| Next changeset 1:72ccb2f848a0 (2018-07-26) |
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Commit message:
planemo upload commit b615ca3bfed9f2115f62d1af30d4726fe8ba08d8 |
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added:
rename_tracks.iml rename_tracks.py rename_tracks.xml test-data/Augustus.gff3 test-data/HISAT.bam test-data/StringTie_assembled_transcripts.gtf test-data/TrfBig.bed test-data/name_mapping.csv test-data/rename_Augustus.gff3 test-data/rename_HISAT.bam test-data/rename_StringTie.gtf test-data/rename_TrfBig.bed test-data/rename_sequence_cov.bigwig test-data/renamed_reference.fasta test-data/sequence_cov.bigwig tool_dependencies.xml |
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| diff -r 000000000000 -r 8b19a698d90e rename_tracks.iml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_tracks.iml Mon Jun 25 15:01:41 2018 -0400 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module type="PYTHON_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="true"> + <exclude-output /> + <content url="file://$MODULE_DIR$" /> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> +</module> \ No newline at end of file |
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| diff -r 000000000000 -r 8b19a698d90e rename_tracks.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_tracks.py Mon Jun 25 15:01:41 2018 -0400 |
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| @@ -0,0 +1,69 @@ +# -*- coding: utf8 -*- + +""" +Rename the custom evidence tracks so that the tracks use the same sequence names as the renamed reference +""" +import sys +import csv +import subprocess +import tempfile + +def rename_interval(inputFile, nameDict, renamedFile): + writer = open(renamedFile, 'w') + with open(inputFile, 'r') as f: + lines = f.readlines() + for l in lines: + if not l.startswith("#"): + scaffold_name = l.split()[0] + if scaffold_name in nameDict: + l = l.replace(scaffold_name, nameDict[scaffold_name]) + writer.write(l) + writer.close() + +def rename_bam(inputFile, nameDict, renamedFile): + header = subprocess.Popen(['samtools', 'view', '-H', inputFile], stdout=subprocess.PIPE) + array_call = ['sed'] + for k,v in nameDict.items(): + substitute = "s/%s/%s/" % (str(k), str(v)) + array_call.append('-e') + array_call.append(substitute) + reheader = subprocess.Popen(array_call, stdin=header.stdout, stdout=subprocess.PIPE) + out = open(renamedFile, 'w') + subprocess.Popen(['samtools', 'reheader', '-', inputFile], stdin=reheader.stdout, stdout=out) + +def rename_bigwig(inputFile, renamedReference, nameDict, renamedFile): + bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0) + chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0) + sorted_bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0) + renamed_sorted_bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0) + + subprocess.call(['bigWigToBedGraph', inputFile, bedGraphFile.name]) + subprocess.call(['faSize', '-detailed', '-tab', renamedReference], stdout=chrom_sizes) + subprocess.call(['sort', '-k1,1', '-k2,2n', bedGraphFile.name], stdout=sorted_bedGraphFile) + rename_interval(sorted_bedGraphFile.name, nameDict, renamed_sorted_bedGraphFile.name) + subprocess.call(['bedGraphToBigWig', renamed_sorted_bedGraphFile.name, chrom_sizes.name, renamedFile]) + +def getNameDict(nameMapping): + nameDict = {} + with open(nameMapping, 'r') as f: + reader = csv.reader(f) + for row in reader: + nameDict[row[0]] = row[1] + return nameDict + +def main(): + inputFile = sys.argv[1] + nameMapping = sys.argv[2] + inputFormat = sys.argv[3] + outputfile = sys.argv[4] + nameDict = getNameDict(nameMapping) + if inputFormat == "bed" or inputFormat == "gff3" or inputFormat == "gtf": + rename_interval(inputFile, nameDict, outputfile) + elif inputFormat == "bam": + rename_bam(inputFile, nameDict, outputfile) + elif inputFormat == "bigwig": + renamedReference = sys.argv[5] + rename_bigwig(inputFile, renamedReference, nameDict, outputfile) + +if __name__ == "__main__": + main() \ No newline at end of file |
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| diff -r 000000000000 -r 8b19a698d90e rename_tracks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_tracks.xml Mon Jun 25 15:01:41 2018 -0400 |
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| @@ -0,0 +1,92 @@ +<tool id="rename_tracks" name="rename the tracks" version="1.2"> +<description>a Galaxy tool to rename the scaffold names in the custom track files</description> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="340">ucsc_rename_bigwig</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/rename_tracks.py "${format_select.input}" "${mapping}" $format_select.format "${output}" + #if $format_select.format == "bigwig" + "${format_select.reference}" + #end if + + + ]]></command> + <inputs> + <conditional name="format_select"> + <param name="format" type="select" label="Select the format of your custom track file"> + <option value="bed">BED</option> + <option value="gff3">GFF3</option> + <option value="gtf">GTF</option> + <option value="bam">BAM</option> + <option value="bigwig">BigWig</option> + </param> + <when value="bed"> + <param name="input" type="data" format="bed" label="Custom track file" /> + </when> + <when value="gff3"> + <param name="input" type="data" format="gff3" label="Custom track file" /> + </when> + <when value="gtf"> + <param name="input" type="data" format="gtf" label="Custom track file" /> + </when> + <when value="bam"> + <param name="input" type="data" format="bam" label="Custom track file" /> + </when> + <when value="bigwig"> + <param name="input" type="data" format="bigwig" label="Custom track file" /> + <param name="reference" type="data" format="fasta" label="Provide the renamed the reference file from 'renamed the scaffolds' tool" /> + </when> + </conditional> + <param name="mapping" type="data" format="csv" label="Provide the name mapping file from 'renamed the scaffolds' tool"/> + </inputs> + <outputs> + <data name="output" format_source="input" label="${tool.name} on ${on_string}: renamed_track" /> + </outputs> + <tests> + <test> + <!-- Test with GFF3 --> + <param name="input" value="Augustus.gff3" /> + <param name="format" value="gff3" /> + <param name="mapping" value="name_mapping.csv" /> + <output name="output" file="rename_Augustus.gff3"/> + </test> + <test> + <!