| Next changeset 1:c784170f3b5e (2021-04-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108" |
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added:
flair_correct.xml flair_macros.xml test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf test-data/chrM.bed12 test-data/chrM.fa test-data/chrM.fa.fai test-data/chrM.fastq.gz test-data/fasta_indexes.loc test-data/flair.collapse.isoforms.bed test-data/flair.collapse.isoforms.fa test-data/flair.collapse.isoforms.gtf test-data/flair_all_corrected.bed test-data/flair_all_inconsistent.bed tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 6927379c9ede flair_correct.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_correct.xml Fri Nov 27 21:55:45 2020 +0000 |
| [ |
| @@ -0,0 +1,137 @@ +<tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@" profile="20.01"> + <description>corrects misaligned splice sites using genome annotations</description> + + <macros> + <import>flair_macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + +@PREPARE_REF@ + +flair.py correct + +########### +## Input ## +########### + +-q '$input_query' +-g reference.fa +-f '$input_gtf' + +#if $input_shortread: + -j '$input_shortread' +#end if + +######################## +## Additional Options ## +######################## + +$additional_options.strand +-w $additional_options.window + +######### +## END ## +######### + + ]]></command> + <inputs> + <param name="input_query" argument="-q" type="data" format="bed12" label="Uncorrected Bed12 file"/> + <expand macro="reference_interface" /> + <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/> + <param name="input_shortread" optional="true" argument="-j" type="data" format="bed" label="Splice junction BED file" /> + + <!-- Additional Options --> + <section name="additional_options" title="Additional Options"> + <param name="strand" argument="-n" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Strand Consistency" help="Keep the strand of a read consistent after correction."/> + <param name="window" argument="-w" type="integer" min="1" value="10" label="Window Size" help="Window size for correcting splice sites (Default=10)" /> + </section> + </inputs> + + + <outputs> + <data name="outfile_1" format="bed12" from_work_dir="flair_all_corrected.bed" label="${tool.name} on ${on_string}: Corrected Reads" /> + <data name="outfile_2" format="bed12" from_work_dir="flair_all_inconsistent.bed" label="${tool.name} on ${on_string}: Inconsistent Reads" /> + </outputs> + + <tests> + <test expect_num_outputs="2"> + <param name="input_query" ftype="bed12" value="chrM.bed12" /> + <param name="ref_selector_genome" value="history" /> + <param name="reffile" ftype="fasta" value="chrM.fa" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" /> + <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" /> + </test> + <!-- Test with cached genome --> + <test expect_num_outputs="2"> + <param name="input_query" ftype="bed12" value="chrM.bed12" /> + <param name="ref_selector_genome" value="cached" /> + <param name="reffile" value="chrM" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" /> + <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" /> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +------------------- + +@description@ + +**flair correct** +Corrects misaligned splice sites using genome annotations and/or short-read splice junctions. Based on common user issues we have encountered, for flair-correct to run properly, please ensure/note that (1) the genome annotation and genome sequences are compatible, (2) gtf is preferred over gff for annotation and annotations that do not split single exons into multiple entries are ideal. + +------------------- + +**Inputs** + +------------------- + +(1) Uncorreced bed12 file. +(2) FASTA file of the reference genome. +(3) GTF annotation file. +(4) BED format splice junctions from short-read sequencing or GTF annotation file. + +----------- + +**Outputs** + +----------- + +(1) bed12 of corrected reads, +(2) bed12 of reads that weren't able to be corrected, +(3) psl of corrected reads if the -c chromsizes file is provided. + +Either (1) or (3) can be supplied to flair-collapse as the query. + +-------------------- + +**More Information** + +-------------------- + +See the excellent `FLAIR documentation`_ + +.. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair + + +-------------------- + +**Galaxy Wrapper Development** + +-------------------- + +@citation@ + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 6927379c9ede flair_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_macros.xml Fri Nov 27 21:55:45 2020 +0000 |
