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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621" |
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added:
get_hrun.py get_hrun.xml macros.xml test-data/in.vcf test-data/out.vcf test-data/reference.fasta |
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| diff -r 000000000000 -r 84f70ce0b830 get_hrun.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_hrun.py Tue Mar 02 21:35:40 2021 +0000 |
| [ |
| @@ -0,0 +1,64 @@ +#!/usr/bin/env python +import argparse + +import vcf +from pyfaidx import Fasta +from vcf.parser import _Info as VcfInfo + + +parser = argparse.ArgumentParser(description='Generate report tables') +parser.add_argument("--reference", + required=True, + help="Filepath to reference FASTA file") +parser.add_argument("--in-vcf", + required=True, + help="Filepath to vcf file to be analyzed") +parser.add_argument("--out-vcf", + required=True, + help="Filepath to vcf file to be output") + +args = parser.parse_args() +ref_path = args.reference +reference = Fasta(ref_path, sequence_always_upper=True, read_ahead=1000) +in_vcf_path = args.in_vcf +in_vcf_handle = open(in_vcf_path) +in_vcf = vcf.Reader(in_vcf_handle) +in_vcf.infos['HRUN'] = VcfInfo( + 'HRUN', 1, 'Integer', + 'Homopolymer length to the right of report indel position', + "get_hrun", "1.0") +out_vcf_path = args.out_vcf +out_vcf_handle = open(out_vcf_path, 'w') +out_vcf = vcf.Writer(out_vcf_handle, in_vcf) +for record in in_vcf: + chrom = record.CHROM + pos = record.POS - 1 + ref = record.REF + calc_hrun = False + for alt in record.ALT: + if len(ref) != len(alt): + calc_hrun = True + if calc_hrun: + window = 50 + hrun = 1 + start = pos + 2 + end = start + window + base = reference[chrom][pos + 1] + seq_len = len(reference[chrom]) + for i in range(start, len(reference)): + base2 = reference[chrom][i] + if base == base2: + hrun += 1 + else: + break + # Extend to left in case not left aligned + for i in range(pos, -1, -1): + if reference[chrom][i] == base: + hrun += 1 + else: + break + record.add_info('HRUN', [hrun]) + out_vcf.write_record(record) +in_vcf_handle.close() +out_vcf.close() +out_vcf_handle.close() |
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| diff -r 000000000000 -r 84f70ce0b830 get_hrun.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_hrun.xml Tue Mar 02 21:35:40 2021 +0000 |
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| @@ -0,0 +1,41 @@ +<?xml version="1.0"?> +<tool id="get_hrun" name="Get homopolymer run length" version="@VERSION@+galaxy0" profile="@PROFILE@" license="MIT"> + <description>Annotate indel variants with homopolymer context</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -s '${reference}' ref.fa && + samtools faidx ref.fa && + python '${__tool_directory__}/get_hrun.py' --reference ref.fa --in-vcf '${in_vcf}' --out-vcf '${out_vcf}' +]]></command> + <inputs> + <param argument="--in-vcf" type="data" format="vcf" label="Input VCF"/> + <param argument="--reference" type="data" format="fasta" label="Input Reference FASTA"/> + </inputs> + <outputs> + <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="in_vcf" value="in.vcf"/> + <param name="reference" value="reference.fasta"/> + <output name="out_vcf" value="out.vcf"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +@WID@ + +**Inputs** +- VCF file +- Reference file for that VCF +**Outputs** +- VCF with annotated homopolymers +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 84f70ce0b830 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 02 21:35:40 2021 +0000 |
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| @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">1.0</token> + <token name="@PROFILE@">20.01</token> + <token name="@TOOL_VERSION@">0.5.9.2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pyfaidx</requirement> + <requirement type="package" version="0.6.8">pyvcf</requirement> + <requirement type="package" version="1.11">samtools</requirement> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.7287/peerj.preprints.970v1</citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + </citations> + </xml> + <!-- + Help + --> + <token name="@WID@"><![CDATA[ +This tools determines the homopolymer context of indels and returns them. +]]></token> +</macros> |
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| diff -r 000000000000 -r 84f70ce0b830 test-data/in.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.vcf Tue Mar 02 21:35:40 2021 +0000 |
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| @@ -0,0 +1,10 @@ +##fileformat=VCFv4.1 +##medaka_version=1.0.3 +##contig=<ID=MN908947.3> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Medaka genotype."> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Medaka genotype quality score"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE +MN908947.3 29748 . TAAAAAAAAAAA TA 243.965 PASS GT:GQ 1:244 +MN908947.3 29749 . A ATTT 243.965 PASS GT:GQ 1:244 +MN908947.3 29765 . TGGGGAACTCG A 243.965 PASS GT:GQ 1:244 +MN908947.3 29789 . TATATGGAAGA A 243.965 PASS GT:GQ 1:244 \ No newline at end of file |
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| diff -r 000000000000 -r 84f70ce0b830 test-data/out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.vcf Tue Mar 02 21:35:40 2021 +0000 |
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| @@ -0,0 +1,11 @@ +##fileformat=VCFv4.1 +##medaka_version=1.0.3 +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Medaka genotype."> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Medaka genotype quality score"> +##contig=<ID=MN908947.3> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE +MN908947.3 29748 . TAAAAAAAAAAA TA 243.965 PASS HRUN=11; GT:GQ 1:244 +MN908947.3 29749 . A ATTT 243.965 PASS HRUN=11; GT:GQ 1:244 +MN908947.3 29765 . TGGGGAACTCG A 243.965 PASS HRUN=4; GT:GQ 1:244 +MN908947.3 29789 . TATATGGAAGA A 243.965 PASS HRUN=1; GT:GQ 1:244 |
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| diff -r 000000000000 -r 84f70ce0b830 test-data/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Tue Mar 02 21:35:40 2021 +0000 |
