| Previous changeset 0:dd513c72ea56 (2016-05-17) |
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Commit message:
planemo upload for repository https://github.com/portiahollyoak/Tools commit 41388a30836a24988ff78645b9446480c1c59990 |
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modified:
test-data/README |
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added:
pindelwrapper.xml test-data/dm6_X.fasta |
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removed:
pindel.xml test-data/dm6.fa |
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| diff -r dd513c72ea56 -r 374bb08157ca pindel.xml --- a/pindel.xml Tue May 17 04:47:23 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,94 +0,0 @@ -<tool id ="pindel" name="Pindel" version="0.2.5b8"> - <description></description> - <requirements> - <requirement type="package" version="0.2.5b8">pindel</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command><![CDATA[ - ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai && - ln -f -s "$input_file" alignment.sorted.bam && - ln -f -s "$reference" ref.fa && - samtools faidx ref.fa && - python $__tool_directory__/create_config_file.py - --input_file alignment.sorted.bam - --insert_size "$insert_size" - --sample_label "$input_file.element_identifier" - --output_config_file output_config_file && - pindel - -f ref.fa - -i output_config_file - -c "$chromosome" - -o prefix && - mv prefix_D $Deletions && - mv prefix_SI $Short_Insertions && - mv prefix_LI $Long_Insertions && - mv prefix_INV $Inversions && - mv prefix_TD $Tandem_Duplications && - mv prefix_RP $Read_Pair && - mv prefix_INT_final $INT_final && - mv prefix_CloseEndMapped $Close_End_Mapped - ]]></command> - <inputs> - <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/> - <param name="insert_size" type="integer" value="" label="Expected Insert size" /> - <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/> - <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes" - label="Which chromosome to operate on"/> - </inputs> - <outputs> - <data format="txt" name="Deletions" type="data" label="${input_file.element_identifier} Deletions"/> - <data format="txt" name="Short_Insertions" type="data" label="${input_file.element_identifier} Short Insertions"/> - <data format="txt" name="Long_Insertions" type="data" label="${input_file.element_identifier} Long Insertions"/> - <data format="txt" name="Inversions" type="data" label="${input_file.element_identifier} Inversions"/> - <data format="txt" name="Tandem_Duplications" type="data" label="${input_file.element_identifier} Tandom Duplications"/> - <data format="txt" name="Breakpoints" type="data" label="${input_file.element_identifier} Breakpoints"/> - <data format="txt" name="Read_Pair" type="data" label="${input_file.element_identifier} Read Pair Evidence"/> - <data format="txt" name="INT_final" type="data" label="${input_file.element_identifier} INT_final"/> - <data format="txt" name="Close_End_Mapped" type="data" label="${input_file.element_identifier} Close End Mapped"/> - </outputs> - <tests> - <test> - <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/> - <param name="insert_size" value="250"/> - <param