-- Test with BED --> + <param name="input" value="TrfBig.bed" /> + <param name="format" value="bed" /> + <param name="mapping" value="name_mapping.csv" /> + <output name="output" file="rename_TrfBig.bed"/> + </test> + <test> + <!-- Test with GTF --> + <param name="input" value="StringTie_assembled_transcripts.gtf" /> + <param name="format" value="gtf" /> + <param name="mapping" value="name_mapping.csv" /> + <output name="output" file="rename_StringTie.gtf" /> + </test> + <test> + <!-- Test with BAM --> + <param name="input" value="HISAT.bam" /> + <param name="format" value="bam" /> + <param name="mapping" value="name_mapping.csv" /> + <output name="output" file="rename_HISAT.bam" /> + </test> + <test> + <!-- Test with BigWig --> + <param name="input" value="sequence_cov.bigwig" /> + <param name="format" value="bigwig" /> + <param name="mapping" value="name_mapping.csv" /> + <param name="reference" value="renamed_reference.fasta" /> + <output name="output" file="rename_sequence_cov.bigwig" /> + </test> + </tests> + <help><![CDATA[ + This tool is to rename scaffold names in the custom track files, so that the tracks use the same scaffold names as the reference genome renamed by "rename the scaffolds" tool + ]]></help> + <citations> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 8b19a698d90e test-data/Augustus.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Augustus.gff3 Mon Jun 25 15:01:41 2018 -0400 |
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| b'@@ -0,0 +1,6937 @@\n+##gff-version 3\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/galaxy/galaxy/database/dependencies/augustus/3.1/iuc/package_augustus_3_1/24009970003a/config/ ...\n+# fly version. Using default transition matrix.\n+# Looks like /home/galaxy/galaxy/database/files/000/dataset_283.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 45179, name = contig1) -----\n+#\n+# Predicted genes for sequence number 1 on both strands\n+# start gene contig1.g1\n+contig1\tAUGUSTUS\tgene\t553\t34688\t0.03\t-\t.\tID=contig1.g1\n+contig1\tAUGUSTUS\ttranscript\t553\t34688\t0.03\t-\t.\tID=contig1.g1.t1;Parent=contig1.g1\n+contig1\tAUGUSTUS\tCDS\t553\t578\t0.41\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t652\t1047\t0.25\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t12541\t12968\t0.87\t-\t1\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t32202\t33826\t0.89\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t33880\t34044\t0.98\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t34107\t34619\t0.99\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t34674\t34688\t0.45\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tstart_codon\t34686\t34688\t.\t-\t0\tParent=contig1.g1.t1\n+# coding sequence = [atggcagcactctcgcaaaaggactttaatgacggaaaccagagaaatcgtcagaggaaaagtactgtcactgagcagc\n+# cctcatcaacatcaggaagcgtggcccaagtagaagcggacagcgcatcgtcacatttgtctgatcgctgttataacaacatagcaagtactaccaaa\n+# agtattgttggtgatgtgaaaacaagcagacgctgtgaagactttataagtagtggatcagcttcgactccattaaatgaatatgattgtgccaacgc\n+# tgatacgacggatattaaagatgaacctggagattttatagaaacaaattgtcattggcgaagttgttgtattgaatttaatacgcaagatgagcttg\n+# ttaaacatatcaataatgaccatatccaaaccaataagaaggcctttgtctgtcgatgggaaaattgtacccgtggtgaaaaacctttcaaagcgcag\n+# tatatgctagttgtgcatatgcgtcgtcataccggcgaaaagccacataaatgcacatttgaaggctgttttaaggcatattcacgcttggaaaacct\n+# aaaaacacatttacggtcacacacaggtgaaaaaccctatatgtgcgagtatccgggatgcagcaaggcgtttagtaatgcaagcgatcgtgcaaagc\n+# atcaaaatcgtactcacagtaatgagaaaccgtacatttgtaaagctcctggttgcacgaaacgttacaccgacccaagttctttgcgtaaacatgtt\n+# aaaacagttcatggtgctgagttttatgctaataaaaaacacaagggattgcccctaaatgatgcgaactctcgcctccaccgagacagtggccaagg\n+# tcggcataatcttcaagagcataatattgactctagcccttgcagcgaagaacttcaggtgggaaaacttataggcatgtctagtcccagtattaaat\n+# ctgaatctgatgaaagttcaccacatcatcagttgttaagtggagttcgagcttcagactgttttttaacatattcacaagatggtgccgccgaacat\n+# ataactttagatgacggctgggattgtgacgatgacgttgacgtggccgacttaccaattgtcttgcgtgctatggtaaatgttggcagcggaaattc\n+# gatggccccgaccattggagggggtgttgttgcgaggcagcgatttagaagtcgtttgcaaactaaaggaataaactctagtatggttatgcttggca\n+# acatccccgaaagcaatcgcaccattggaataagcgaacttaaccagcgtataacagaacttaagatggagcctggtaccgcttgtgatattacagtt\n+# ccattgaatacggggctggaaaggatttcagaagacttatcacaaaatcaatcaaatataacattaaataagcaaagcttctttaccgcttccggctc\n+# tctccaaggacattttcgtcgcgatagccagaactccactgcaagtacatattatggtagcatgcaaagtcgccgcagtagtcaatcatctcaggtgt\n+# cttctatatctacaatgcgtccaggcccatcgtacaacacaaccacagcttccctctatgatccaatttccccaggatgctctcgacgctctagccaa\n+# atgtctaatgtagtcaactcctacgcacttacatcaacatcaggattgactgcaattaacaaggacttaaatgcaaacagcagcccaaatgcttctat\n+# taataaaccgggtcttggtggtcagtactttggtttttacaataacagtcttcctccacctccatcgtctcatttaattgccaccaatttgaagcatc\n+# tgcaggacacagactctaggagttgttatcacaacacaactggcggtcgattttccattcccaattgtacgccatctctacatttagactacaatgga\n+# ccggctggagagcaggaaattgataaagaaatcccgaataacatattacgacgtcaatctgagccaatgccaaacataagtttg'..b'gt\n+# tttcgtgttggacgaatattgcgctcgctatggtgtgcggggatgctaccgacatttatgctacctttctgatttactggatcgtgcagaaaagcaac\n+# acatgatagatccaacactaattcactattcatttgcgttttgcgcaagccacgttcacggaaatcgacctgatggggtaggaagcattacgcatgag\n+# gaaaaggaaaaattttctgaaatcaaagaacgcctacgtcagttactggagtttcaaataaccaattttagatactgttttcctttcggtcgccccga\n+# aggcgctcttaaagcgacattatctttactagagagagtgctaatgaaagacattgttacccctgttccacctgaagaagttcgtcaaatgattaaaa\n+# aaagtttagagacggcagcgcttgtaaattacacccgtctctccaataaagctaagattgaaggcacttttccgttcaagggacacgtgccagggaaa\n+# tcctatcggaatttcaaaatttttccaagcactttcctgtacacgggaaacgtcccagggaaagcctatcggaaaggtcccagggaaatcccgtcgga\n+# tattcaggatttgcgaggagaggttattgttccgcccccaaaaaaactagaggacctaattcacttagcagaactttgtgttgatctgttgcaacaaa\n+# atgaagagcactatggagaactgcgcaaacatgacaaaatggataaaattaaaatgcgtaaggaagatgatgatgtaccaaaaggccacaatgaaagc\n+# gatattgatttaaccgccaatactggactcagtagcacatcagacctggcttctgcagcatcaactaatggatcgtcatttcgttattataatttgag\n+# gaatgggcgttttcatcagcacctgcgagacacattcgcaccattagtcgtgcggtacgtggatctgatggaatcttcaatagctcagtcgattcata\n+# agggatttgaaaaagaacgctgggaaagtaaagggaacggatgtgccacctctgaagacttattttggaaactagatgctctacagtcgtttataaga\n+# gacctgcactggccagacgcagagtttcgacaacatttagaacagcgtcttaaaatgatggccgtcgatatgatagagcaatgtatacaacgaactga\n+# ttcgtcttttcagtcgtggctaaaaaaaaacattgccttcatatcaactgattatattttaccttcagaaatgtgcgctatggtcaatgtgatattag\n+# atgctaaaaatcaaagctttaaattgactactattgacggcattgatttgtataaatttcatgcaaaaattgacgaccaaatcgacaaagcgaatgta\n+# gctatgacacaaggtctaactggtaaacttatgtcagtgctagagtcgactttgtcaaaattagcacgatacgacgaaggtagcctaatcggctcgat\n+# tcttagttttacaaatgtatcgagctcgggaaaggatctcgggcaaggatatgtaaatttctttagaaataatatggatcaagtacgaggaaaaattg\n+# gcgacgatttatggaccctgaatttctttgagcagtggtactcgcagcagattaacatgctatgtaattggctttcggaacgtttggaccacgctctg\n+# cactacgctcaagtttcatctatttctcacattatcaagaaaatatattcagacttcgaattacaaggtgtattagaagataaattaaactctaaagc\n+# atatcaagcagtcgcacagcgaatggcgacagaggaagcgacatgtgctttgacaatgcctgatgttagcgaagatgaaccctgtgacgacattcgag\n+# aaggggaagaagaagatactggcgacgaatctacctctaacataccaaggggcttaccaaaaccaaaaattgctgccgctcaagctgctgctgttacc\n+# aacgttgttgccggccgtgtgggtaatttactcggcaaaggcattggcggccttagttcaaagttgggaagtggaagttggttttaa]\n+# protein