)\n+ -Q for -M option, no longer require boundary containment when assessing\n+ redundancy (can be combined with -K); only introns have to match for\n+ multi-exon transcripts, and >=80% overlap for single-exon transcripts\n+ -Y for -M option, enforce -Q but also discard overlapping single-exon \n+ transcripts, even on the opposite strand (can be combined with -K)\n+ \n+ Output options:\n+ --force-exons: make sure that the lowest level GFF features are considered\n+ "exon" features\n+ --gene2exon: for single-line genes not parenting any transcripts, add an\n+ exon feature spanning the entire gene (treat it as a transcript)\n+ --t-adopt: try to find a parent gene overlapping/containing a transcript\n+ that does not have any explicit gene Parent\n+ -D decode url encoded characters within attributes\n+ -Z merge very close exons into a single exon (when intron size<4)\n+ -g full path to a multi-fasta file with the genomic sequences\n+ for all input mappings, OR a directory with single-fasta files\n+ (one per genomic sequence, with file names matching sequence names)\n+ -w write a fasta file with spliced exons for each GFF transcript\n+ -x write a fasta file with spliced CDS for each GFF transcript\n+ -y write a protein fasta file with the translation of CDS for each record\n+ -W for -w and -x options, write in the FASTA defline the exon\n+ coordinates projected onto the spliced sequence;\n+ for -y option, write transcript attributes in the FASTA defline\n+ -S for -y option, use \'*\' instead of \'.\' as stop codon translation\n+ -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n+ -m <chr_replace> is a name mapping table for converting reference \n+ sequence names, having this 2-column format:\n+ <original_ref_ID> <new_ref_ID>\n+ WARNING: all GFF records on reference sequences whose original IDs\n+ are not found in the 1st column of this table will be discarded!\n+ -t use <trackname> in the 2nd column of each GFF/GTF output line\n+ -o write the records into <outfile> instead of stdout\n+ -T main output will be GTF instead of GFF3\n+ --bed output records in BED format instead of default GFF3\n+ --tlf output "transcript line format" which is like GFF\n+ but exons, CDS features and related data are stored as GFF \n+ attributes in the transcript feature line, like this:\n+ exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> \n+ <exons> is a comma-delimited list of exon_start-exon_end coordinates;\n+ <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>\n+ --table output a simple tab delimited format instead of GFF, with columns\n+ having the values of GFF attributes given in <attrlist>; special\n+ pseudo-attributes (prefixed by @) are recognized:\n+ @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\n+ -v,-E expose (warn about) duplicate transcript IDs and other potential\n+ problems with the given GFF/GTF records\n ]]>\n </help>\n <citations>\n' |
| b |
| diff -r 69e0806b63a4 -r 6ea09f60dee9 test-data/Homo_sapiens.GRCh37_19.71.gff3 --- a/test-data/Homo_sapiens.GRCh37_19.71.gff3 Tue Oct 01 12:20:13 2019 -0400 +++ b/test-data/Homo_sapiens.GRCh37_19.71.gff3 Fri Nov 01 12:54:52 2019 -0400 |
| b |