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| @@ -0,0 +1,60 @@ +<macros> + <token name="@TOOL_VERSION@">1.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">flair</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>flair.py --version</version_command> + </xml> + + <token name="@PREPARE_REF@"><![CDATA[ + #if str($reference_source_genome.ref_selector_genome) == 'history': + ln -s '$reference_source_genome.reffile' reference.fa && + samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 && + #else + ln -s '${reference_source_genome.reffile.fields.path}' reference.fa && + #end if + ]]></token> + + <xml name="reference_interface"> + <conditional name="reference_source_genome"> + <param name="ref_selector_genome" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="reffile" argument="-g" type="select" label="Reference genome"> + <options from_data_table="fasta_indexes"> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param name="reffile" argument="-g" type="data" format="fasta" label="Reference" help="Reference sequence" /> + </when> + </conditional> + </xml> + + <token name="@description@"> + +**FLAIR** FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads. +FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from Tang et al. (2018). +It is recommended to combine all samples together prior to running flair-collapse for isoform assembly by concatenating corrected read psl or bed files together. Following the creation of an isoform reference from flair-collapse, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses. + + </token> + + <token name="@citation@"> + +Author: Florian Heyl + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-020-15171-6</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 6927379c9ede test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf Fri Nov 27 21:55:45 2020 +0000 |
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| b'@@ -0,0 +1,76 @@\n+chrM\thg38_knownGene\texon\t577\t647\t0.000000\t+\t.\tgene_id "ENST00000387314.1"; transcript_id "ENST00000387314.1"; \n+chrM\thg38_knownGene\texon\t648\t1601\t0.000000\t+\t.\tgene_id "ENST00000389680.2"; transcript_id "ENST00000389680.2"; \n+chrM\thg38_knownGene\texon\t1602\t1670\t0.000000\t+\t.\tgene_id "ENST00000387342.1"; transcript_id "ENST00000387342.1"; \n+chrM\thg38_knownGene\texon\t1671\t3229\t0.000000\t+\t.\tgene_id "ENST00000387347.2"; transcript_id "ENST00000387347.2"; \n+chrM\thg38_knownGene\texon\t3230\t3304\t0.000000\t+\t.\tgene_id "ENST00000386347.1"; transcript_id "ENST00000386347.1"; \n+chrM\thg38_knownGene\tstart_codon\t3307\t3309\t0.000000\t+\t.\tgene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; \n+chrM\thg38_knownGene\tCDS\t3307\t4259\t0.000000\t+\t0\tgene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; \n+chrM\thg38_knownGene\tstop_codon\t4260\t4262\t0.000000\t+\t.\tgene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; 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transcript_id "ENST00000361789.2"; \n+chrM\thg38_knownGene\texon\t14747\t15887\t0.000000\t+\t.\tgene_id "ENST00000361789.2"; transcript_id "ENST00000361789.2"; \n+chrM\thg38_knownGene\texon\t15888\t15953\t0.000000\t+\t.\tgene_id "ENST00000387460.2"; transcript_id "ENST00000387460.2"; \n+chrM\thg38_knownGene\texon\t15956\t16023\t0.000000\t-\t.\tgene_id "ENST00000387461.2"; transcript_id "ENST00000387461.2"; \n' |
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| diff -r 000000000000 -r 6927379c9ede test-data/chrM.bed12 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.bed12 Fri Nov 27 21:55:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,1348 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|