name="reference" value="dm6.fa" ftype="fasta"/> - <param name="chromosome" value="ALL"/> - <output name="Deletions" file="X_100000_Hum1.bam_Deletions" ftype="txt"/> - <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions" ftype="txt"/> - <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions" ftype="txt"/> - <output name="Inversions" file="X_100000_Hum1.bam_Inversions" ftype="txt"/> - <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications" ftype="txt"/> - <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints" ftype="txt"/> - <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence" ftype="txt"/> - <output name="INT_Final" file="X_100000_Hum1.bam_INT_final" ftype="txt"/> - <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped" ftype="txt"/> - </test> - </tests> - <help> <![CDATA[ - -Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequencing data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. - -The following inputs/parameters are required: -- One or more BAM alignment files produced by BWA -- Expected Insert Size for each alignment file -- Sample label for each alignment file -- Reference genome in fasta format (same one used in alignment) -- Which chromosome to operate on - -The following output files are produced by Pindel: -- Deletions -- Short Insertions -- Long Insertions -- Inversions -- Tandom Duplications -- Breakpoints -- Read Pair Evidence -- INT_final -- Close End Mapped - - ]]> </help> - <citations> - <citation type="doi">doi:10.1093/bioinformatics/btp394</citation> - </citations> -</tool> \ No newline at end of file |
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| diff -r dd513c72ea56 -r 374bb08157ca pindelwrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pindelwrapper.xml Fri May 20 04:55:23 2016 -0400 |
| [ |
| @@ -0,0 +1,95 @@ +<tool id ="pindel" name="Pindel" version="0.2.5b8"> + <description></description> + <requirements> + <requirement type="package" version="0.2.5b8">pindel</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai && + ln -f -s "$input_file" alignment.sorted.bam && + ln -f -s "$reference" ref.fa && + samtools faidx ref.fa && + python $__tool_directory__/create_config_file.py + --input_file alignment.sorted.bam + --insert_size "$insert_size" + --sample_label "$input_file.element_identifier" + --output_config_file output_config_file && + pindel + -f ref.fa + -i output_config_file + -c "$chromosome" + -o prefix && + mv prefix_D $Deletions && + mv prefix_SI $Short_Insertions && + mv prefix_LI $Long_Insertions && + mv prefix_INV $Inversions && + mv prefix_TD $Tandem_Duplications && + mv prefix_RP $Read_Pair && + mv prefix_INT_final $INT_final && + mv prefix_CloseEndMapped $Close_End_Mapped + ]]></command> + <inputs> + <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/> + <param name="insert_size" type="integer" value="" label="Expected Insert size" /> + <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/> + <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes" + label="Which chromosome to operate on"/> + </inputs> + <outputs> + <data format="txt" name="Deletions" type="data" label="${input_file.element_identifier} Deletions"/> + <data