| b'@@ -1,4 +1,5 @@\n-# gffread test-data/Homo_sapiens.GRCh37_19.71.gtf -o test-data/Homo_sapiens.GRCh37_19.71.gff3\n+# gffread /tmp/tmpq6d_yfqc/files/9/2/2/dataset_922cd54b-d77c-48fb-abf7-6fc8d8fdb97c.dat -o output.gff3\n+# gffread v0.11.4\n ##gff-version 3\n 19\tsnRNA\ttranscript\t223158\t223261\t.\t-\t.\tID=ENST00000410397;geneID=ENSG00000222329;gene_name=U6\n 19\tsnRNA\texon\t223158\t223261\t.\t-\t.\tParent=ENST00000410397\n@@ -9,55 +10,55 @@\n 19\tprocessed_pseudogene\texon\t239145\t239247\t.\t-\t.\tParent=ENST00000588755\n 19\tprocessed_pseudogene\ttranscript\t279495\t280170\t.\t+\t.\tID=ENST00000589981;geneID=ENSG00000267447;gene_name=VN2R11P\n 19\tprocessed_pseudogene\texon\t279495\t280170\t.\t+\t.\tParent=ENST00000589981\n-19\tprotein_coding\tmRNA\t281043\t291386\t.\t-\t.\tID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C\n+19\tprotein_coding\ttranscript\t281043\t291386\t.\t-\t.\tID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C\n 19\tprotein_coding\texon\t281043\t281537\t.\t-\t.\tParent=ENST00000269812\n 19\tprotein_coding\texon\t282134\t282310\t.\t-\t.\tParent=ENST00000269812\n 19\tprotein_coding\texon\t282752\t282809\t.\t-\t.\tParent=ENST00000269812\n 19\tprotein_coding\texon\t287474\t287751\t.\t-\t.\tParent=ENST00000269812\n 19\tprotein_coding\texon\t288020\t288171\t.\t-\t.\tParent=ENST00000269812\n 19\tprotein_coding\texon\t291285\t291386\t.\t-\t.\tParent=ENST00000269812\n-19\tprotein_coding\tCDS\t281391\t281537\t.\t-\t0\tParent=ENST00000269812\n+19\tprotein_coding\tCDS\t281388\t281537\t.\t-\t0\tParent=ENST00000269812\n 19\tprotein_coding\tCDS\t282134\t282310\t.\t-\t0\tParent=ENST00000269812\n 19\tprotein_coding\tCDS\t282752\t282809\t.\t-\t1\tParent=ENST00000269812\n 19\tprotein_coding\tCDS\t287474\t287751\t.\t-\t0\tParent=ENST00000269812\n 19\tprotein_coding\tCDS\t288020\t288171\t.\t-\t2\tParent=ENST00000269812\n 19\tprotein_coding\tCDS\t291285\t291336\t.\t-\t0\tParent=ENST00000269812\n-19\tprotein_coding\tmRNA\t281345\t291393\t.\t-\t.\tID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C\n+19\tprotein_coding\ttranscript\t281345\t291393\t.\t-\t.\tID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C\n 19\tprotein_coding\texon\t281345\t281537\t.\t-\t.\tParent=ENST00000434325\n 19\tprotein_coding\texon\t282134\t282310\t.\t-\t.\tParent=ENST00000434325\n 19\tprotein_coding\texon\t282752\t282809\t.\t-\t.\tParent=ENST00000434325\n 19\tprotein_coding\texon\t287474\t287751\t.\t-\t.\tParent=ENST00000434325\n 19\tprotein_coding\texon\t288020\t288171\t.\t-\t.\tParent=ENST00000434325\n 19\tprotein_coding\texon\t291326\t291393\t.\t-\t.\tParent=ENST00000434325\n-19\tprotein_coding\tCDS\t281391\t281537\t.\t-\t0\tParent=ENST00000434325\n+19\tprotein_coding\tCDS\t281388\t281537\t.\t-\t0\tParent=ENST00000434325\n 19\tprotein_coding\tCDS\t282134\t282310\t.\t-\t0\tParent=ENST00000434325\n 19\tprotein_coding\tCDS\t282752\t282809\t.\t-\t1\tParent=ENST00000434325\n 19\tprotein_coding\tCDS\t287474\t287751\t.\t-\t0\tParent=ENST00000434325\n 19\tprotein_coding\tCDS\t288020\t288055\t.\t-\t0\tParent=ENST00000434325\n-19\tprotein_coding\tmRNA\t281388\t291200\t.\t-\t.\tID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C\n+19\tprotein_coding\ttranscript\t281388\t291200\t.\t-\t.\tID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C\n 19\tprotein_coding\texon\t281388\t281537\t.\t-\t.\tParent=ENST00000327790\n 19\tprotein_coding\texon\t282134\t282310\t.\t-\t.\tParent=ENST00000327790\n 19\tprotein_coding\texon\t282752\t282809\t.\t-\t.\tParent=ENST00000327790\n 19\tprotein_coding\texon\t287474\t287751\t.\t-\t.\tParent=ENST00000327790\n 19\tprotein_coding\texon\t288020\t288171\t.\t-\t.\tParent=ENST00000327790\n 19\tprotein_coding\texon\t290952\t291200\t.\t-\t.\tParent=ENST00000327790\n-19\tprotein_coding\tCDS\t281391\t281537\t.