sequence = [MIDPSSSEEEGEDDPIANVSSKGRLTHAPKGTNTVSILGGVSGPGVGSNMAISGSNGDLAGNQRQSNISSISNRNDAG\n+# NVAGVGGSSNKNEQIHGSRVDGGNLEVPNSCIPSGVSQETLNQSIGSSRANSLPRPLSPSPSLTSEKPDTGDPHAFLKGETQIMADEAFQNAVQSYHD\n+# VFLKSERVLKMVQSGASSQHDFREVFRNNIEKRVRSLPEIDGLSKETVLTSWMAKFDIILKGTGEEDSKRPSRMQQSLNSELILSKEQLYDMFQQILL\n+# VKKFEHQILYNALMLDSADEQAAAIRRELDGRMQRVGEMEKNRKLMPKFVLKEMESLYVEELKSSINLLMANLESLPVSKGNMDSKYGLQKLKRYNHR\n+# KLILRSHGSLSKLEGDSEDGSTQLTKLDVVLTFQLEVIVMEVKGLKSLAPNRIVYCTMEVENGEKLQTDQAEASKPMWDTQGDFTTTHPLPVVKVKLY\n+# TENPGMLALEDKELGKVILKPTPLSSKSPEWHRMVIPKNLPDQDIRIKIACRLDKPLNMKHCGYKEKKSEPSEMMQLDGYTVDYIEAASANLMFGIDL\n+# NGGRFFFNAVREGDSISFACDDENECSLWVMAMYRATGQSHKPTPPITQDKNSAMSKIQGARVAPDGSIFLWASFFVAAATRNSSSYHWFRVGGRLNP\n+# MVVSAAARMEWDMCAQSPLASTWRGIGWWSSSERGQPYDLVDVEVPKSGATHYHVSCRGEVNQPETVVRDGLMEAESTDGGVKDAFATELCVEVPEDK\n+# LHVVVWGWFSPGQVFVLDEYCARYGVRGCYRHLCYLSDLLDRAEKQHMIDPTLIHYSFAFCASHVHGNRPDGVGSITHEEKEKFSEIKERLRQLLEFQ\n+# ITNFRYCFPFGRPEGALKATLSLLERVLMKDIVTPVPPEEVRQMIKKSLETAALVNYTRLSNKAKIEGTFPFKGHVPGKSYRNFKIFPSTFLYTGNVP\n+# GKAYRKGPREIPSDIQDLRGEVIVPPPKKLEDLIHLAELCVDLLQQNEEHYGELRKHDKMDKIKMRKEDDDVPKGHNESDIDLTANTGLSSTSDLASA\n+# ASTNGSSFRYYNLRNGRFHQHLRDTFAPLVVRYVDLMESSIAQSIHKGFEKERWESKGNGCATSEDLFWKLDALQSFIRDLHWPDAEFRQHLEQRLKM\n+# MAVDMIEQCIQRTDSSFQSWLKKNIAFISTDYILPSEMCAMVNVILDAKNQSFKLTTIDGIDLYKFHAKIDDQIDKANVAMTQGLTGKLMSVLESTLS\n+# KLARYDEGSLIGSILSFTNVSSSGKDLGQGYVNFFRNNMDQVRGKIGDDLWTLNFFEQWYSQQINMLCNWLSERLDHALHYAQVSSISHIIKKIYSDF\n+# ELQGVLEDKLNSKAYQAVAQRMATEEATCALTMPDVSEDEPCDDIREGEEEDTGDESTSNIPRGLPKPKIAAAQAAAVTNVVAGRVGNLLGKGIGGLS\n+# SKLGSGSWF]\n+# end gene contig70.g117\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /home/galaxy/galaxy/database/files/000/dataset_283.dat --UTR=off --genemodel=complete --species=fly\n' |
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| diff -r 000000000000 -r 8b19a698d90e test-data/HISAT.bam |
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| Binary file test-data/HISAT.bam has changed |
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| diff -r 000000000000 -r 8b19a698d90e test-data/StringTie_assembled_transcripts.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/StringTie_assembled_transcripts.gtf Mon Jun 25 15:01:41 2018 -0400 |
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| @@ -0,0 +1,11 @@ +# stringtie /home/galaxy/galaxy/database/files/000/dataset_328.dat -o /home/galaxy/galaxy/database/files/000/dataset_332.dat -p 1 +# StringTie version 1.2.3 +contig16 StringTie transcript 1751 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "14.618678"; FPKM "322160.531250"; TPM "866155.937500"; +contig16 StringTie exon 1751 1897 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "6.787892"; +contig16 StringTie exon 11285 11463 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "19.860081"; +contig16 StringTie exon 11518 11705 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "23.926477"; +contig16 StringTie exon 11759 11858 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "17.452721"; +contig16 StringTie exon 11922 11975 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "11.461867"; +contig16 StringTie exon 12601 12811 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "11.876496"; +contig16 StringTie exon 17222 17337 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "15.915709"; +contig16 StringTie exon 17406 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "8"; cov "11.738873"; |
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| diff -r 000000000000 -r 8b19a698d90e test-data/TrfBig.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TrfBig.bed Mon Jun 25 15:01:41 2018 -0400 |
| b |
| b'@@ -0,0 +1,602 @@\n+contig1\t9130\t9428\ttrf\t163\t1.8\t164\t86\t2\t438\t36\t12\t13\t37\t1.82\tAAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT\n+contig1\t15707\t15757\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig1\t16261\t16302\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig1\t23387\t23483\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig1\t23451\t23520\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig1\t24200\t24233\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig1\t29159\t29628\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig1\t37571\t37606\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig1\t38436\t38491\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig1\t38436\t38491\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig1\t38436\t38491\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig1\t43116\t43168\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t540\t590\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig2\t1094\t1135\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig2\t8220\t8316\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig2\t8284\t8353\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig2\t9033\t9066\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig2\t13992\t14461\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig2\t22404\t22439\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig2\t23269\t23324\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig2\t23269\t23324\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig2\t23269\t23324\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig2\t27949\t28001\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t38280\t38311\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t3265\t3296\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t17933\t17958\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig3\t19067\t19124\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig3\t23368\t23418\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig3\t24889\t25322\