format="txt" name="Short_Insertions" type="data" label="${input_file.element_identifier} Short Insertions"/> + <data format="txt" name="Long_Insertions" type="data" label="${input_file.element_identifier} Long Insertions"/> + <data format="txt" name="Inversions" type="data" label="${input_file.element_identifier} Inversions"/> + <data format="txt" name="Tandem_Duplications" type="data" label="${input_file.element_identifier} Tandom Duplications"/> + <data format="txt" name="Breakpoints" type="data" label="${input_file.element_identifier} Breakpoints"/> + <data format="txt" name="Read_Pair" type="data" label="${input_file.element_identifier} Read Pair Evidence"/> + <data format="txt" name="INT_final" type="data" label="${input_file.element_identifier} INT_final"/> + <data format="txt" name="Close_End_Mapped" type="data" label="${input_file.element_identifier} Close End Mapped"/> + </outputs> + <tests> + <test> + <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/> + <param name="insert_size" value="250"/> + <param name="reference" value="dm6.fa" ftype="fasta"/> + <param name="chromosome" value="ALL"/> + <output name="Deletions" file="X_100000_Hum1.bam_Deletions" ftype="txt"/> + <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions" ftype="txt"/> + <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions" ftype="txt"/> + <output name="Inversions" file="X_100000_Hum1.bam_Inversions" ftype="txt"/> + <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications" ftype="txt"/> + <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints" ftype="txt"/> + <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence" ftype="txt"/> + <output name="INT_Final" file="X_100000_Hum1.bam_INT_final" ftype="txt"/> + <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped" ftype="txt"/> + </test> + </tests> + <help> <![CDATA[ + +Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequencing data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. + +The following inputs/parameters are required: +- One or more BAM alignment files produced by BWA +- Expected Insert Size for each alignment file +- Sample label for each alignment file +- Reference genome in fasta format (the same one used in alignment) +- Which chromosome to operate on + +The following output files are produced by Pindel: +- Deletions +- Short Insertions +- Long Insertions +- Inversions +- Tandom Duplications +- Breakpoints +- Read Pair Evidence +- INT_final +- Close End Mapped + + + ]]> </help> + <citations> + <citation type="doi">doi:10.1093/bioinformatics/btp394</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r dd513c72ea56 -r 374bb08157ca test-data/README --- a/test-data/README Tue May 17 04:47:23 2016 -0400 +++ b/test-data/README Fri May 20 04:55:23 2016 -0400 |
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| @@ -1,8 +1,9 @@ This folder contains test data for the pindel galaxy tool. X_100000_Hum1.bam = The first 100,000 nucleotides of the X chromosome of the 'Hum' sample sequence in bam format. -X_1000000_dm6.fasta = The first 1,000,0000 nucleotides of X chromosome of Drosophila Melanogaster genome release 6 (dm6) in fasta format. +X_dm6.fasta = The X chromosome sequence of the Drosophila Melanogaster reference genome release 6 (dm6) in fasta format. Information: The readlength for the test data alignment file is 250 + |