\t-\t0\tParent=ENST00000327790\n+19\tprotein_coding\tCDS\t281388\t281537\t.\t-\t0\tParent=ENST00000327790\n 19\tprotein_coding\tCDS\t282134\t282310\t.\t-\t0\tParent=ENST00000327790\n 19\tprotein_coding\tCDS\t282752\t282809\t.\t-\t1\tParent=ENST00000327790\n 19\tprotein_coding\tCDS\t287474\t287751\t.\t-\t0\tParent=ENST00000327790\n 19\tprotein_coding\tCDS\t288020\t288171\t.\t-\t2\tParent=ENST00000327790\n 19\tprotein_coding\tCDS\t290952\t291066\t.\t-\t0\tParent=ENST00000327790\n-19\tprotein_coding\tmRNA\t281991\t287636\t.\t-\t.\tID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C\n+19\tprotein_coding\ttranscript\t281991\t287636\t.\t-\t'..b'000315489\n 19\tprotein_coding\tCDS\t474621\t474747\t.\t-\t0\tParent=ENST00000315489\n-19\tprotein_coding\tmRNA\t463467\t474880\t.\t-\t.\tID=ENST00000382696;geneID=ENSG00000181781;gene_name=ODF3L2\n+19\tprotein_coding\ttranscript\t463467\t474880\t.\t-\t.\tID=ENST00000382696;geneID=ENSG00000181781;gene_name=ODF3L2\n 19\tprotein_coding\texon\t463467\t464364\t.\t-\t.\tParent=ENST00000382696\n 19\tprotein_coding\texon\t467649\t467762\t.\t-\t.\tParent=ENST00000382696\n 19\tprotein_coding\texon\t474621\t474880\t.\t-\t.\tParent=ENST00000382696\n-19\tprotein_coding\tCDS\t463847\t464364\t.\t-\t2\tParent=ENST00000382696\n+19\tprotein_coding\tCDS\t463844\t464364\t.\t-\t2\tParent=ENST00000382696\n 19\tprotein_coding\tCDS\t467649\t467762\t.\t-\t2\tParent=ENST00000382696\n 19\tprotein_coding\tCDS\t474621\t474747\t.\t-\t0\tParent=ENST00000382696\n 19\tretained_intron\ttranscript\t464146\t472631\t.\t-\t.\tID=ENST00000591681;geneID=ENSG00000181781;gene_name=ODF3L2\n@@ -277,7 +278,7 @@\n 19\tantisense\texon\t490046\t490353\t.\t-\t.\tParent=ENST00000592413\n 19\tantisense\texon\t501541\t501624\t.\t-\t.\tParent=ENST00000592413\n 19\tantisense\texon\t507376\t507813\t.\t-\t.\tParent=ENST00000592413\n-19\tprotein_coding\tmRNA\t496454\t505207\t.\t+\t.\tID=ENST00000346144;geneID=ENSG00000099866;gene_name=MADCAM1\n+19\tprotein_coding\ttranscript\t496454\t505207\t.\t+\t.\tID=ENST00000346144;geneID=ENSG00000099866;gene_name=MADCAM1\n 19\tprotein_coding\texon\t496454\t496551\t.\t+\t.\tParent=ENST00000346144\n 19\tprotein_coding\texon\t497833\t498117\t.\t+\t.\tParent=ENST00000346144\n 19\tprotein_coding\texon\t498496\t498825\t.\t+\t.\tParent=ENST00000346144\n@@ -285,8 +286,8 @@\n 19\tprotein_coding\tCDS\t496500\t496551\t.\t+\t0\tParent=ENST00000346144\n 19\tprotein_coding\tCDS\t497833\t498117\t.\t+\t2\tParent=ENST00000346144\n 19\tprotein_coding\tCDS\t498496\t498825\t.\t+\t2\tParent=ENST00000346144\n-19\tprotein_coding\tCDS\t504745\t504963\t.\t+\t2\tParent=ENST00000346144\n-19\tprotein_coding\tmRNA\t496454\t505347\t.\t+\t.\tID=ENST00000215637;geneID=ENSG00000099866;gene_name=MADCAM1\n+19\tprotein_coding\tCDS\t504745\t504965\t.\t+\t2\tParent=ENST00000346144\n+19\tprotein_coding\ttranscript\t496454\t505347\t.\t+\t.\tID=ENST00000215637;geneID=ENSG00000099866;gene_name=MADCAM1\n 19\tprotein_coding\texon\t496454\t496551\t.\t+\t.\tParent=ENST00000215637\n 19\tprotein_coding\texon\t497833\t498117\t.\t+\t.\tParent=ENST00000215637\n 19\tprotein_coding\texon\t498496\t498825\t.\t+\t.\tParent=ENST00000215637\n@@ -296,18 +297,18 @@\n 19\tprotein_coding\tCDS\t497833\t498117\t.\t+\t2\tParent=ENST00000215637\n 19\tprotein_coding\tCDS\t498496\t498825\t.\t+\t2\tParent=ENST00000215637\n 19\tprotein_coding\tCDS\t501669\t501929\t.\t+\t2\tParent=ENST00000215637\n-19\tprotein_coding\tCDS\t504745\t504963\t.