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig3\t26816\t26900\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig3\t26816\t26887\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig3\t26816\t26900\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT\n+contig3\t26820\t26887\ttrf\t17\t3.7\t19\t80\t20\t74\t20\t4\t0\t74\t0.99\tTTTATATATTTTTTTTTCA\n+contig3\t29468\t29515\ttrf\t25\t2.0\t23\t84\t12\t60\t34\t0\t17\t48\t1.47\tATTATAATTATGATGTTATGATG\n+contig3\t38756\t38791\ttrf\t10\t3.6\t10\t92\t7\t63\t40\t0\t0\t60\t0.97\tATTTATTTAA\n+contig3\t38758\t38788\ttrf\t9\t3.2\t9\t95\t4\t51\t40\t0\t0\t60\t0.97\tTTATTTAAA\n+contig4\t7931\t7956\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig4\t9065\t9122\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig4\t13366\t13416\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig4\t14887\t15320\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig4\t16814\t16898\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig4\t16814\t16885\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig4\t16814\t16898\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT'..b'\n+contig69\t18503\t18850\ttrf\t163\t2.1\t163\t88\t3\t502\t36\t12\t16\t35\t1.86\tCTTTGGTGCTATTTGACATATAACCTCCTAAGCTTGGAAATATCATTTTTTAATTGATTTTGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAG\n+contig69\t18536\t18888\ttrf\t163\t2.2\t161\t85\t4\t472\t36\t9\t16\t37\t1.82\tTTGGAAATACAATTTTTTATATTTATGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAGCTTTGGAGCTGTTTGACATATAACCCTATAAGA\n+contig69\t19781\t19812\ttrf\t15\t2.1\t14\t94\t5\t53\t58\t0\t0\t41\t0.98\tATATAATTATAATA\n+contig69\t23637\t24060\ttrf\t162\t2.7\t156\t83\t6\t496\t37\t11\t12\t38\t1.79\tAAAAAAATTATATCTTCGGTGCTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTAATTAGTTCTGAATTTCAATTAAATTTTATCAAAATCGGACGACTTATAGCTGCCATAGGAACGATCGAAAAATTGATGGGAAAATAAATAT\n+contig69\t36863\t36892\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+contig69\t38645\t39124\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+contig69\t43653\t44084\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t6910\t6939\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+contig70\t8692\t9171\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+contig70\t13700\t14131\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t17962\t18295\ttrf\t161\t2.1\t160\t83\t5\t413\t37\t12\t13\t35\t1.84\tAAAAAATTATATCTCTGGTGTTTTTAAACATATAACCTCCTAAACTTGGAAATAACATTTTATAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAACCCGACGACTATATCATACATGTAACTGTAACGATCGGAAAATTGATGGGAAAATAATATG\n+contig70\t19030\t19306\ttrf\t137\t2.0\t137\t94\t1\t482\t39\t13\t13\t34\t1.83\tTTTAACACATACCTTTCTAAGCTTGGATATAACATTTTTAAACTGGTTCTGAATTTCAAATTAAATTCAATTAAAATCGGACGACTATATCATATAGCTCCCATAGGAAAAATCGGAAAATTAGTGAGAAAATAATA\n+contig70\t22269\t22308\ttrf\t19\t2.1\t19\t100\t0\t78\t58\t15\t15\t10\t1.62\tAACTAAGGAAATACCAGAA\n+contig70\t22812\t23252\ttrf\t162\t2.8\t156\t84\t5\t562\t37\t11\t13\t37\t1.81\tTTCTAAGCTTGAAATAACATTTTTTAATTAGTTCTGAATTTCGAATTTAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAAATAAAAATTATATTTGTATTTTTAACATATAACC\n+contig70\t23421\t23486\ttrf\t13\t4.7\t13\t70\t20\t51\t38\t0\t0\t61\t0.96\tATATATATAATTT\n+contig70\t23426\t23479\ttrf\t7\t7.4\t7\t79\t12\t54\t35\t0\t0\t64\t0.94\tTATATTT\n+contig70\t23430\t23486\ttrf\t27\t2.0\t27\t83\t10\t69\t35\t0\t0\t64\t0.94\tATTTATATATTTATTAATATATTTTAT\n+contig70\t25576\t25606\ttrf\t12\t2.5\t12\t94\t0\t51\t33\t26\t36\t3\t1.73\tACGGACGGACAG\n+contig70\t27263\t27382\ttrf\t63\t1.9\t63\t85\t3\t168\t27\t25\t21\t26\t1.99\tATTTTTCCAAGCACTTTCCTGTACAAGGGAAACGTCCCAGGGAAAGCCTATCGGAATTTCAAA\n+contig70\t27353\t27406\ttrf\t25\t2.1\t25\t85\t0\t70\t30\t26\t32\t11\t1.91\tGGAAACGTCCCAGGGAAAGCCCATC\n+contig70\t27848\t27878\ttrf\t12\t2.5\t12\t88\t0\t51\t30\t30\t40\t0\t1.57\tACGGACGGACAG\n+contig70\t35504\t35713\ttrf\t102\t2.0\t102\t99\t0\t409\t37\t12\t13\t36\t1.82\tAAAACGATGGTAGACAAATATGCATATATTTTTTACACAAAACGAAATATAATGGACTTTTAAAAATTCTTTTTTCTATCTTTCCTGGTGGGAGATATATAT\n+contig70\t43333\t43446\ttrf\t57\t2.0\t57\t94\t0\t199\t30\t17\t22\t29\t1.97\tAATATTGGGAATAACATATTATCTTATAATATGGGAGCGCGAAGGCTCCTCGCCCAT\n+contig70\t44242\t44281\ttrf\t7\t5.7\t7\t81\t6\t53\t28\t20\t12\t38\t1.89\tTACATGT\n+contig70\t44241\t44281\ttrf\t13\t2.9\t14\t85\t7\t55\t27\t22\t12\t37\t1.90\tCTACATGTTACATG\n+contig70\t44485\t44531\ttrf\t14\t3.3\t14\t84\t0\t65\t41\t21\t10\t26\t1.86\tAACCGTATATGACT\n+contig70\t45147\t45181\ttrf\t16\t2.0\t17\t88\t11\t52\t52\t0\t2\t44\t1.16\tAAATATTAGTAATATAT\n+contig70\t46706\t46990\ttrf\t147\t1.9\t147\t100\t0\t568\t39\t10\t9\t40\t1.72\tTTCTTTATTTTTTTTATTTTAAAATACTTAGTACTTAGTAATGTCGCTAAAACCAATATAATATTCTTTAAAATTTAGAAAATATATTCAGACTTCGAATTACAAGGTGTATTAGAAGATAAATTAAACTCTAAAGCTTAATTTATC\n+contig70\t53900\t53978\ttrf\t28\t2.8\t28\t80\t5\t97\t15\t43\t5\t35\t1.69\tCTCTGTCACCCTCTCTTTACCTACCTCA\n' |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/name_mapping.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name_mapping.csv Mon Jun 25 15:01:41 2018 -0400 |
| b |
| @@ -0,0 +1,71 @@ +Original sequence name,Renamed sequence name +contig1,scaffold_1 +contig2,scaffold_2 +contig3,scaffold_3 +contig4,scaffold_4 +contig5,scaffold_5 +contig6,scaffold_6 +contig7,scaffold_7 +contig8,scaffold_8 +contig9,scaffold_9 +contig10,scaffold_10 +contig11,scaffold_11 +contig12,scaffold_12 +contig13,scaffold_13 +contig14,scaffold_14 +contig15,scaffold_15 +contig16,scaffold_16 +contig17,scaffold_17 +contig18,scaffold_18 +contig19,scaffold_19 +contig20,scaffold_20 +contig21,scaffold_21 +contig22,scaffold_22 +contig23,scaffold_23 +contig24,scaffold_24 +contig25,scaffold_25 +contig26,scaffold_26 +contig27,scaffold_27 +contig28,scaffold_28 +contig29,scaffold_29 +contig30,scaffold_30 +contig31,scaffold_31 +contig32,scaffold_32 +contig33,scaffold_33 +contig34,scaffold_34 +contig35,scaffold_35 +contig36,scaffold_36 +contig37,scaffold_37 +contig38,scaffold_38 +contig39,scaffold_39 +contig40,scaffold_40 +contig41,scaffold_41 +contig42,scaffold_42 +contig43,scaffold_43 +contig44,scaffold_44 +contig45,scaffold_45 +contig46,scaffold_46 +contig47,scaffold_47 +contig48,scaffold_48 +contig49,scaffold_49 +contig50,scaffold_50 +contig51,scaffold_51 +contig52,scaffold_52 +contig53,scaffold_53 +contig54,scaffold_54 +contig55,scaffold_55 +contig56,scaffold_56 +contig57,scaffold_57 +contig58,scaffold_58 +contig59,scaffold_59 +contig60,scaffold_60 +contig61,scaffold_61 +contig62,scaffold_62 +contig63,scaffold_63 +contig64,scaffold_64 +contig65,scaffold_65 +contig66,scaffold_66 +contig67,scaffold_67 +contig68,scaffold_68 +contig69,scaffold_69 +contig70,scaffold_70 |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/rename_Augustus.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rename_Augustus.gff3 Mon Jun 25 15:01:41 2018 -0400 |