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Fri Nov 27 21:55:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,333 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT\n+TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG\n+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC\n+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT\n+GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n+AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT\n+TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT\n+ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC\n+CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA\n+ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA\n+GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT\n+AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA\n+ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC\n+ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT\n+AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC\n+GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA\n+GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT\n+CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC\n+TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC\n+CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG\n+AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC\n+AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA\n+GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG\n+GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC\n+TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC\n+AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA\n+GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA\n+CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA\n+ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT\n+TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG\n+AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT\n+GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA\n+CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT\n+CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC\n+CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA\n+AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT\n+AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA\n+GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA\n+ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG\n+TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA\n+TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC\n+AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA\n+CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA\n+GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata\n+atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc\n+agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg\n+ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT\n+GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT\n+ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC\n+AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT\n+ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA\n+GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT\n+AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT\n+ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT\n+ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt\n+aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt\n+aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT\n+CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC\n+AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC\n+TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG\n+CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC\n+AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC\n+AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG\n+CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC\n+ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT\n+TATCACAACACAAGAACACCT'..b'CTTAGTTACCGCTAACAACCTATTC\n+CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT\n+CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA\n+TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA\n+TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG\n+GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA\n+GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC\n+AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC\n+TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA\n+GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC\n+CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA\n+CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA\n+TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT\n+CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT\n+TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA\n+CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT\n+ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA\n+ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA\n+TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC\n+ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA\n+CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT\n+TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC\n+TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT\n+CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC\n+CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC\n+TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT\n+CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC\n+ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA\n+TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC\n+ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA\n+TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA\n+ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT\n+AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG\n+GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC\n+AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA\n+CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC\n+ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC\n+ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG\n+CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC\n+ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA\n+TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC\n+CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG\n+AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG\n+CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC\n+TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT\n+GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG\n+AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT\n+CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG\n+ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC\n+AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC\n+TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG\n+CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC\n+CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC\n+AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT\n+ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT\n+AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG\n+ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG\n+ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT\n+ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC\n+CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA\n+CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC\n+CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA\n+CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA\n+ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC\n+CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT\n+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT\n+TAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/chrM.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chrM 16569 6 50 51 |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/chrM.fastq.gz |
| b |