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| diff -r dd513c72ea56 -r 374bb08157ca test-data/dm6.fa --- a/test-data/dm6.fa Tue May 17 04:47:23 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,2877329 +0,0 @@\n->2L\n-Cgacaatgcacgacagaggaagcagaacagatatttagattgcctctcat\n-tttctctcccatattatagggagaaatatgatcgcgtatgcgagagtagt\n-gccaacatattgtgctctttgattttttggcaacccaaaatggtggcgga\n-tgaaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCA\n-TTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTG\n-CCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCG\n-CAAACCCAAAAAgacaatacacgacagagagagagagcagcggagatatt\n-tagattgcctattaaatatgatcgcgtatgcgagagtagtgccaacatat\n-tgtgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAA\n-ACCCAAatcgacaatgcacgacagaggaagcagaacagatatttagattg\n-cctctcattttctctcccatattatagggagaaatatgatcgcgtatgcg\n-agagtagtgccaacatattgtgctctttgattttttggcaacccaaaatg\n-gtggcggatgaaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAA\n-TAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGA\n-GAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTA\n-TATTACCGCAAACCCAAAAAgacaatacacgacagagagagagagcagcg\n-gagatatttagattgcctattaaatatgatcgcgtatgcgagagtagtgc\n-caacatattgtgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTT\n-TACCGCAAACCCAAatcgacaatgcacgacagaggaagcagaacagatat\n-ttagattgcctctcattttctctcccatattatagggagaaatatgatcg\n-cgtatgcgagagtagtgccaacatattgtgctctttgattttttggcaac\n-ccaaaatggtggcggatgaaCGAGATGATAATATATTCAAGTTGCCGCTA\n-ATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGC\n-GTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCT\n-CTGTCTTATATTACCGCAAACCCAAAAAgacaatacacgacagagagaga\n-gagcagcggagatatttagattgcctattaaatatgatcgcgtatgcgag\n-agtagtgccaacatattgtgctctCTATATAATGACTGCCTCTCATTCTG\n-TCTTATTTTACCGCAAACCCAAatcgacaatgcacgacagaggaagcaga\n-acagatatttagattgcctctcattttctctcccatattatagggagaaa\n-tatgatcgcgtatgcgagagtagtgccaacatattgtgctctttgatttt\n-ttggcaacccaaaatggtggcggatgaaCGAGATGATAATATATTCAAGT\n-TGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATAT\n-ATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCT\n-CTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAgacaatacacgaca\n-gagagagagagcagcggagatatttagattgcctattaaatatgatcgcg\n-tatgcgagagtagtgccaacatattgtgctctCTATATAATGACTGCCTC\n-TCATTCTGTCTTATTTTACCGCAAACCCAAatcgacaatgcacgacagag\n-gaagcagaacagatatttagattgcctctcattttctctcccatattata\n-gggagaaatatgatcgcgtatgcgagagtagtgccaacatattgtgctct\n-ttgattttttggcaacccaaaatggtggcggatgaaCGAGATGATAATAT\n-ATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAG\n-CACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAAT\n-GAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAgacaat\n-acacgacagagagagagagcagcggagatatttagattgcctattaaata\n-tgatcgcgtatgcgagagtagtgccaacatattgtgctctCTATATAATG\n-ACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAatcgacaatgca\n-cgacagaggaagcagaacagatatttagattgcctctcattttctctccc\n-atattatagggagaaatatgatcgcgtatgcgagagtagtgccaacatat\n-tgtgctctttgattttttggcaacccaaaatggtggcggatgaaCGAGAT\n-GATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTT\n-AAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATT\n-GTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAA\n-AAgacaatacacgacagagagagagagcagcggagatatttagattgcct\n-attaaatatgatcgcgtatgcgagagtagtgccaacatattgtgctctCT\n-ATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAatcg\n-acaatgcacgacagaggaagcagaacagatatttagattgcctctcattt\n-tctctcccatattatagggagaaatatgatcgcgtatgcgagagtagtgc\n-caacatattgtgctctttgattttttggcaacccaaaatggtggcggatg\n-aaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATT\n-GCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCC\n-AACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCA\n-AACCCAAAAAgacaatacacgacagagagagagagcagcggagatattta\n-gattgcctattaaatatgatcgcgtatgcgagagtagtgccaacatattg\n-tgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAAC\n-CCAAatcgacaatgcacgacagaggaagcagaacagatatttagattgcc\n-tctcattttctctcccatattatagggagaaatatgatcgcgtatgcgag\n-agtagtgccaacatattgtgctctttgattttttggcaacccaaaatggt\n-ggcggatgaaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATA\n-AATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGA\n-GTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATA\n-TTACCGCAAACCCAAAAAgacaatacacgacagagagagagagcagcgga\n-gatatttagattgcctattaaatatgatcgcgtatgcgagagtagtgcca\n-acatattgtgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTTTA\n-CCGCAAACCCAAatcgacaatgcacgacagaggaagcagaacagatattt\n-agattgcctctcattttctctcccatattatagggagaaatatgatcgcg\n-tatgcgagagtagtgccaacatattgtgctctttgattttttggcaaccc\n-aaaatggtggcggatgaaC'..b'gggaccccatccg\n-gaagacagactggctgcaaatcaaatacacaggactggactactttgggc\n-cactgctggggactgtgtcccgtcacaaggagaagcgttgggtcgccttg\n-tttacgtgtttgacgacaagggcgattcacctgtagctggcgcatgacct\n-gtcgacggattcctgcataattgcgatcaggaacttcgtctgccgtagag\n-gggcggtatatagactgcgcagcgataacggcaagaacttcgtgggagct\n-gacagggaagccaggcgctttggcgacgtattcgagatggggaagcttca\n-gagtgagttgtcaagcagaagcattgaatgggtgtttaattgtccagcga\n-acccgtctgagggcagagtttgggagcgcatggtgcagtgcgtcaagaga\n-ttgaggcggagaatattgtaaactcgcgtgaaacattgaattcttccaga\n-ataaaacgtgttctactaccacggattagtctgccctttctttcgggaac\n-caatgtgtggggtagccgtttaaggcaactccctgtgacgcacgacgaca\n-gatacaatacaggattagtatcaagtactgtatttatattttctgttgtt\n-gtgttattttgttgttctatttgttgtgaattctcttttttatatttaac\n-aattagttttttgggaatgcctttatatttataaataaaatatagtaaaa\n-gtgtaagtattataatagcaagtatagttaatataataagttgtaatggg\n-ttgtatgtattagtgtgttcattaattatttctttagcatttagatatga\n-taatggttctaattttgttacattgttattgatatagaccgtttgtgtgt\n-agtctagtgttgtgcttgtaattaatatgttttctatttgaacagaacaa\n-ttaaaagcttttattatatggtctccttctattataatttctctattaat\n-tatacagttttgatttaatacaatttttgatattttccaagttaaaatta\n-tgtttggttctacataagttattccaatattgaatatccgcattctgttg\n-gtatttgatttaatattcctgtaattcatttgtttattattggttttcct\n-gagttttgtttgtaaacttgattatcttgaatataatacatttacatttt\n-ctataagtaatttattatctttgtctggatatggtacgatgttaaaaagt\n-gcagtttttataatgtctctaggaatatgggaaataataagtatttcatt\n-tgcatctgattttaaccacgtagaagtttttatatttagcaatttttcgg\n-aatttacatgtaataatggatcatgtcttaataatttgggattaaaaata\n-ccaagtcttgttaattgcataccaagttctatatcttcaatgtactaaac\n-taaactaaaagttctagtcttctgtcaccttcacttattgcgtttaaatg\n-gttgattacttcaatgcctctattgactacttctattacttcattcaatt\n-cattaatttgaatactatgttgagaaagatcgtatattttttgttctaat\n-tcttctttgtcattttgatctaaagtgccaaaaaggtatttatatgcggt\n-acctataaccgcttttattgagttttattattcttattccattcatttct\n-ctgtctaatttttcagttaaatattggatttgggctatagtaccatattc\n-ttcagcttgtttaattaaatttgcaaaagtttgttcggtctttgataagt\n-ttacggagaaatagtgatattcatagtttataggtatatNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNatgttcaactt\n-ttcttcctctatttgtttcttcgtaatgtttctcatctatttgttctacg\n-tgtcctgttttcttaaatgggttagttgttttactttttaccaatggtgc\n-ttgtttatatctagtatctacttcatagctatgtctatctttattcaact\n-tatctatttttaattgtttctctttttgggtgtcatatgcaggtgttcct\n-gcataaaggaaaatatcagctggtgttctcccagttgtattgtgtttagt\n-tttgtggttatatacatagagaatagtttcaaattgtgttatcttatttt\n-ctgggtcggactcactattaatgattcttaacttttcattgactgtttta\n-tggaatctttcaatttttacatttatacaacaacatttttacttgttgtg\n-atatttatattcacattctcggacttaagccataaatgtaacgcggaaca\n-tataaaagatgaatctttatcggcctttatttcggacggttttcccattt\n-cattgaaaattttaaggagagctctttttgcttccagccagtctctacta\n-ctgacttcaatcaaagcggcatattttgaataaatgtcaatgaatgagag\n-gaacgttttattattgattaaataaaaatctataacatatttttctctgg\n-gattagtatcttagtttagtatctctatgttctgttttggatatgttaca\n-tacttcgcattcattaataatgttctgtataaacttttggtagtctgggt\n-aataatatttttgtttaaaaagattagtttgttttctattcctcggtgta\n-aaagttctctgtgactttttataattatttctttaaattctgaatatgtt\n-tcaatgtcttttaatttgatgtttgatttcataactttagttatgttatt\n-cggactgacaatttctatgtaagcgttttgaaatgtaaggaaatctattt\n-cgttatgaaagaaaattacgattcttttggtacataaatattatttattt\n-aattctttggcaaggacatttgtcatttcta\n' 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| diff -r dd513c72ea56 -r 374bb08157ca test-data/dm6_X.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dm6_X.fasta Fri May 20 04:55:23 2016 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>X\n+gaattcgtcagaaatgagctaaacaaatttaaatcattaaatgcgagcggcgaatccggaaacagcaacttcaaaccagtcactctggctgaactaaatggcctgataaactcactggaattaaagaaagccccaggaactgacaatcttaacaacaagaccataataaacttacctacaaaggccagaatatatttaatacttatttataacaacatcctgagaactggacatttcccgaacaaatggaagcacgctagcatctcaatgattcccaaaccagggaaatcaccatttgctctaaattcataccgcccaatcagcttactctctggtctttccaaactactcgaaagaatactactgaaacgactgtatgacattgactcttttgccaaagcaatcccttcccatcaatttggtttcagaaaggatcatggagcggaacatcagctggccagggtgacccaatttattctaaaagcttttgatgaaaaagatgtctgttctgccacattccttgacattacggaagcctttgaccgagtatggcacgacggcttgctatataaactatccagactcatccccagatacctattcgacctacttgaaaactatttatctaatagaaccttctcagtaaggatcgacggtgaaacaacgtctaggataggtaatattagagcaggagtgccccagggcagcatactgggaccggtcctctactcaatatactcatccgacatgccctatcccatcgtaaaagactatatgcgtaacatatccttccctgattaccacccaactaatattatcttagctacatatgcagatgataccataattcttagccggtccaaatataccaagcttgcgatcaacctaaatcaaaactaccttaacgtcttctgtaggtggtcaaaaaaatgggacatagcaattaatgcaaaaaaaaccggacacattcttttctccctaaaaaaagaacaaactaatatatacactcccccactaatcaacggacaaagagctgccaaactaaacaaacaacgctatctcggacttatgctagacagaagactgaccttttgtgcacacatgacgctgctaaagggaaagactatagctgcatataaaaaactggaatggctaataggaaaaaacagccacctacccaaaaatgcaaaaattctcctctggaagcaaattgtctcccccatctggcattacgccatagcaatctggggctcgctggtatctgacacccaagcaaagaaaattcaaacaatggaaaacaaatacatcagacgaatcataaacgccagcagatacacgagacaagcagacataaggacaaaatataacattaaatcatttgatgaaatttttgacaaagcaagccaacgctacgccaactccctcactgaccatgaaaaccctttaatatatgacctccttatcaacgcctacaagccgaacagactggaactaagcaaaaacagatacgtcaagcaattatcaaaatatatactgccccttcaacaacaccgacctaaaccacccgcagaacccatctacagctccatacataattatacaaaaaaggaagaagctgaaatagtcgccaaaatgagaaccaaattcagacagacccttccaaccctcctccggatcgctgaccaagaattggaaataagacaatccatagctgaggaaaagagaaaggaaaaagaaaaatccgaaaggagaaaagccttagagaagggaccgccagatagatggtgtgaacttcaaataaacaaatacagcaaattatacagaaaaggactaagggccagagaggaaatccttgaattaatgctcggacaacccgccactgtaatcaaaatagtaatcccagactatgaacccgaagacgacctaacaaaaaagtcttgaaaactaaataaaagcaaataaaaccaaaagtacatgtatttacaataatcattgattgtataattggtgattataatataacaattataattattaatataattgattgtcataattgttagctattgattataaataactaatcaaaatacaaactacaaactatgaccgacggaaagacgcacgccgacctgcttctcttcctacaatagcgatacacatctccttctccatagtcagcatctttctgtggaaaaacaaaccaattagatggatgatacaaaaacacaaataataaccacacctcaacgcatccggataaaaacaaccaacgacaacgcattccagctgatcatgacgaagtgatgcgaataaaatcaccacctggacataaaagaagaatcggtagatggatatgaaaaggattggtgcggcgaaagcatgatgaatataaggcgactcgctgcagcaatatatgcacaacgtcacttacctgaatcttcttgccgcacagtcttttgaagatccttatcaccgctgcaatccacacacatcgccgcattgctaaagacaggccatctaagctgacccagcgccgattaggacactctgttcgacgagcgcctacagcgaattgccgctaaaacctaaaaacaaaaaatttattaacaaatgaaatacaaatatacaaaattcaaataaaacaaagcacttacctcactgaccgcatccaactgcacgcaacacatccatatccaacataacagacaagaggagacgggccctcaaacgtaaaacaatatcgccaactttgcgcttacaaacacaaaaaaatttacaattttatgatgccgtctcctcttcccgatgccactgcctcaatatggattactagcgcggagccgacagcacactaaaaggctgaaaaatttgtcctcaaaattaatatttttccttagtaccactatcccaacgaattttccgcaaacctgaaataaaaagaaaattaataagaaagtgatacaaaattaactaaaaacaaatagaaaatagcaaaccggacaagcaaagtaacagatataaatatgctacttcatcctgctgaagacacgcatccatgcatccttcttccaagactgcaaaacagaaagaaggaaacacaagctatactgggaaaaatatattaaatcacaatacttatctaattgccaatttgaagaatcctaaaccacggcatcccagcggcgatggccttatctttagctgctacaaatgtacctgaaaacaaaaatcaaaaaacaaaaagtaattcaactataaaaacaaacataatacttacctccagactattttcctcccgaaaaacatacctggaaaacaaaaacaatgcaactatataaacaaataaatacacaaataatacttacctccgaactgcattccacctaatgtacctgaaaaaatacaaaaattacagaaatcacaaaaataaataacaaatgctatacttacctaattttaatattacacccattcccatggcccaatctttgggcggtccccagcaacaattcctgacccggaacattctaaaataataggaaaataaataagattgcgactcaaaattaagcaataacacaaaaaaaaaaacaacaaacctggcagacaaattagctgacgataaattacaacaccatcctgctgacgtcacgcacgaaaattctctctcctaaaacacgggatcccagcggcgatgtccttaactttagctgctacaaatgtacctgaaaacaaaaaaacaaaaattaattcaattataaaaacaaacataatacttacctccagactatttttcctcccgaaaaacatacctggaaaacaaaaacaaggcaactatataaacaaataaatacatatataatacttacatccaaactacattccacctaatgtatctgagaaatacaaaaattagagaaatcacaaaaataaataacaaaggttatacttacctaaaatttaatattacatcca'..b'ATAAATGTATTTTTATACCTAAAATAAATGTTGCGAAATGTCGTAGTTTCATATAAGCATTATGTATCATAATAATCTGGTTGGTTATGGGGTTTGCTATTTTGGGTGACACATACTGCAATTTATATAAAACATTAACCTGATGGATGCCAGGTACAACATTGTTTATTTCAGGTTGTTGCATTAGCCAACGTATGCCCATAACTAAGATGAACAATACATATTCGCAACGCGTGTATAGTAATAAATACACACAAATTTTAAAAATTAGTTAATATCTACCAATTATATTAACACTTATTTCGATGATTACCACATGCGAAATTATTTTATTTTGATTCGACTTCCACTTTCGAATTTTGTTTCTTCGATTTTCATGTTCGAAACATTATTTCTATAGGAAACGCCGTTGTTGTAAGTACTCGCCACAAAAACGCACAACATACtgtagcatattggactaatctaccctaagaatacaatagatgattgggtataacatagcgtcaatacattgtgacactttgtcataataaatataaatatacaaatatacaaaaagaccaccaaaaactacgtaagcactccagcgccccagtaatacgatctaacgcttatacataagccgatagcggagcgtgggaatgctgagcatgcactttgcagctcaagtggtcaatgccttctgcatacatatgtatatgtataaatgtaagtaagaatacatagatataagcaatgtatgtgcgggttagctgaacccaacttcagcacactttgatcattcgaataaacagattcaaacagagcagaggttctgagctcggaaaccaaatctattacatctatacctgttacatttttaaaacaattacatggcgaccgtgactcggtctcgagtctgtctctgtgttgtgtgtgtccgtgtatGTGCGAGGGTCTTTAAACGGTGCTAACTGTGCTGCAAGCGATGTTCGCGCTGCCTGCTGCATTTTCTAATAAAATGCGTTTGAGTAAAACAATTACATGGCAAGCAAGATAACTGTGCACCAAACCAGATTGTGTGGCATGCCACGTGTAGCAACTGATGACCAGACAGCAAAACGATCAGCAAGCACCaaacgcacaaaaacacacagacacaagcggcaattgatggcagacgagccacaattgaccgaggcgcaacccgaggtacagagggaccagccaacgctgggagaagcactggaattaaaccccgccgatggaccgcgcccactcacaatagctgagtaccgggcacgtcaggagaagcgccaacccaggaaacataaacgctctggacgtagagtgaaattactacaacaacgccgactggtcaaggaaatgacccagttggccaaggaggaatcatcccgacaacgctacaaagagcgtcttgaggacatcgaaagcaagatttcgcatggtgcgaaacaacgcaaacgggctgcataaataaatgccaatgcccaaatttgccttaattttaatttctaaacccaagccgatgcgggaaaccgctgcttgaaaaacactaatatctgttaggctttttactaacaatgcggttggacaatttttttttatattgtaaacaaatatgtgagccaaccacatttattaacaactaatatttccacgtctccgctactgagtatatatattcagctgcaaaaatttttttttaatgacagaatataacaattcttatcttcattaaacgtaaacattttttatatttttgattttctagaagaataaattaatatcataataatgagaaaaaactcataaaaaggaaacaaaaacgtttcattgaaaataaacaaaataatatgggatggtttagcgattctagtgaggcaaaggacaatactgccaacgtagttaataacgtaaaaattatagatcacacagacgatataaatgcgttgtggatcttattgctgatcattacaatagtactacttctacaatttctgcttacaatttatgttaagcataacaagatcatcaaaagacgttatataaatagggcaaatcgtttagaccagatttaaaaaaaaaaaataatatggattagaagaaagcttaataaaaactttttttttacgacaagaatggaatggagcgaagtagcgatacgaatagacgaatttcgcttcaggttcgctaagtcttataaatgtatcaatagagacgcagtaataaaatccgaaactttgaaaaatcatatagagatattagtaggagaatataataatatagttacattagtaaataaatatgcaaataggctcacatctgaacataataacaaatgtttgagggttataaaatccctaaacacaagattaaataacatcagaaaaagaaggcatattctgatagatgtaccagaaagtctaagtcaattggttgaattcaacacagaccagttcaaagaactagacgaatctgttcaatcaagcggcgctgagtccgatagtgacattgaaacgctagaaggaggcgaccgaattgaatttaagtctgaaccaataaaaatttctgagatggcacagacattgatagaatttatcaggctagccacatctctgataccagagttcgatggtaaaccagaaaatctacaaagttttttggatgctctaggtctactagatagcttaaagagcacacatgaaacgacagcagtaagcctaataaaaactaaacttaaaggccatgtaagaaaccttataagtaatgagcagacgattgctgcaatcattacccaactgtcgagtgcagtaaaaggagaatcggtagaagtgatatctgccaagcttctgaatctacaacagagaaataaaacggctaaccaatacacccaagaggtggagaaactgacaaaggcccttgaaggtgcctatatcagtgaaggtctcaaccagtccttagcaaataaatacagcactacaacagctgtaaaagcaatgacacagaattgctccattgataaggtaaaacttatcatgcaagcaggcacattcacaaacatgaatgatgccatctccaaatttgtaaacagttgcacagagataacaggtcaaagtaacactgtactctattatcgacgaggtgcaaataattataatagaggcgcccggggttataaccgtggaagaaataactaccacaacaattacaaccgaggcagcaataacaacaataataataactataataaccgtggaggtaggcgaggccaaaaccaagggagaggccgcggaaactacaaccatggtaataataataatagcagtgtgagaatcgcgcaaaatacgtcggaaaactaacagaaccctttaggaaacaaccaataaatgtaaaagttcattccatcaattatagtcttaatatattcgtaaccttctataatcattcaactgaaaataaactaacatttctcatagatactggtgcagatatctcacttttgaaagtaaattctgataacttcataattcaaaatgaaaaaataataaacatcgaaggcataggccaaggaacaaccttaatagaactccaatcaacaaaatatattatcccacatgaatttcatttggtaaacccaaattttgcaataccatgtgatggaataataggcattgattttataaagaaattcaattgtcaactagatttcaaaccaagtgaagactggtttataattagtccccaaaatttaaattatccaatatatgttccgataacatatagcgcttgcaacaatacagttcttctgccagccagatcacaagttattcggaaaatagacattaatgttgtaaatgatttcatatttgttcctaatcaagaaatacacagtgggatttatgttgcaaatacaatagcagcatccaaacatgtatacgttcgacttctaaatacaactaatttcgaccaagtggtcaaagtaaataaaatac\n' |