| [ |
| b'@@ -0,0 +1,6937 @@\n+##gff-version 3\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/galaxy/galaxy/database/dependencies/augustus/3.1/iuc/package_augustus_3_1/24009970003a/config/ ...\n+# fly version. Using default transition matrix.\n+# Looks like /home/galaxy/galaxy/database/files/000/dataset_283.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 45179, name = contig1) -----\n+#\n+# Predicted genes for sequence number 1 on both strands\n+# start gene contig1.g1\n+scaffold_1\tAUGUSTUS\tgene\t553\t34688\t0.03\t-\t.\tID=scaffold_1.g1\n+scaffold_1\tAUGUSTUS\ttranscript\t553\t34688\t0.03\t-\t.\tID=scaffold_1.g1.t1;Parent=scaffold_1.g1\n+scaffold_1\tAUGUSTUS\tCDS\t553\t578\t0.41\t-\t2\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tCDS\t652\t1047\t0.25\t-\t2\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tCDS\t12541\t12968\t0.87\t-\t1\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tCDS\t32202\t33826\t0.89\t-\t0\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tCDS\t33880\t34044\t0.98\t-\t0\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tCDS\t34107\t34619\t0.99\t-\t0\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tCDS\t34674\t34688\t0.45\t-\t0\tID=scaffold_1.g1.t1.cds;Parent=scaffold_1.g1.t1\n+scaffold_1\tAUGUSTUS\tstart_codon\t34686\t34688\t.\t-\t0\tParent=scaffold_1.g1.t1\n+# coding sequence = [atggcagcactctcgcaaaaggactttaatgacggaaaccagagaaatcgtcagaggaaaagtactgtcactgagcagc\n+# cctcatcaacatcaggaagcgtggcccaagtagaagcggacagcgcatcgtcacatttgtctgatcgctgttataacaacatagcaagtactaccaaa\n+# agtattgttggtgatgtgaaaacaagcagacgctgtgaagactttataagtagtggatcagcttcgactccattaaatgaatatgattgtgccaacgc\n+# tgatacgacggatattaaagatgaacctggagattttatagaaacaaattgtcattggcgaagttgttgtattgaatttaatacgcaagatgagcttg\n+# ttaaacatatcaataatgaccatatccaaaccaataagaaggcctttgtctgtcgatgggaaaattgtacccgtggtgaaaaacctttcaaagcgcag\n+# tatatgctagttgtgcatatgcgtcgtcataccggcgaaaagccacataaatgcacatttgaaggctgttttaaggcatattcacgcttggaaaacct\n+# aaaaacacatttacggtcacacacaggtgaaaaaccctatatgtgcgagtatccgggatgcagcaaggcgtttagtaatgcaagcgatcgtgcaaagc\n+# atcaaaatcgtactcacagtaatgagaaaccgtacatttgtaaagctcctggttgcacgaaacgttacaccgacccaagttctttgcgtaaacatgtt\n+# aaaacagttcatggtgctgagttttatgctaataaaaaacacaagggattgcccctaaatgatgcgaactctcgcctccaccgagacagtggccaagg\n+# tcggcataatcttcaagagcataatattgactctagcccttgcagcgaagaacttcaggtgggaaaacttataggcatgtctagtcccagtattaaat\n+# ctgaatctgatgaaagttcaccacatcatcagttgttaagtggagttcgagcttcagactgttttttaacatattcacaagatggtgccgccgaacat\n+# ataactttagatgacggctgggattgtgacgatgacgttgacgtggccgacttaccaattgtcttgcgtgctatggtaaatgttggcagcggaaattc\n+# gatggccccgaccattggagggggtgttgttgcgaggcagcgatttagaagtcgtttgcaaactaaaggaataaactctagtatggttatgcttggca\n+# acatccccgaaagcaatcgcaccattggaataagcgaacttaaccagcgtataacagaacttaagatggagcctggtaccgcttgtgatattacagtt\n+# ccattgaatacggggctggaaaggatttcagaagacttatcacaaaatcaatcaaatataacattaaataagcaaagcttctttaccgcttccggctc\n+# tctccaaggacattttcgtcgcgatagccagaactccactgcaagtacatattatggtagcatgcaaagtcgccgcagtagtcaatcatctcaggtgt\n+# cttctatatctacaatgcgtccaggcccatcgtacaacacaaccacagcttccctctatgatccaatttccccaggatgctctcgacgctctagccaa\n+# atgtctaatgtagtcaactcctacgcacttacatcaacatcaggattgactgcaattaacaaggacttaaatgcaaacagcagcccaaatgcttctat\n+# taataaaccgggtcttggtggtcagtactttggtttttacaataacagtcttcctccacctccatcgtctcatttaattgccaccaatttgaagcatc\n+# tgcaggacacagactctaggagttgttatcacaacacaactggcggtcgattttccattcccaattgtacgccatctctacatttagactacaatgga\n+# '..b'gt\n+# tttcgtgttggacgaatattgcgctcgctatggtgtgcggggatgctaccgacatttatgctacctttctgatttactggatcgtgcagaaaagcaac\n+# acatgatagatccaacactaattcactattcatttgcgttttgcgcaagccacgttcacggaaatcgacctgatggggtaggaagcattacgcatgag\n+# gaaaaggaaaaattttctgaaatcaaagaacgcctacgtcagttactggagtttcaaataaccaattttagatactgttttcctttcggtcgccccga\n+# aggcgctcttaaagcgacattatctttactagagagagtgctaatgaaagacattgttacccctgttccacctgaagaagttcgtcaaatgattaaaa\n+# aaagtttagagacggcagcgcttgtaaattacacccgtctctccaataaagctaagattgaaggcacttttccgttcaagggacacgtgccagggaaa\n+# tcctatcggaatttcaaaatttttccaagcactttcctgtacacgggaaacgtcccagggaaagcctatcggaaaggtcccagggaaatcccgtcgga\n+# tattcaggatttgcgaggagaggttattgttccgcccccaaaaaaactagaggacctaattcacttagcagaactttgtgttgatctgttgcaacaaa\n+# atgaagagcactatggagaactgcgcaaacatgacaaaatggataaaattaaaatgcgtaaggaagatgatgatgtaccaaaaggccacaatgaaagc\n+# gatattgatttaaccgccaatactggactcagtagcacatcagacctggcttctgcagcatcaactaatggatcgtcatttcgttattataatttgag\n+# gaatgggcgttttcatcagcacctgcgagacacattcgcaccattagtcgtgcggtacgtggatctgatggaatcttcaatagctcagtcgattcata\n+# agggatttgaaaaagaacgctgggaaagtaaagggaacggatgtgccacctctgaagacttattttggaaactagatgctctacagtcgtttataaga\n+# gacctgcactggccagacgcagagtttcgacaacatttagaacagcgtcttaaaatgatggccgtcgatatgatagagcaatgtatacaacgaactga\n+# ttcgtcttttcagtcgtggctaaaaaaaaacattgccttcatatcaactgattatattttaccttcagaaatgtgcgctatggtcaatgtgatattag\n+# atgctaaaaatcaaagctttaaattgactactattgacggcattgatttgtataaatttcatgcaaaaattgacgaccaaatcgacaaagcgaatgta\n+# gctatgacacaaggtctaactggtaaacttatgtcagtgctagagtcgactttgtcaaaattagcacgatacgacgaaggtagcctaatcggctcgat\n+# tcttagttttacaaatgtatcgagctcgggaaaggatctcgggcaaggatatgtaaatttctttagaaataatatggatcaagtacgaggaaaaattg\n+# gcgacgatttatggaccctgaatttctttgagcagtggtactcgcagcagattaacatgctatgtaattggctttcggaacgtttggaccacgctctg\n+# cactacgctcaagtttcatctatttctcacattatcaagaaaatatattcagacttcgaattacaaggtgtattagaagataaattaaactctaaagc\n+# atatcaagcagtcgcacagcgaatggcgacagaggaagcgacatgtgctttgacaatgcctgatgttagcgaagatgaaccctgtgacgacattcgag\n+# aaggggaagaagaagatactggcgacgaatctacctctaacataccaaggggcttaccaaaaccaaaaattgctgccgctcaagctgctgctgttacc\n+# aacgttgttgccggccgtgtgggtaatttactcggcaaaggcattggcggccttagttcaaagttgggaagtggaagttggttttaa]\n+# protein sequence = [MIDPSSSEEEGEDDPIANVSSKGRLTHAPKGTNTVSILGGVSGPGVGSNMAISGSNGDLAGNQRQSNISSISNRNDAG\n+# NVAGVGGSSNKNEQIHGSRVDGGNLEVPNSCIPSGVSQETLNQSIGSSRANSLPRPLSPSPSLTSEKPDTGDPHAFLKGETQIMADEAFQNAVQSYHD\n+# VFLKSERVLKMVQSGASSQHDFREVFRNNIEKRVRSLPEIDGLSKETVLTSWMAKFDIILKGTGEEDSKRPSRMQQSLNSELILSKEQLYDMFQQILL\n+# VKKFEHQILYNALMLDSADEQAAAIRRELDGRMQRVGEMEKNRKLMPKFVLKEMESLYVEELKSSINLLMANLESLPVSKGNMDSKYGLQKLKRYNHR\n+# KLILRSHGSLSKLEGDSEDGSTQLTKLDVVLTFQLEVIVMEVKGLKSLAPNRIVYCTMEVENGEKLQTDQAEASKPMWDTQGDFTTTHPLPVVKVKLY\n+# TENPGMLALEDKELGKVILKPTPLSSKSPEWHRMVIPKNLPDQDIRIKIACRLDKPLNMKHCGYKEKKSEPSEMMQLDGYTVDYIEAASANLMFGIDL\n+# NGGRFFFNAVREGDSISFACDDENECSLWVMAMYRATGQSHKPTPPITQDKNSAMSKIQGARVAPDGSIFLWASFFVAAATRNSSSYHWFRVGGRLNP\n+# MVVSAAARMEWDMCAQSPLASTWRGIGWWSSSERGQPYDLVDVEVPKSGATHYHVSCRGEVNQPETVVRDGLMEAESTDGGVKDAFATELCVEVPEDK\n+# LHVVVWGWFSPGQVFVLDEYCARYGVRGCYRHLCYLSDLLDRAEKQHMIDPTLIHYSFAFCASHVHGNRPDGVGSITHEEKEKFSEIKERLRQLLEFQ\n+# ITNFRYCFPFGRPEGALKATLSLLERVLMKDIVTPVPPEEVRQMIKKSLETAALVNYTRLSNKAKIEGTFPFKGHVPGKSYRNFKIFPSTFLYTGNVP\n+# GKAYRKGPREIPSDIQDLRGEVIVPPPKKLEDLIHLAELCVDLLQQNEEHYGELRKHDKMDKIKMRKEDDDVPKGHNESDIDLTANTGLSSTSDLASA\n+# ASTNGSSFRYYNLRNGRFHQHLRDTFAPLVVRYVDLMESSIAQSIHKGFEKERWESKGNGCATSEDLFWKLDALQSFIRDLHWPDAEFRQHLEQRLKM\n+# MAVDMIEQCIQRTDSSFQSWLKKNIAFISTDYILPSEMCAMVNVILDAKNQSFKLTTIDGIDLYKFHAKIDDQIDKANVAMTQGLTGKLMSVLESTLS\n+# KLARYDEGSLIGSILSFTNVSSSGKDLGQGYVNFFRNNMDQVRGKIGDDLWTLNFFEQWYSQQINMLCNWLSERLDHALHYAQVSSISHIIKKIYSDF\n+# ELQGVLEDKLNSKAYQAVAQRMATEEATCALTMPDVSEDEPCDDIREGEEEDTGDESTSNIPRGLPKPKIAAAQAAAVTNVVAGRVGNLLGKGIGGLS\n+# SKLGSGSWF]\n+# end gene contig70.g117\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /home/galaxy/galaxy/database/files/000/dataset_283.dat --UTR=off --genemodel=complete --species=fly\n' |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/rename_HISAT.bam |
| b |
| Binary file test-data/rename_HISAT.bam has changed |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/rename_StringTie.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rename_StringTie.gtf Mon Jun 25 15:01:41 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ +# stringtie /home/galaxy/galaxy/database/files/000/dataset_328.dat -o /home/galaxy/galaxy/database/files/000/dataset_332.dat -p 1 +# StringTie version 1.2.3 +scaffold_16 StringTie transcript 1751 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "14.618678"; FPKM "322160.531250"; TPM "866155.937500"; +scaffold_16 StringTie exon 1751 1897 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "6.787892"; +scaffold_16 StringTie exon 11285 11463 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "19.860081"; +scaffold_16 StringTie exon 11518 11705 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "23.926477"; +scaffold_16 StringTie exon 11759 11858 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "17.452721"; +scaffold_16 StringTie exon 11922 11975 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "11.461867"; +scaffold_16 StringTie exon 12601 12811 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "11.876496"; +scaffold_16 StringTie exon 17222 17337 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "15.915709"; +scaffold_16 StringTie exon 17406 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "8"; cov "11.738873"; |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/rename_TrfBig.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rename_TrfBig.bed Mon Jun 25 15:01:41 2018 -0400 |
| b |
| b'@@ -0,0 +1,602 @@\n+scaffold_1\t9130\t9428\ttrf\t163\t1.8\t164\t86\t2\t438\t36\t12\t13\t37\t1.82\tAAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT\n+scaffold_1\t15707\t15757\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+scaffold_1\t16261\t16302\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+scaffold_1\t23387\t23483\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+scaffold_1\t23451\t23520\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+scaffold_1\t24200\t24233\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+scaffold_1\t29159\t29628\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+scaffold_1\t37571\t37606\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+scaffold_1\t38436\t38491\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+scaffold_1\t38436\t38491\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+scaffold_1\t38436\t38491\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+scaffold_1\t43116\t43168\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+scaffold_2\t540\t590\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+scaffold_2\t1094\t1135\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+scaffold_2\t8220\t8316\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+scaffold_2\t8284\t8353\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+scaffold_2\t9033\t9066\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+scaffold_2\t13992\t14461\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+scaffold_2\t22404\t22439\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+scaffold_2\t23269\t23324\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+scaffold_2\t23269\t23324\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+scaffold_2\t23269\t23324\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+scaffold_2\t27949\t28001\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+scaffold_2\t38280\t38311\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+scaffold_3\t3265\t3296\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+scaffold_3\t17933\t17958\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+scaffold_3\t19067\t19124\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+scaffold_3\t23368\t23418\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+scaffold_3\t24889\t25322\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+scaffold_3\t26816\t26900\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+scaffold_3\t26816\t26887\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+scaffold_3\t26816\t26900\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT\n+scaffold_3\t26820\t26887\ttrf\t17\t3.7\t19\t80\t20\t74\t20\t4\t0\t74\t0.99\tTTTATATATTTTTTTTTCA\n+scaffold_3\t29468\t29515\ttrf\t25\t2.0\t23\t84\t12\t60\t34\t0\t17\t48\t1.47\tATTATAATTATGATGTTATGATG\n+scaffold_3\t38756\t38791\ttrf\t10\t3.6\t10\t92\t7\t63\t40\t0\t0\t60\t0.97\tATTTATTTAA\n+scaffold_3\t38758\t38788\ttrf\t9\t3.2\t9\t95\t4\t51\t40\t0\t0\t60\t0.97\tTTATTTAAA\n+scaffold_4\t7931\t7956\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+scaffold_4\t9065\t9122\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+scaffold_4\t13366\t13416\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+scaffold_4\t14887\t15320\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+scaffold_4\t16814\t16898\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