| Binary file test-data/chrM.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/flair.collapse.isoforms.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.bed Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,14 @@ +chrM 661 1341 ca7655f0-1077-4546-850f-be0f10f50a81_chrM:000 60 + 661 1341 14 1 680, 0, +chrM 1274 1601 07a2d20a-8f33-4283-87e2-ee2b28b771f2_chrM:1000 60 + 1274 1601 11 1 327, 0, +chrM 1681 3211 7739a708-0dd8-4e16-856c-0488b9378738_ENST00000387347.2 60 + 1681 3211 31 1 1530, 0, +chrM 3315 4220 13557349-20c1-42e2-8477-a31c29e524a3_ENST00000361390.2 60 + 3315 4220 58 1 905, 0, +chrM 4482 5439 7c64296d-12c2-49bd-a404-70478fff9a62_ENST00000361453.3 60 - 4482 5439 33 1 957, 0, +chrM 5591 5865 272f11a9-f8b7-4c23-8526-a36936b8527f_chrM:5000 29 + 5591 5865 66 1 274, 0, +chrM 5911 7518 1804a832-0ae7-4760-bd8c-2b8250455c48_ENST00000361624.2 60 + 5911 7518 167 1 1607, 0, +chrM 7596 8294 3065b2ed-affa-4e42-8c6e-b385487325f6_ENST00000361739.1 45 + 7596 8294 116 1 698, 0, +chrM 8377 9207 08c5eaa2-47a2-4813-ae6d-e579904d6416_ENST00000361899.2 42 + 8377 9207 77 1 830, 0, +chrM 9221 9991 29af7e32-7b11-4c36-ae11-25b54575faea_ENST00000362079.2 60 + 9221 9991 148 1 770, 0, +chrM 10070 10404 7258b7cf-cbd2-4dab-928d-bbb5bc115c4c_ENST00000361227.2 60 + 10070 10404 78 1 334, 0, +chrM 10482 12053 ccdaa81a-848a-4da0-abef-6411c5c3a01e_ENST00000361381.2 60 + 10482 12053 54 1 1571, 0, +chrM 12350 14748 81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5_ENST00000361567.2 60 + 12350 14748 20 1 2398, 0, +chrM 15971 16569 2f14a1a9-c356-4568-9a4e-150c8d2038d0_chrM:15000 60 + 15971 16569 3 1 598, 0, |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/flair.collapse.isoforms.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.fa Fri Nov 27 21:55:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,28 @@\n+>ca7655f0-1077-4546-850f-be0f10f50a81_chrM:000\n+TAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCC\n+>07a2d20a-8f33-4283-87e2-ee2b28b771f2_chrM:1000\n+AAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAAC\n+>7739a708-0dd8-4e16-856c-0488b9378738_ENST00000387347.2\n+CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggctccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcgggcataacacagcaagacgagaagaccctatggagctttaatttaTTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACC\n+>13557349-20c1-42e2-8477-a31c29e524a3_ENST00000361390.2\n+GCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATTACTTATATGATATGT\n+>7c64296d-12c2-49bd-a404-70478fff9a62_ENST00000361453.3\n+GGGTGGGTTTTGTATGTTCAAACTGTCATTTTATTTTTACGTTGTTAGATATGGGGAGTAGTGTGATTGAGGTGGAGTAGATTAGGCGTAGGTAGAAGTAGAGGTTAAGGAGGGTGATGGTGGCTATGATGGTGGGGATGATGAGGCTATTGTTTTTTGTGAATTCTTCGATAATGGCCCATTTGGGCAAAAAGCCGGTTAGCGGGGGCAGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTTAGC'..b'GATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACAC\n+>81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5_ENST00000361567.2\n+TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAAT\n+>2f14a1a9-c356-4568-9a4e-150c8d2038d0_chrM:15000\n+TAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/flair.collapse.isoforms.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.gtf Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,28 @@ +chrM FLAIR transcript 662 1341 . + . gene_id "chrM:000"; transcript_id "ca7655f0-1077-4546-850f-be0f10f50a81"; +chrM FLAIR exon 662 1341 . + 60 gene_id "chrM:000"; transcript_id "ca7655f0-1077-4546-850f-be0f10f50a81"; exon_number "0"; +chrM FLAIR transcript 1275 1601 . + . gene_id "chrM:1000"; transcript_id "07a2d20a-8f33-4283-87e2-ee2b28b771f2"; +chrM FLAIR exon 1275 1601 . + 60 gene_id "chrM:1000"; transcript_id "07a2d20a-8f33-4283-87e2-ee2b28b771f2"; exon_number "0"; +chrM FLAIR transcript 1682 3211 . + . gene_id "ENST00000387347.2"; transcript_id "7739a708-0dd8-4e16-856c-0488b9378738"; +chrM FLAIR exon 1682 3211 . + 60 gene_id "ENST00000387347.2"; transcript_id "7739a708-0dd8-4e16-856c-0488b9378738"; exon_number "0"; +chrM FLAIR transcript 3316 4220 . + . gene_id "ENST00000361390.2"; transcript_id "13557349-20c1-42e2-8477-a31c29e524a3"; +chrM FLAIR exon 3316 4220 . + 60 gene_id "ENST00000361390.2"; transcript_id "13557349-20c1-42e2-8477-a31c29e524a3"; exon_number "0"; +chrM FLAIR transcript 4483 5439 . - . gene_id "ENST00000361453.3"; transcript_id "7c64296d-12c2-49bd-a404-70478fff9a62"; +chrM FLAIR exon 4483 5439 . - 60 gene_id "ENST00000361453.3"; transcript_id "7c64296d-12c2-49bd-a404-70478fff9a62"; exon_number "0"; +chrM FLAIR transcript 5592 5865 . + . gene_id "chrM:5000"; transcript_id "272f11a9-f8b7-4c23-8526-a36936b8527f"; +chrM FLAIR exon 5592 5865 . + 29 gene_id "chrM:5000"; transcript_id "272f11a9-f8b7-4c23-8526-a36936b8527f"; exon_number "0"; +chrM FLAIR transcript 5912 7518 . + . gene_id "ENST00000361624.2"; transcript_id "1804a832-0ae7-4760-bd8c-2b8250455c48"; +chrM FLAIR exon 5912 7518 . + 60 gene_id "ENST00000361624.2"; transcript_id "1804a832-0ae7-4760-bd8c-2b8250455c48"; exon_number "0"; +chrM FLAIR transcript 7597 8294 . + . gene_id "ENST00000361739.1"; transcript_id "3065b2ed-affa-4e42-8c6e-b385487325f6"; +chrM FLAIR exon 7597 8294 . + 45 gene_id "ENST00000361739.1"; transcript_id "3065b2ed-affa-4e42-8c6e-b385487325f6"; exon_number "0"; +chrM FLAIR transcript 8378 9207 . + . gene_id "ENST00000361899.2"; transcript_id "08c5eaa2-47a2-4813-ae6d-e579904d6416"; +chrM FLAIR exon 8378 9207 . + 42 gene_id "ENST00000361899.2"; transcript_id "08c5eaa2-47a2-4813-ae6d-e579904d6416"; exon_number "0"; +chrM FLAIR transcript 9222 9991 . + . gene_id "ENST00000362079.2"; transcript_id "29af7e32-7b11-4c36-ae11-25b54575faea"; +chrM FLAIR exon 9222 9991 . + 60 gene_id "ENST00000362079.2"; transcript_id "29af7e32-7b11-4c36-ae11-25b54575faea"; exon_number "0"; +chrM FLAIR transcript 10071 10404 . + . gene_id "ENST00000361227.2"; transcript_id "7258b7cf-cbd2-4dab-928d-bbb5bc115c4c"; +chrM FLAIR exon 10071 10404 . + 60 gene_id "ENST00000361227.2"; transcript_id "7258b7cf-cbd2-4dab-928d-bbb5bc115c4c"; exon_number "0"; +chrM FLAIR transcript 10483 12053 . + . gene_id "ENST00000361381.2"; transcript_id "ccdaa81a-848a-4da0-abef-6411c5c3a01e"; +chrM FLAIR exon 10483 12053 . + 60 gene_id "ENST00000361381.2"; transcript_id "ccdaa81a-848a-4da0-abef-6411c5c3a01e"; exon_number "0"; +chrM FLAIR transcript 12351 14748 . + . gene_id "ENST00000361567.2"; transcript_id "81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5"; +chrM FLAIR exon 12351 14748 . + 60 gene_id "ENST00000361567.2"; transcript_id "81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5"; exon_number "0"; +chrM FLAIR transcript 15972 16569 . + . gene_id "chrM:15000"; transcript_id "2f14a1a9-c356-4568-9a4e-150c8d2038d0"; +chrM FLAIR exon 15972 16569 . + 60 gene_id "chrM:15000"; transcript_id "2f14a1a9-c356-4568-9a4e-150c8d2038d0"; exon_number "0"; |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/flair_all_corrected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair_all_corrected.bed Fri Nov 27 21:55:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,1340 @@\n+chrM\t569\t1461\t1fb96112-b5ee-46ac-9ca4-c3e170512e4d;0\t60\t+\t569\t1461\t99,99,99\t1\t892,\t0,\n+chrM\t570\t1631\tca7655f0-1077-4546-850f-be0f10f50a81;0\t60\t+\t570\t1631\t99,99,99\t1\t1061,\t0,\n+chrM\t570\t3149\t07a2d20a-8f33-4283-87e2-ee2b28b771f2;0\t60\t+\t570\t3149\t99,99,99\t1\t2579,\t0,\n+chrM\t571\t1180\tfd4b26fc-72f9-4060-8c6d-deca2e55cceb;0\t60\t+\t571\t1180\t99,99,99\t1\t609,\t0,\n+chrM\t571\t1041\tec1423b2-49e7-4751-81b6-39614fd8991d;0\t60\t+\t571\t1041\t99,99,99\t1\t470,\t0,\n+chrM\t578\t1601\t550708cd-84a1-40c0-aed9-b6b38faca411;0\t49\t+\t578\t1601\t99,99,99\t1\t1023,\t0,\n+chrM\t658\t1215\t2dc80131-77c9-4dd4-b6ab-26de0d91afc5;0\t60\t+\t658\t1215\t99,99,99\t1\t557,\t0,\n+chrM\t660\t1118\t31d34648-3f54-4a65-9878-2ae72795dba4;0\t58\t+\t660\t1118\t99,99,99\t1\t458,\t0,\n+chrM\t661\t1258\tf7ee2b0a-5e47-4c55-a70b-60fc2a8d9d5f;0\t52\t+\t661\t1258\t99,99,99\t1\t597,\t0,\n+chrM\t661\t1191\t385a6115-47fa-45f1-a64e-6bf9e9e8f716;0\t60\t+\t661\t1191\t99,99,99\t1\t530,\t0,\n+chrM\t661\t1341\tf3b281ca-2587-46ce-8f37-4019909debad;0\t6\t+\t661\t1341\t99,99,99\t1\t680,\t0,\n+chrM\t661\t1214\t0dea8b5d-78d3-42d6-9284-458c574f8e26;0\t60\t+\t661\t1214\t99,99,99\t1\t553,\t0,\n+chrM\t661\t1223\t3f02c2e6-10dc-426b-b9dd-dd180be4d84d;0\t55\t+\t661\t1223\t99,99,99\t1\t562,\t0,\n+chrM\t661\t1236\t4d24b700-6645-44a4-bdeb-c8f1f82fd43a;0\t60\t+\t661\t1236\t99,99,99\t1\t575,\t0,\n+chrM\t661\t1215\ta3113469-53e5-4399-8dd1-3e80e6cd4840;0\t42\t+\t661\t1215\t99,99,99\t1\t554,\t0,\n+chrM\t661\t1562\tc2ac6756-bf06-40ee-b116-629cb06dc938;0\t60\t+\t661\t1562\t99,99,99\t1\t901,\t0,\n+chrM\t661\t1365\t36639f99-fc00-48ae-9e41-a716f3c85183;0\t60\t+\t661\t1365\t99,99,99\t1\t704,\t0,\n+chrM\t661\t1218\t16c2c9d6-4694-4810-9277-dcfb6c0bf1be;0\t60\t+\t661\t1218\t99,99,99\t1\t557,\t0,\n+chrM\t661\t1300\tf189c761-c080-4b56-a655-f9510205a098;0\t60\t+\t661\t1300\t99,99,99\t1\t639,\t0,\n+chrM\t661\t1476\t56c4f0a0-919a-47d7-9301-efedea78d911;0\t58\t+\t661\t1476\t99,99,99\t1\t815