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| b'@@ -0,0 +1,500 @@\n+>MN908947.3\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT\n+GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT\n+CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC\n+TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT\n+CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC\n+ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG\n+AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA\n+ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT\n+CGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGG\n+CGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGG\n+TGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGA\n+TCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGA\n+ACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTC\n+ATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCG\n+TGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCA\n+GACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAA\n+TTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAA\n+GCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATG\n+CAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGA\n+AGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGC\n+ATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGG\n+CTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTC\n+TTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGG\n+TTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGA\n+AATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAA\n+AGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTAC\n+AAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCC\n+TCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCT\n+TGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGG\n+AATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTAC\n+TAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n+GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGA\n+AGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTAT\n+CTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAA\n+GGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTC\n+TATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCA\n+CTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCC\n+TCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGA\n+AGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGA\n+AATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATAC\n+CTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGA\n+AGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGT\n+ACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGC\n+CTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n+ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGG\n+TGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGA\n+AGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGA\n+AGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGA\n+AGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGA\n+CGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATT\n+AGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n+AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGT\n+AAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGC\n+AGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGC\n+TACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAA\n+ACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAA\n+GAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGG\n+TATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA\n+TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGA\n'..b'GGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATT\n+GTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTT\n+AATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAA\n+GCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTA\n+ATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCC\n+ATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTA\n+AAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n+CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAG\n+CCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAAT\n+GGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATG\n+CCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAG\n+TAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAA\n+TTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT\n+TCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n+TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAA\n+TCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTG\n+ACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACA\n+AATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACA\n+GGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGC\n+TTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAG\n+ATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n+AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGAT\n+GAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTG\n+ATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTA\n+CTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTA\n+GCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGAC\n+GGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGA\n+CAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACT\n+TCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTT\n+GGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAAT\n+TTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTAC\n+AGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATT\n+CTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGG\n+ATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n+GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTT\n+CGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAA\n+CGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTAC\n+GTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCG\n+ATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCT\n+CACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACAC\n+CAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n+TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGG\n+GCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGA\n+GGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGC\n+AATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAG\n+CAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAA\n+TTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGA\n+TGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n+TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAA\n+GAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAG\n+ACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAAC\n+TGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGG\n+AATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGC\n+CATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCA\n+TATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n+TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCC\n+TGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTC\n+AACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGC\n+TTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGC\n+ACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTA\n+GGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAAAAAAAAAAAT\n+ACAGTGGGGAACTCGAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n+TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAA\n\\ No newline at end of file\n' |