\t+\t2\tParent=ENST00000215637\n-19\tprotein_coding\tmRNA\t496500\t504965\t.\t+\t.\tID=ENST00000382683;geneID=ENSG00000099866;gene_name=MADCAM1\n+19\tprotein_coding\tCDS\t504745\t504965\t.\t+\t2\tParent=ENST00000215637\n+19\tprotein_coding\ttranscript\t496500\t504965\t.\t+\t.\tID=ENST00000382683;geneID=ENSG00000099866;gene_name=MADCAM1\n 19\tprotein_coding\texon\t496500\t496551\t.\t+\t.\tParent=ENST00000382683\n 19\tprotein_coding\texon\t498496\t498825\t.\t+\t.\tParent=ENST00000382683\n 19\tprotein_coding\texon\t504745\t504965\t.\t+\t.\tParent=ENST00000382683\n 19\tprotein_coding\tCDS\t496500\t496551\t.\t+\t0\tParent=ENST00000382683\n 19\tprotein_coding\tCDS\t498496\t498825\t.\t+\t2\tParent=ENST00000382683\n-19\tprotein_coding\tCDS\t504745\t504963\t.\t+\t2\tParent=ENST00000382683\n-19\tprotein_coding\tmRNA\t507299\t519654\t.\t+\t.\tID=ENST00000359315;geneID=ENSG00000141933;gene_name=TPGS1\n+19\tprotein_coding\tCDS\t504745\t504965\t.\t+\t2\tParent=ENST00000382683\n+19\tprotein_coding\ttranscript\t507299\t519654\t.\t+\t.\tID=ENST00000359315;geneID=ENSG00000141933;gene_name=TPGS1\n 19\tprotein_coding\texon\t507299\t507844\t.\t+\t.\tParent=ENST00000359315\n 19\tprotein_coding\texon\t518889\t519654\t.\t+\t.\tParent=ENST00000359315\n 19\tprotein_coding\tCDS\t507507\t507844\t.\t+\t0\tParent=ENST00000359315\n-19\tprotein_coding\tCDS\t518889\t519421\t.\t+\t1\tParent=ENST00000359315\n+19\tprotein_coding\tCDS\t518889\t519423\t.\t+\t1\tParent=ENST00000359315\n 19\tretained_intron\ttranscript\t507500\t510372\t.\t+\t.\tID=ENST00000588278;geneID=ENSG00000141933;gene_name=TPGS1\n 19\tretained_intron\texon\t507500\t510372\t.\t+\t.\tParent=ENST00000588278\n' |
| b |
| diff -r 69e0806b63a4 -r 6ea09f60dee9 test-data/ecoli-k12.processed.gff3 --- a/test-data/ecoli-k12.processed.gff3 Tue Oct 01 12:20:13 2019 -0400 +++ b/test-data/ecoli-k12.processed.gff3 Fri Nov 01 12:54:52 2019 -0400 |
| b |
| b'@@ -1,32 +1,33 @@\n-# gffread /home/hxr/arbeit/galaxy/database/files/000/dataset_791.dat -F -D -E -o output.gff3\n+# gffread /tmp/tmpq6d_yfqc/files/2/7/7/dataset_277f6e18-b25a-4b59-b712-49b5c202a183.dat -F -o output.gff3\n+# gffread v0.11.4\n ##gff-version 3\n-NC_000913.3\tRefSeq\tgene\t190\t255\t.\t+\t.\tID=gene-b0001;geneID=gene-b0001;gene_name=thrL;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001;protein_id=NP_414542.1\n-NC_000913.3\tRefSeq\tCDS\t190\t255\t.\t+\t0\tParent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;transl_table=11\n-NC_000913.3\tRefSeq\tgene\t337\t2799\t.\t+\t.\tID=gene-b0002;geneID=gene-b0002;gene_name=thrA;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002;protein_id=NP_414543.1\n-NC_000913.3\tRefSeq\tCDS\t337\t2799\t.\t+\t0\tParent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;transl_table=11\n-NC_000913.3\tRefSeq\tgene\t2801\t3733\t.\t+\t.\tID=gene-b0003;geneID=gene-b0003;gene_name=thrB;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003;protein_id=NP_414544.1\n-NC_000913.3\tRefSeq\tCDS\t2801\t3733\t.\t+\t0\tParent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;transl_table=11\n-NC_000913.3\tRefSeq\tgene\t3734\t5020\t.\t+\t.\tID=gene-b0004;geneID=gene-b0004;gene_name=thrC;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004;protein_id=NP_414545.1\n-NC_000913.3\tRefSeq\tCDS\t3734\t5020\t.\t+\t0\tParent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;transl_table=11\n-NC_000913.3\tRefSeq\tgene\t5234\t5530\t.\t+\t.\tID=gene-b0005;geneID=gene-b0005;gene_name=yaaX;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005;protein_id=NP_414546.1\n-NC_000913.3\tRefSeq\tCDS\t5234\t5530\t.\t+\t0\tParent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;transl_table=11\n-NC_000913.3\tRefSeq\tgene\t5683\t6459\t.\t-\t.\tID=gene-b0006;geneID=gene-b0006;gene_name=yaaA;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006;protein_id=NP_414547.1\n-NC_000913.3\tRefSeq\tCDS\t5683\t6459\t.\t-\t0\tParent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;transl_table=11\n-NC_000913.3\tRefSeq\tgene\t6529\t7959\t.\t-\t.\tID=gene-b0007;geneID=gene-b0007;gene_name=yaaJ;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007;protein_id='..b'306\t9893\t.\t+\t0\tParent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;gene=mog;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;protein_id=NP_414550.1;transl_table=11\n+NC_000913.3\tRefSeq\tgene\t9928\t10494\t.\t-\t.\tID=gene-b0010;geneID=gene-b0010;gene_name=satP;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene=satP;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010\n+NC_000913.3\tRefSeq\tCDS\t9928\t10494\t.\t-\t0\tParent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;gene=satP;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;protein_id=NP_414551.1;transl_table=11\n+NC_000913.3\tRefSeq\tgene\t10643\t11356\t.\t-\t.\tID=gene-b0011;geneID=gene-b0011;gene_name=yaaW;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene=yaaW;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011\n+NC_000913.3\tRefSeq\tCDS\t10643\t11356\t.\t-\t0\tParent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;gene=yaaW;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;protein_id=NP_414552.1;transl_table=11\n+NC_000913.3\tRefSeq\tgene\t10830\t11315\t.\t+\t.\tID=gene-b0012;geneID=gene-b0012;gene_name=mbiA;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene=mbiA;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012\n+NC_000913.3\tRefSeq\tCDS\t10830\t11315\t.\t+\t0\tParent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;gene=mbiA;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;protein_id=YP_009518733.1;transl_table=11\n+NC_000913.3\tRefSeq\tgene\t11382\t11786\t.\t-\t.\tID=gene-b0013;geneID=gene-b0013;gene_name=yaaI;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene=yaaI;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013\n+NC_000913.3\tRefSeq\tCDS\t11382\t11786\t.\t-\t0\tParent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;gene=yaaI;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;protein_id=NP_414554.1;transl_table=11\n+NC_000913.3\tRefSeq\tgene\t12163\t14079\t.\t+\t.\tID=gene-b0014;geneID=gene-b0014;gene_name=dnaK;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene=dnaK;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014\n+NC_000913.3\tRefSeq\tCDS\t12163\t14079\t.\t+\t0\tParent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;gene=dnaK;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;protein_id=NP_414555.1;transl_table=11\n+NC_000913.3\tRefSeq\tgene\t14168\t15298\t.\t+\t.\tID=gene-b0015;geneID=gene-b0015;gene_name=dnaJ;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene=dnaJ;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015\n+NC_000913.3\tRefSeq\tCDS\t14168\t15298\t.\t+\t0\tParent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;gene=dnaJ;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;protein_id=NP_414556.1;transl_table=11\n' |