,\t0,\n+chrM\t661\t1319\t1eac4a10-986b-4f42-b3dd-3e2b607fea06;0\t60\t+\t661\t1319\t99,99,99\t1\t658,\t0,\n+chrM\t661\t1042\t6ba621b6-fd6c-4796-adbf-067fcf2e5056;0\t60\t+\t661\t1042\t99,99,99\t1\t381,\t0,\n+chrM\t661\t1231\t94ed9dc9-c718-4cb6-a1a1-9d09589a85de;0\t60\t+\t661\t1231\t99,99,99\t1\t570,\t0,\n+chrM\t661\t1000\t3978ce5e-977d-4ba4-9f8c-3964a85eb6a2;0\t51\t+\t661\t1000\t99,99,99\t1\t339,\t0,\n+chrM\t663\t1119\t3364bed4-f737-4e16-a4ff-4e040854792a;0\t60\t+\t663\t1119\t99,99,99\t1\t456,\t0,\n+chrM\t667\t1479\tbb9afd60-09db-421c-ab2e-82246c288f76;0\t60\t+\t667\t1479\t99,99,99\t1\t812,\t0,\n+chrM\t670\t1191\t8645727c-31ca-40c3-ba14-b55aceeaaf24;0\t60\t+\t670\t1191\t99,99,99\t1\t521,\t0,\n+chrM\t670\t1188\te1e06242-962d-4c16-adf2-b9c2d04393e7;0\t60\t+\t670\t1188\t99,99,99\t1\t518,\t0,\n+chrM\t671\t1033\tbecad4cf-9e68-43ac-b445-50c77d90599b;0\t24\t+\t671\t1033\t99,99,99\t1\t362,\t0,\n+chrM\t672\t1237\t5f0a6f3e-08b6-43fb-b2fe-6a22d69b9f13;0\t20\t+\t672\t1237\t99,99,99\t1\t565,\t0,\n+chrM\t682\t1229\tf7783e60-4446-471d-be7a-768b6076b0b1;0\t60\t+\t682\t1229\t99,99,99\t1\t547,\t0,\n+chrM\t683\t1157\te874ce99-235c-4fc9-8d00-1917eda2b03f;0\t56\t+\t683\t1157\t99,99,99\t1\t474,\t0,\n+chrM\t709\t1003\t6570595e-650e-4b85-9e7e-723b9a727b28;0\t60\t+\t709\t1003\t99,99,99\t1\t294,\t0,\n+chrM\t722\t1001\t78fd7765-20aa-4906-b329-cbeef0a1a84b;0\t60\t+\t722\t1001\t99,99,99\t1\t279,\t0,\n+chrM\t736\t1027\t90fef919-6bc3-48f9-85c8-87d8a5251967;0\t60\t+\t736\t1027\t99,99,99\t1\t291,\t0,\n+chrM\t743\t1194\t038a94b2-8d27-48e9-b319-8f5afab370de;0\t47\t+\t743\t1194\t99,99,99\t1\t451,\t0,\n+chrM\t843\t1182\t11555bed-0cd5-466b-bc33-e1471c67069f;0\t60\t+\t843\t1182\t99,99,99\t1\t339,\t0,\n+chrM\t853\t1601\tbd1bd54a-7196-440b-a210-9049b19561f2;0\t60\t+\t853\t1601\t99,99,99\t1\t748,\t0,\n+chrM\t873\t1371\ta470bde4-ddda-452d-9960-34ae9bb8d8cd;0\t42\t+\t873\t1371\t99,99,99\t1\t498,\t0,\n+chrM\t883\t1601\t8fef762f-f8ee-4493-afcf-3876480619d9;0\t60\t+\t883\t1601\t99,99,99\t1\t718,\t0,\n+chrM\t899\t1514\t75c7d0bb-b9c9-44f4-a7cc-0c90b2939b1a;0\t41\t+\t899\t1514\t99,99,99\t1\t615,\t0,\n+chrM\t905\t1480\t91067ece-d6e2-4755-9d58-7ce8c5e1269d;0\t47\t+\t905\t1480\t99,99,99\t1\t575,\t0,\n+chrM\t906\t1600\t2a2aa7e2-9392-4d18-80c2-6ecb196f0c3a;0\t21\t+\t906\t1600\t99,99,99\t1\t694,\t0,\n+chrM\t916\t1404\t88e10926-72ef-44e0-8aea-3087ae881943;0\t60\t+\t916\t1404\t99,99,99\t1\t488,\t0,\n+chrM\t933\t1340\t4eca6002-439f-4e4c-985d-49836304090a;0\t41\t+\t933\t1340\t99,99,99\t1\t407,\t0,\n+chrM\t1002\t1183\ta98eb040-7def-41e7-875f-869f697626e0;0\t28\t+\t100'..b'\tcf24a281-b665-4b8f-a3a3-528576c3067c;0\t60\t+\t14757\t15887\t99,99,99\t1\t1130,\t0,\n+chrM\t14757\t16045\tfb76bcd3-041c-4e20-9175-ae434cbb3210;0\t60\t+\t14757\t16045\t99,99,99\t1\t1288,\t0,\n+chrM\t14757\t15670\tf993603f-03f0-4fe4-9de0-4de82f7a0d0d;0\t60\t+\t14757\t15670\t99,99,99\t1\t913,\t0,\n+chrM\t14757\t15822\ta6f7c93a-69a7-494b-a49a-eb8a64ce3918;0\t60\t+\t14757\t15822\t99,99,99\t1\t1065,\t0,\n+chrM\t14757\t15856\t01c13ab7-ef27-4e62-ac39-638653276f7e;0\t60\t+\t14757\t15856\t99,99,99\t1\t1099,\t0,\n+chrM\t14757\t15869\t5dac3f00-ff98-4945-944e-71670bc92587;0\t60\t+\t14757\t15869\t99,99,99\t1\t1112,\t0,\n+chrM\t14758\t15887\td69cbde2-2d60-4e19-ac83-817b0c69f28e;0\t60\t+\t14758\t15887\t99,99,99\t1\t1129,\t0,\n+chrM\t14758\t15886\t016bc55b-7a52-4f24-b3d6-9132df099d80;0\t60\t+\t14758\t15886\t99,99,99\t1\t1128,\t0,\n+chrM\t14758\t15883\t64e15f2e-0069-43b5-9dab-7940ef61c849;0\t60\t+\t14758\t15883\t99,99,99\t1\t1125,\t0,\n+chrM\t14758\t15887\t6f6d8722-287e-4445-a9c8-94238428138f;0\t60\t+\t14758\t15887\t99,99,99\t1\t1129,\t0,\n+chrM\t14758\t15879\tc072360c-3ac0-4097-8733-362a494a988e;0\t60\t+\t14758\t15879\t99,99,99\t1\t1121,\t0,\n+chrM\t14760\t15887\t45bb9527-2be5-4272-b819-48a7971c6fbe;0\t60\t+\t14760\t15887\t99,99,99\t1\t1127,\t0,\n+chrM\t14760\t15883\t7f6ec223-0a7f-415e-bdd8-0b2e2c4985ff;0\t60\t+\t14760\t15883\t99,99,99\t1\t1123,\t0,\n+chrM\t14761\t15847\t95cb889c-4a97-4c29-a77c-3312a219a6ad;0\t60\t+\t14761\t15847\t99,99,99\t1\t1086,\t0,\n+chrM\t14766\t15887\tf81dd59c-c08b-4c7d-8c23-1e47857afb92;0\t60\t+\t14766\t15887\t99,99,99\t1\t1121,\t0,\n+chrM\t14766\t15887\t4a1cc098-aa5d-4ad9-87a6-fba57c10c7d7;0\t60\t+\t14766\t15887\t99,99,99\t1\t1121,\t0,\n+chrM\t14770\t15887\tce4659c3-382a-4361-b5ea-28c442883218;0\t60\t+\t14770\t15887\t99,99,99\t1\t1117,\t0,\n+chrM\t14770\t16075\t90808752-db98-4215-b707-b0944c0a7272;0\t60\t+\t14770\t16075\t99,99,99\t1\t1305,\t0,\n+chrM\t14778\t14984\t774ce748-fca6-4046-8daa-da7c6e91765a;0\t60\t+\t14778\t14984\t99,99,99\t1\t206,\t0,\n+chrM\t14846\t15115\t76dc9f46-8b7b-48a8-9225-bca23777bda2;0\t60\t+\t14846\t15115\t99,99,99\t1\t269,\t0,\n+chrM\t14924\t15659\t79eea848-d3ff-4e7b-9c01-9a3710c20732;0\t60\t+\t14924\t15659\t99,99,99\t1\t735,\t0,\n+chrM\t14982\t15842\tdd484c35-375e-47a8-b9e8-31c0b4d39b4b;0\t60\t+\t14982\t15842\t99,99,99\t1\t860,\t0,\n+chrM\t15009\t15887\t3bd3e3d3-132c-43e2-872a-8a41e25d8805;0\t60\t+\t15009\t15887\t99,99,99\t1\t878,\t0,\n+chrM\t15169\t15886\tcdb71c09-5f6e-4145-99c6-3e0cbfd90739;0\t60\t+\t15169\t15886\t99,99,99\t1\t717,\t0,\n+chrM\t15194\t15883\t2622775b-65c9-4cae-9a3b-c6be3e0faa17;0\t60\t+\t15194\t15883\t99,99,99\t1\t689,\t0,\n+chrM\t15213\t15876\t3b1ef952-41fe-4d83-808c-76caa7f7b83d;0\t60\t+\t15213\t15876\t99,99,99\t1\t663,\t0,\n+chrM\t15461\t15887\t9f0d3300-a9c3-41aa-af9b-00403ffbeacb;0\t60\t+\t15461\t15887\t99,99,99\t1\t426,\t0,\n+chrM\t15496\t15876\tfbd51668-5fe6-431a-ad8b-fe1165eebf19;0\t60\t+\t15496\t15876\t99,99,99\t1\t380,\t0,\n+chrM\t15587\t15887\t3c97e997-9eed-405b-b40e-28122064980c;0\t60\t+\t15587\t15887\t99,99,99\t1\t300,\t0,\n+chrM\t15589\t15887\t32c06f69-94bc-4023-8ae7-f66dc584d355;0\t30\t+\t15589\t15887\t99,99,99\t1\t298,\t0,\n+chrM\t15670\t15874\t4a827e6b-259e-4723-8860-f978ceaaa5f7;0\t58\t+\t15670\t15874\t99,99,99\t1\t204,\t0,\n+chrM\t15695\t15877\t7e44209b-aae3-4993-91e4-fe5b37ab2eb2;0\t55\t+\t15695\t15877\t99,99,99\t1\t182,\t0,\n+chrM\t15800\t16569\ta78fb847-612c-42c0-9b73-d59b91a9e9df;0\t60\t+\t15800\t16569\t99,99,99\t1\t769,\t0,\n+chrM\t15963\t16569\tf6bd411a-d419-4197-a525-324568f7944a;0\t60\t+\t15963\t16569\t99,99,99\t1\t606,\t0,\n+chrM\t15963\t16540\tccdfb0ae-54fb-4e3d-8f92-587d4cdc7141;0\t60\t+\t15963\t16540\t99,99,99\t1\t577,\t0,\n+chrM\t15968\t16271\t37432238-4f0a-4817-b648-73cb476a71d7;0\t60\t+\t15968\t16271\t99,99,99\t1\t303,\t0,\n+chrM\t15970\t16311\ta446bc9e-f22d-40ca-a502-d78b06fc8dd4;0\t60\t+\t15970\t16311\t99,99,99\t1\t341,\t0,\n+chrM\t15970\t16557\t2f14a1a9-c356-4568-9a4e-150c8d2038d0;0\t60\t+\t15970\t16557\t99,99,99\t1\t587,\t0,\n+chrM\t15970\t16296\t19cc5328-7604-445f-b261-7e71a02273c6;0\t60\t+\t15970\t16296\t99,99,99\t1\t326,\t0,\n+chrM\t15971\t16569\t46a0710f-c426-4f83-902b-a99be8273b34;0\t60\t+\t15971\t16569\t99,99,99\t1\t598,\t0,\n+chrM\t15971\t16569\td52a572f-79ca-4109-a247-55ab7b0ceda6;0\t60\t+\t15971\t16569\t99,99,99\t1\t598,\t0,\n+chrM\t15972\t16569\t8bf3eb49-3aeb-4bc6-9bcc-1cfb1a896618;0\t60\t+\t15972\t16569\t99,99,99\t1\t597,\t0,\n+chrM\t15976\t16291\tf051705e-4230-4631-84e3-7e014eb98f35;0\t48\t+\t15976\t16291\t99,99,99\t1\t315,\t0,\n' |
| b |
| diff -r 000000000000 -r 6927379c9ede test-data/flair_all_inconsistent.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair_all_inconsistent.bed Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,8 @@ +chrM 1692 16233 8e95941f-3681-40f9-98c2-f5dee4c29acd;0 60 + 1692 16233 27,158,119 2 881,20, 0,14521, +chrM 2011 10881 4d2c4cb6-5652-4bff-aeaa-1a7501b9203e;0 60 + 2011 10881 99,99,99 2 1237,30, 0,8840, +chrM 3258 4226 a6aa00e3-7d42-431e-aa9b-f974416c184b;0 60 - 3258 4226 217,95,2 2 563,338, 0,630, +chrM 3328 4257 c2a3dfdd-b7b9-4af8-b933-d7042384d0cc;0 60 - 3328 4257 217,95,2 2 187,628, 0,301, +chrM 4482 9899 d49d098d-20e2-471c-b621-aea607dcf717;0 58 - 4482 9899 217,95,2 2 1016,46, 0,5371, +chrM 4737 8145 8c9e8a40-b47d-43f7-bc54-d15976e27c0c;0 60 - 4737 8145 217,95,2 2 725,15, 0,3393, +chrM 5911 12712 78cc6deb-e14a-479f-a24e-7941deded72c;0 60 + 5911 12712 27,158,119 2 1609,72, 0,6729, +chrM 11384 12143 af53d265-544a-420b-ae7b-8b56aebe1ac7;0 60 - 11384 12143 217,95,2 2 65,642, 0,117, |
| b |
| diff -r 000000000000 -r 6927379c9ede tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r 000000000000 -r 6927379c9ede tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 6927379c9ede tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 27 21:55:45 2020 +0000 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> |