+scaffold_4\t16814\t16885\ttrf\t'..b'ATAACCTCCTAAGCTTGGAAATATCATTTTTTAATTGATTTTGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAG\n+scaffold_69\t18536\t18888\ttrf\t163\t2.2\t161\t85\t4\t472\t36\t9\t16\t37\t1.82\tTTGGAAATACAATTTTTTATATTTATGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAGCTTTGGAGCTGTTTGACATATAACCCTATAAGA\n+scaffold_69\t19781\t19812\ttrf\t15\t2.1\t14\t94\t5\t53\t58\t0\t0\t41\t0.98\tATATAATTATAATA\n+scaffold_69\t23637\t24060\ttrf\t162\t2.7\t156\t83\t6\t496\t37\t11\t12\t38\t1.79\tAAAAAAATTATATCTTCGGTGCTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTAATTAGTTCTGAATTTCAATTAAATTTTATCAAAATCGGACGACTTATAGCTGCCATAGGAACGATCGAAAAATTGATGGGAAAATAAATAT\n+scaffold_69\t36863\t36892\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+scaffold_69\t38645\t39124\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+scaffold_69\t43653\t44084\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+scaffold_70\t6910\t6939\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+scaffold_70\t8692\t9171\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+scaffold_70\t13700\t14131\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+scaffold_70\t17962\t18295\ttrf\t161\t2.1\t160\t83\t5\t413\t37\t12\t13\t35\t1.84\tAAAAAATTATATCTCTGGTGTTTTTAAACATATAACCTCCTAAACTTGGAAATAACATTTTATAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAACCCGACGACTATATCATACATGTAACTGTAACGATCGGAAAATTGATGGGAAAATAATATG\n+scaffold_70\t19030\t19306\ttrf\t137\t2.0\t137\t94\t1\t482\t39\t13\t13\t34\t1.83\tTTTAACACATACCTTTCTAAGCTTGGATATAACATTTTTAAACTGGTTCTGAATTTCAAATTAAATTCAATTAAAATCGGACGACTATATCATATAGCTCCCATAGGAAAAATCGGAAAATTAGTGAGAAAATAATA\n+scaffold_70\t22269\t22308\ttrf\t19\t2.1\t19\t100\t0\t78\t58\t15\t15\t10\t1.62\tAACTAAGGAAATACCAGAA\n+scaffold_70\t22812\t23252\ttrf\t162\t2.8\t156\t84\t5\t562\t37\t11\t13\t37\t1.81\tTTCTAAGCTTGAAATAACATTTTTTAATTAGTTCTGAATTTCGAATTTAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAAATAAAAATTATATTTGTATTTTTAACATATAACC\n+scaffold_70\t23421\t23486\ttrf\t13\t4.7\t13\t70\t20\t51\t38\t0\t0\t61\t0.96\tATATATATAATTT\n+scaffold_70\t23426\t23479\ttrf\t7\t7.4\t7\t79\t12\t54\t35\t0\t0\t64\t0.94\tTATATTT\n+scaffold_70\t23430\t23486\ttrf\t27\t2.0\t27\t83\t10\t69\t35\t0\t0\t64\t0.94\tATTTATATATTTATTAATATATTTTAT\n+scaffold_70\t25576\t25606\ttrf\t12\t2.5\t12\t94\t0\t51\t33\t26\t36\t3\t1.73\tACGGACGGACAG\n+scaffold_70\t27263\t27382\ttrf\t63\t1.9\t63\t85\t3\t168\t27\t25\t21\t26\t1.99\tATTTTTCCAAGCACTTTCCTGTACAAGGGAAACGTCCCAGGGAAAGCCTATCGGAATTTCAAA\n+scaffold_70\t27353\t27406\ttrf\t25\t2.1\t25\t85\t0\t70\t30\t26\t32\t11\t1.91\tGGAAACGTCCCAGGGAAAGCCCATC\n+scaffold_70\t27848\t27878\ttrf\t12\t2.5\t12\t88\t0\t51\t30\t30\t40\t0\t1.57\tACGGACGGACAG\n+scaffold_70\t35504\t35713\ttrf\t102\t2.0\t102\t99\t0\t409\t37\t12\t13\t36\t1.82\tAAAACGATGGTAGACAAATATGCATATATTTTTTACACAAAACGAAATATAATGGACTTTTAAAAATTCTTTTTTCTATCTTTCCTGGTGGGAGATATATAT\n+scaffold_70\t43333\t43446\ttrf\t57\t2.0\t57\t94\t0\t199\t30\t17\t22\t29\t1.97\tAATATTGGGAATAACATATTATCTTATAATATGGGAGCGCGAAGGCTCCTCGCCCAT\n+scaffold_70\t44242\t44281\ttrf\t7\t5.7\t7\t81\t6\t53\t28\t20\t12\t38\t1.89\tTACATGT\n+scaffold_70\t44241\t44281\ttrf\t13\t2.9\t14\t85\t7\t55\t27\t22\t12\t37\t1.90\tCTACATGTTACATG\n+scaffold_70\t44485\t44531\ttrf\t14\t3.3\t14\t84\t0\t65\t41\t21\t10\t26\t1.86\tAACCGTATATGACT\n+scaffold_70\t45147\t45181\ttrf\t16\t2.0\t17\t88\t11\t52\t52\t0\t2\t44\t1.16\tAAATATTAGTAATATAT\n+scaffold_70\t46706\t46990\ttrf\t147\t1.9\t147\t100\t0\t568\t39\t10\t9\t40\t1.72\tTTCTTTATTTTTTTTATTTTAAAATACTTAGTACTTAGTAATGTCGCTAAAACCAATATAATATTCTTTAAAATTTAGAAAATATATTCAGACTTCGAATTACAAGGTGTATTAGAAGATAAATTAAACTCTAAAGCTTAATTTATC\n+scaffold_70\t53900\t53978\ttrf\t28\t2.8\t28\t80\t5\t97\t15\t43\t5\t35\t1.69\tCTCTGTCACCCTCTCTTTACCTACCTCA\n' |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/rename_sequence_cov.bigwig |
| b |
| Binary file test-data/rename_sequence_cov.bigwig has changed |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/renamed_reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/renamed_reference.fasta Mon Jun 25 15:01:41 2018 -0400 |
| b |
| b'@@ -0,0 +1,66784 @@\n+>scaffold_1\n+AAAACTAATTTTATCAAAATCGGACAACTATATCATATAGCTGCCATACG\n+AACGATCGGAAAATTGGTAAGTAAATAATTAAAAATATTATATCTTTGGT\n+GTGTTTTTGGAAATAACATTTTTTAATATGTTTTGAATTTTGAATTAAAT\n+TCTATCAAAATCGGACGACTATATCATATAGCTGCCATACAAACGATCGG\n+AAAATTGGTGAATAAATAATATGAAAAAATTATATCTTTGGTTATTTTTT\n+AGACAAATAACCTCCAACGCTTGGAAATAACATTTTTTAATTAGTTATAA\n+ATTTGATATTTTAATTTTATCAAAATCGGACGAATATAGCATATAGCTGT\n+TAAAATAATATGAAACAAATTATAGCTCCGGTGTTTTTTACATATTATCT\n+TATACTATTGGGAAAATAGTTTATTATATTTTAAAGAATTTCCAATTAAA\n+CTCTAACATATAGCTTTCAAAGAAACGGTCAAAAAAGTAAAGAAATCATT\n+TTTTTTTAACATCACTGAAGCTAGAAACAATCCTTAAAAATGTAACATGG\n+TGTTAGTAGCATTGAAAATTGCTTATAACTGCAAAGGGAAAACAAACATC\n+GGCTTGCCGAATGTAATTTCCATTCTTGTTTGACTTGAGTTTATAACTTA\n+CAATTATGGTAAGGTGCCTGATTTTGGTTTTTGCCATACGGTATGTGGTA\n+GTTATCATTTTGCCGTGCTATAAGTGACATCACAGCCGATTCTTTTACTC\n+CATAATGGGCCAATGTGTTGAGGCGTTTCCATCCATTTATTGTTTTTGTA\n+GTTAGGTCTTCATCTTGTAATGTGAGATGACCTCCTCTTCCATGCCTCCA\n+TTCTAAGTCAACTTCGTGCACAGATGGTCTCATAGAAAACGGAGTATTTT\n+TAAAAATTGCGTCCAAAATTTTTAATTTAACTTGCGATATGGTATCCAAA\n+TCGTTTACACGACATTGGACTTTTTCATCAAGATCATCTTGTAAAATGTG\n+CAAAATTACAACAGAATGGGTAACTTGTTCGTGGAGAAGTCGTTCCTCTG\n+AAAGTGAATAACGAGCATCGTGGGTTATTGCGTCCACCAAACCCTTTTCA\n+ATTTGATGCTTAATTGCCTTGAACAGCAAAAATAAATTAGATCCAGCATA\n+TTCTTTTAGGTAGTCGTACATACAAATTGCTAAGTAGTTTGTTAACATTT\n+TTTCAACTACGCTCTCAGTGCGTCGTAGCATTAGCTGAGGATGCTTGCTG\n+GCGAGCGATTTGTCAATTAATCGCAATAAAAGGGACTTTAAAATTTCCGT\n+CGCATATTCCATTTTGTTCATTAGAACAACCATAAGTAAAGAGGCGACGT\n+TAACTCGATCGCGAATTGAGAAAGATGACCGTTGAGCTTCTAAAGTTTCT\n+ATGAACAATAGTAAAAAATATTTGTTTCCAATAAGTTGCTCGAATTGTAT\n+CATAGCTGCATCATAGTTAGTGTGCGGGCTACTTCCACAAAATTTTCGGG\n+AGTTTAGAATAGGATGATCTGATACACCGGGAAAGAAAACTTTCATAATG\n+TAATTGACGTGATCTAACGTTGGTATACCGGTGCTCTCCAAATCTGCTGT\n+TAGATCGGTCATGTCCGTTTGGAGCTCAGCAAATGCCTGTTTACACTCAG\n+AACGAACGTTGCTTTCCAATGTTATCATCTGTATCTGAATTCGTTTGTAT\n+TCCCGTTCTGCTTGGGTCGATTTCCTTCTAAATATTATTAGTACGACAAC\n+CAAAACGATGACAAGCACTGCAACTGTCAATATAACGACAAACATGGCAT\n+GTGAAAAAACATAGGGTTTATTTAAATCATATTTCAAATATCCTATGGCG\n+AAACGAAGATTTCGCCCTACTTTAACCACAACTAGAGGTAAATCTGTCGA\n+TTGATCCACACCATTTTCATCAGTTGGGAGTGGTTGATGTTCCGGTGGAA\n+TGCACAAAAGTTGAGTTAGTGTAAGGCTTGTTATATTGCATTGAGTAGTA\n+CCAATGGTTACATTAACGTCGTATTCATCAGCTGCCAAATTTAGTAGCTC\n+GCCTTCAATAACCAAGCTGTCACCCTTGTATAGTTTAATTCCGTCATTTG\n+GAAATGGTAAATATTTTGGATCGGCTAAATAAACAATAGTGCTCCTGATA\n+TCATGAAAGTATTTATTTAGATCTCGAACAAGCTGTACATTGTCCATTAC\n+AAAACTAAGTTGTAAATTCAGTTGCGTTTCATGGACCTTTACAAAAGTTG\n+TAACATCCATATTATTATTGACGAAATAGCTAGGCGCAGTTCCCCCTGTT\n+GTGTATATATGAAAGTTGTCTACGAAGTCTGCTTTTCGCTTTCGTCTAGA\n+ATATTCGTTCTGATGCGCACTTTCATTTTTAAAGTCAAATTCCGAATCCA\n+TCACTCTGTTAGAACTTTTAAATGCTTGAAATTTATCATTTACCGGAGGA\n+GATGGGCATTCCATTTGATTTGAATTGATTACTACGCAAGATGTTTTGTT\n+TACTCTTTCATTATCAAAAAAAACTTCAAGTTCAGGCTTTTGAATTGAAT\n+TAAGATACATTCCATGAACGGTCAGAACGCGACCACCACTTACAAAACTG\n+CGTAAAGGCTTAATCTGCATTATACGCGGGTCTTGGGTATAGTTAAAAAT\n+AGAACAGGGCTGCCTTGGTAACGTACGAAATTGGTATGAACCGAAATTAC\n+TTCGAGTTAGATTTTTATTGGGTATAGTTGCGGGTGAGATATGACATTCT\n+AAAGTTCGGTTGGCACCGTCAATAAGAAGGTGTAGAGACCGTATTGGTTC\n+TGGCTGGGTCGCCTCTGATGTAGTACTACTAACTTGAGTTGAAGAAGCTT\n+GTGTAACGTTTATATGACACTCGTACTCATCTAAATATGCTCGCATGGTT\n+GATCCAATGTTCAAAAACTTTCCTATTAACGACAATTGTGTTCCTCCCGA\n+CCTGGGCCCAATCGTGGGATATAATCCTGTTAGCAAAACATTCTTAAAGT\n+GAAATTGTACACTAGATTCAGTATACCCTGCATCATTTGCAACCTTTATA\n+GGCGCTGACATTTCATACATCACTGCTCCAGTGCGGCATTCGATCTTTAC\n+AGAAATTTGGTAGTTGACTAGTTCACAAGGCACAGACCCAATAAATATTT\n+TTCCACGCACATCTCCTTCGCGAATGCCCAAATTACTGCCTTCAATTGTA\n+ATAAGGGTACCACCCTCAATAGGTCCAGATAACGGTTTAATAATATCGAT\n+CCTTGGTAAAGGGCACTCGTTTTCTTTAGTTGTTTTTGATCCTGCACTAA\n+TAGCACGATCACTGTCTGCTATGCAAGTCTCGTTATATACACATGAGTTG\n+CTGCACCAAGCACATTGGTATTTTGGATCACGAGTGACACACAAACTGCA\n+ATCAGCATGATCCCGATGTGAGCCCAGTACGTCGCATTTATATAATGTAA\n+CAATCGCCGTGTCCACATAGTGCTGGAAATTCCATGTAATTACAACCTTT\n+GCTTGGTATTCATGTGTATTAGTCTCGTAGAAATAAGGTGTTTTTTCACA\n+AACAACAATCTTGTTTGACTCAATGTGGGCAGGCAATAGCATCTGAGCAG\n+CTTCAATATGAACTGTACACAAGAATCCAGCGTGAGCGCTTTTGGGTTTT\n+GGTAAGTTTTCTATCTCTAAACGAATTTCTTTTGGCACCCGCACCGGTAA\n+AAGAATCGCCGGACGATTGCTTTTTAAATGGGGGCATTGACCAACACTAG\n+TTACCGAATTTTCTATATTACGACATTGTATTGATTGATGGACACATTTA\n+TTGTCAAAAATAC'..b'CCACTGGACCCGTTGGATAGCGTC\n+GGCACTTTTCTGTTTGGTGCCATTCACTGGTCACTAGTAGGACCGCTCTG\n+CCTATTAAAATAGGAGTGCTGCTTAGAATTTATTTCAGCAAGACAGCCGT\n+AAGATATATATGAATAGTATTTAACGGCAGTGGCAGAGGCCTTTACAATA\n+TAAGGCTTTACGGGATTTTAAACAATGAAAAACAAAAATATTTTTATAGA\n+GTCGAGATAAAATACTTTTTACAATAAATACTAAGTATTTTTAAAAGATA\n+AAAATATTTAAAAGTAAATACTGAATATTTTAACAGGTGTTAAGTACTGG\n+GAACTGTGACTAAGGACGGCGGTATATCGCTACCATAATATTTTTAAAGG\n+AACTGAATACTGAAAGATGTGACCAAAATGGTAGAATATCGCTAACGAAA\n+ATCACAGACGCAAATATCGATAGTGGCCTAGAGACCCGATATCGCCGCCG\n+TGATTATCGATGAAACTACAGCTGAGCTGCTTGTTTACATTCTAAAGTTA\n+AAATTTTTAAAAATTTCCAATACAAAAAAAAATTCTTCGTATTAACACGG\n+CTGTTTGCCGGTAAGATCTGAAGTGGATTCAAGTTGCAGCACCCTCAGGA\n+AAAGAATAAATTATTATAATATAATAATATAATATAAAGAATTTAAATTC\n+GAACCAAACGCGGTATGTCACTCTTCATTTAGAGAATTTGTGGCTTTGTT\n+TTGTACAAAAAACTATTCTTTTTTCTTGAAAATTAGCATCAAGAATTTAT\n+TGCCAAAACAGAACGCAATTCTGCTAAATCTGGTTACCCTGCCAAATGGC\n+TGGCCGTTCTGTGCATTCAATAACACAAGCTAACGGCTTACGGCACATTC\n+GGAAAGATCCAAAAGAATTTCTATTCCGGCATTTTTTATGTATTATCGTC\n+CAATTTTTGTATGTGTATTCATTCTTTTGGCTGTCCGTTATTAAGCTTTT\n+CTTATCCACATAAGCTGACCAGCTGCCAAAAAGCCGACCGTTTTGTGCAG\n+CCAATAACCCAAGCTAACTATCAACAGCAATTTCGAAAAATCCAGAAGAA\n+GCTATCCTTCGGCAATTTTTTCTTATATTATAATTTTTTTGTCACAATTT\n+TTTGTCAAAAAATCGACAATAATTAAGTGTTTACATTTTAATGCGATTTA\n+ATTGGAAATTTGAATTCGAATCAAACGCGGTGTCACTCTACATATGGACA\n+ATTTGTGGCTACAAAATTAGTTGAAAGTGCATGTTTTTTTTTAAGTGAAA\n+TAAAACAAAAACAGCAATAACAGGCCAAAATGTTGTTTTATAAATAAATA\n+CTTACATATCCGCATATAAATATGAATGAAAAAAAAAACAGCAAGACTGG\n+GCCAAAATATTGTTCTTTAATATGTAAATAAATACATATCTACATATACA\n+TATGTGGACAAAAGTGTTAAAATTAGTTAATAGTGCATGTTTTTTAAATG\n+AAAAAATAAAACAAAAAAAGCAAGCAAATATAAATTATATTCCACACACA\n+TTTACAATAATTTCAAACTACGCTAAAAATACCCAACAGAAAAAACATAG\n+AAAGGTAAACAAAATACAAGAATATCAAAAAAAATCTAATTTTCACGTTG\n+TTGTGGCCGGTACCACCGGTCATACATACATATAGATACATATTTAGATT\n+CTCACAAAAAGAATAGAAAATTACCGCTAATTTCCTTATATACGTTTTTG\n+TTTTCAGTGTTTTGAAATAGTATTTTTCAAACAAAAAACAATACAAAAGG\n+GTTAAAAAAATTGTTCGATTGGCTTTAACATACTAATTAAAAAAAATCAC\n+AATTTTTTGGCAAAATATCGAAAAAAATTAAGTGTTTACATTTTTATGCG\n+AATTATTTGGAAATTTAAATAAGAACCCAACGCGGTTTGTCACTCTACAT\n+ATGGACAATTTGTGGCTTTGTTTTGAACAAAAAATGAATTTTTTTTTACT\n+CAAAATTAACAAGAAGAAACAGTAATGCGGGTTTTGATCGCAATTCTGCT\n+AAATCGAATTTCCGTGCCCAAAGGCTGACCTTTTTGTGCAGCAAATAGCC\n+CAAGCTAATAATCTACAGCAATTTCTTAAAGACCGAAAATGTATCAACTT\n+CGGCAAAATATGAAAATTTAACATTTATTTTTCAACATTTTTTGCCAAAT\n+AATCGACAAAAATTTCAGTGTCCCGATTTGGATGCGAATTAATTGAGGAC\n+AATTGTGACTTTGTTTTGTAAAAAAACTATTTTTTTTACTGAAAATTACA\n+ATCAAGAATCTAAGGCCAAATCAGAATATTTTCACTGCGGTTTTTTGATC\n+GCAATTCTGCTAAATCGGGTTCCGTGCCAAAAAGCTGACTATTTTTTTTA\n+CTGAGAATTAGCATCAAGAATTTATTGCCAAAACAGAACGCAATTCTGCT\n+AAATCGGGTTGCCCTGCCAAAAGGCTGGCCGTTTTGCGCATTCAATAACA\n+CAAGCTAACGGTTTACAGCACATTCGGAAAGATCCAAAAGAATTTCTATT\n+TCGGCATTTTTTATGTATTATCGTCTAATTTTGGTATGTGTATTCATTCT\n+TTTGGCTGTCCGTTATTAAGCTGCTTTTCTTATTCACATATTCAATGGCG\n+CAGTACATAAAAAGAATGAACCGTGGTTTTCTTGCCCTCTCCATCTCCCT\n+CTACCACTTCCCCTCTCAACAACTATCTCACGCACTCTGTCCCTTCTCGT\n+CTCTGTCACCCTCTCTTTACCTACCTCACTCTGGCACACTCTCTCTACCT\n+ATCTCACTCTGTCACCTTCTTCTACCTAATTCTCTCTGTCGCGCTCGCTC\n+TCTCAACATGCCTTTCGCACCGTATCTCTTCGTTTCTCTGTATGCTTGCT\n+CTCTTAATTTAAGTTTCTCTTTCTTTGTGTTCAATATCTTTCGCGCTCGT\n+GACTCCTATTGACCGGACTCTGAGCGGTGCTCATTAAGAGTGGAGTTTTC\n+GATGATGGCGGGTGGCGCGAACGAGAATTTTTTACATAAAGGTAAGTTGC\n+CAATTCTTTTTTAAATGTGACATACAGCATGCATATTTTATTTATTGTAA\n+TTATATGTGAAAGAATAAAATTATATGTACTTTTATCTAATCTATTGCAT\n+CTATTTTTTCACAGGTAAACGAGTCACACGAGAAGTAAAACACAAACACA\n+AGGATCAAAATAAAATTCAGGTGAGTGAACGAACGTGTTGAAAGTAGTTA\n+ATAGTGCATGTCTATTTAAGTGTAAGAAACAAAAAAGACACAAATGGGCC\n+AATAATTCGTTTCTTTAATAGATAACTGCCTATATTATGTTCAAACTATG\n+CTAAAAAGACCCAAAAGGAAAACATAAAGTATATACCTTGCAAAATGAAT\n+AAAAAGAAATCATATATATTCATATACGTTTGACCGGTACCACCGGTCAT\n+ACATACATAAACATAAACACAAAAAGACTAGAATATAAATACCATATTTT\n+TGATTGGCTTAAAAATGGCACAAAAAAAAGATAAAAACTAGAGTGTCTAG\n+CTTTAAGTGACAATCGACTCGGAAAATGATCAAGAAATAAATGAAAAATT\n+TGTCTTGCGGCTTTTTGGTCGCAATTCTAAATCGGTTTGTATGTATGTCA\n+CTCTTCATGTATACAATTTGGTGGCTTTGTATTCCACAAAAGTCACAGTA\n+GTCACAAAAGTTTTTTTTACTGAAAATTACCATCAAGAGTCTATGGCCAA\n+ATCAGAATATTTTCACTGCGGTTTTTTATTTCAATTCTGCTAAATCGGGT\n+TTCCGTGCCAAAAAGCTTTTGCAGCCAACAACAATATTCAATTTTTTGGC\n+AAAAAATCGACAAAAAAATT\n' |
| b |
| diff -r 000000000000 -r 8b19a698d90e test-data/sequence_cov.bigwig |
| b |
| Binary file test-data/sequence_cov.bigwig has changed |
| b |
| diff -r 000000000000 -r 8b19a698d90e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 25 15:01:41 2018 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ucsc_rename_bigwig" version="340"> + <repository changeset_revision="39d26518c84b" name="package_ucsc_rename_bigwig_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |