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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat commit 6946d81de9419c90e9bc4ea2f7bd5e4168dd6dd6 |
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added:
macros.xml necat.xml test-data/test1.fa test-data/test1_head.fastq test-data/test1_tail.fasta |
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| diff -r 000000000000 -r 6ee7eb5821f0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Nov 25 14:24:27 2022 +0000 |
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| b'@@ -0,0 +1,250 @@\n+<?xml version="1.0"?>\r\n+\r\n+<macros>\r\n+ <token name="@TOOL_VERSION@">0.0.1_update20200803</token>\r\n+ <token name="@VERSION_SUFFIX@">0</token>\r\n+ <xml name="job_conf">\r\n+ <configfile name="job_configfile">\r\n+ <![CDATA[\r\n+ PROJECT=project\r\n+ ONT_READ_LIST=read_list.txt\r\n+ GENOME_SIZE=${genome_size}\r\n+ THREADS=\\${GALAXY_SLOTS:-4}\r\n+ \r\n+ MIN_READ_LENGTH=${min_read_length}\r\n+ PREP_OUTPUT_COVERAGE=${correction_coverage}\r\n+ \r\n+ OVLP_FAST_OPTIONS=-k ${adv.ovf.k} -z ${adv.ovf.z} -q ${adv.ovf.q} -b ${adv.ovf.b} -n ${adv.ovf.n} -a ${adv.ovf.a} -d ${adv.ovf.d} -e ${adv.ovf.e} -m ${adv.ovf.m} -j 0 -u 1\r\n+\r\n+ OVLP_SENSITIVE_OPTIONS=-k ${adv.ovs.k} -z ${adv.ovs.z} -q ${adv.ovs.q} -b ${adv.ovs.b} -n ${adv.ovs.n} -a ${adv.ovs.a} -d ${adv.ovs.d} -e ${adv.ovs.e} -m ${adv.ovs.m} -j 0 -u 1\r\n+\r\n+ CNS_FAST_OPTIONS=-a ${adv.cnf.a} -x ${adv.cnf.x} -y ${adv.cnf.y} -l ${adv.cnf.l} -e ${adv.cnf.e} -p ${adv.cnf.p} -r ${adv.cnf.r} -u ${adv.cnf.u} \r\n+ \r\n+ CNS_SENSITIVE_OPTIONS=-a ${adv.cns.a} -x ${adv.cns.x} -y ${adv.cns.y} -l ${adv.cns.l} -e ${adv.cns.e} -p ${adv.cns.p} -r ${adv.cns.r} -u ${adv.cns.u} \r\n+\r\n+ TRIM_OVLP_OPTIONS=-n ${adv.tov.n} -a ${adv.tov.a} -z ${adv.tov.z} -b ${adv.tov.b} -e ${adv.tov.e} -j 1 -u 1\r\n+ \r\n+ ASM_OVLP_OPTIONS=-n ${adv.aov.n} -a ${adv.aov.a} -z ${adv.aov.z} -b ${adv.aov.b} -e ${adv.aov.e} -j 1 -u 0\r\n+\r\n+ NUM_ITER=2\r\n+ \r\n+ #if $assembly.should_assemble == "yes":\r\n+ CNS_OUTPUT_COVERAGE=$assembly.assembly_coverage\r\n+ POLISH_CONTIGS=$assembly.polish_contigs\r\n+ #else:\r\n+ CNS_OUTPUT_COVERAGE=30\r\n+ POLISH_CONTIGS=false\r\n+ #end if \r\n+\r\n+ CLEANUP=1\r\n+ USE_GRID=false \r\n+ GRID_NODE=0 \r\n+ GRID_OPTIONS=\r\n+ SMALL_MEMORY=0 \r\n+ FSA_OL_FILTER_OPTIONS=\r\n+ --min_length={adv.fol.min_length} \r\n+ --max_length={adv.fol.max_length} \r\n+ --min_identity={adv.fol.min_identity}\r\n+ --min_aligned_length={adv.fol.min_aligned_length}\r\n+ --max_overhang={adv.fol.max_overhang}\r\n+ --min_coverage={adv.fol.min_coverage}\r\n+ --max_coverage={adv.fol.max_coverage}\r\n+ --max_diff_coverage={adv.fol.max_diff_coverage}\r\n+ --coverage_discard={adv.fol.coverage_discard}\r\n+ --bestn={adv.fol.bestn}\r\n+ --genome_size={adv.fol.genome_size}\r\n+ --coverage={adv.fol.coverage}\r\n+ --thread_size=\\${GALAXY_SLOTS:-4}\r\n+ --identity_global_deviation1={adv.fol.identity_global_deviation1}\r\n+ --identity_global_deviation2={adv.fol.identity_global_deviation2}\r\n+ --overhang_global_deviation1={adv.fol.overhang_global_deviation1}\r\n+ --overhang_global_deviation2={adv.fol.overhang_global_deviation2}\r\n+ --identity_local_deviation1={adv.fol.identity_local_deviation1}\r\n+ --identity_local_deviation2={adv.fol.identity_local_deviation2}\r\n+ --overhang_local_deviation1={adv.fol.overhang_local_deviation1}\r\n+ --overhang_local_deviation2={adv.fol.overhang_local_deviation2}\r\n+ --identity_local_condition={adv.fol.identity_local_condition}\r\n+ --local_low_coverage={adv.fol.local_low_coverage}\r\n+ --overlap_file_type=m4\r\n+\r\n+ FSA_ASSEMBLE_OPTIONS= \r\n+ --min_length={adv.fa.min_length}\r\n+ --min_identity={adv.fa.min_identity}\r\n+ --min_aligned_length={adv.fa.min_aligned_length}\r\n+ --min_contig_length={adv.fa.min_contig_length}\r\n+ --max_spur_length={adv.fa.max_spur_length}\r\n+ --select_branch={adv.fa.select_branch}\r\n+ --overlap_file_type=m4\r\n+ --thread_size=\\${GALAXY_SLO'..b'<param argument="--local_low_coverage" type="integer" min="0" value="25" label="local low coverage" help="If the coverage of reads is less than local_low_coverage, min_identity and max_overhang are used to filter out low-quality overlaps. Otherwise, the local threshold is used. default: 25" />\r\n+ </section>\r\n+ </xml>\r\n+\r\n+\r\n+ <xml name="contig_assembly">\r\n+ <section name="fa" title="Contig Assembly Options (for fsa_assemble subprogram)" expanded="false" help="Passed to fsa_assemble subprogram. Constructs contigs from filtered overlaps and corrected reads. ">\r\n+ <param argument="--min_length" type="integer" min="0" value="0" label="min read length" help="minimum length of reads" />\r\n+ <param argument="--min_identity" type="float" min="0" max="100" value="0" label="min overlap identity" help="minimum identity of overlaps" />\r\n+ <param argument="--min_contig_length" type="integer" min="1" value="500" label="min contig length" help="minimum length of contigs" />\r\n+ <param argument="--max_spur_length" type="integer" min="1" value="50000" label="max spur length" help="branches less the threshod are treated as spurs" />\r\n+ <param argument="--select_branch" type="boolean" truevalue="best" falsevalue="no" label="select branch" help="select the most probable branch. default is no." />\r\n+ </section>\r\n+ </xml>\r\n+\r\n+\r\n+\r\n+ <xml name="contig_bridging">\r\n+ <section name="fcb" title="Contig Bridging Options (for fsa_ctg_bridge subprogram)" expanded="false" help="Passed to fsa_ctg_bridge subprogram. Bridges contigs using long reads ">\r\n+ <param argument="--read_min_length" type="integer" min="1" value="5000" label="read min length" help="minimum rawread length" />\r\n+ <param argument="--ctg_min_length" type="integer" min="1" value="500" label="contig min length" help="minimum contig length" />\r\n+\r\n+ <param argument="--ctg2ctg_min_identity" type="float" min="1" max="100" value="95" label="ctg2ctg_min_identity" help="minimum identity of overlaps between contigs" />\r\n+ <param argument="--ctg2ctg_max_overhang" type="integer" min="1" value="100" label="contig-contig max overhang" help="maximum overhang of overlaps between contigs" />\r\n+ <param argument="--ctg2ctg_min_aligned_length" type="integer" min="1" value="2000" label="contig-contig min aligned length" help="minimum aligned length of overlaps between contigs" />\r\n+\r\n+ <param argument="--read2ctg_min_identity" type="float" min="1" max="100" value="80" label="read-contig min identity" help="minimum identity of overlaps between rawreads and contigs" />\r\n+ <param argument="--read2ctg_max_overhang" type="integer" min="1" value="500" label="read-contig max overhang" help="maximum overhang of overlaps between rawreads and contigs" />\r\n+ <param argument="--read2ctg_min_aligned_length" type="integer" min="1" value="5000" label="read-contig min aligned length" help="minimum aligned length of overlaps between rawreads and contigs" />\r\n+ <param argument="--read2ctg_min_coverage" type="integer" min="1" value="3" label="read-contig min coverage" help="minimum coverage of links between rawreads and contigs" />\r\n+\r\n+ <param argument="--min_contig_length" type="integer" min="1" value="500" label="min contig length" help="minimum length of bridged contigs" />\r\n+ <param argument="--window_size" type="integer" min="1" value="1000" label="window size" help="threshold is used to group rawreads that bridge contigs" />\r\n+ <param argument="--select_branch" type="boolean" truevalue="best" falsevalue="no" label="select branch" help="select the most probable branch. default is no." />\r\n+ </section>\r\n+ </xml>\r\n+\r\n+\r\n+\r\n+ <xml name="citations">\r\n+ <citations>\r\n+ <citation type="doi">10.1038/s41467-020-20236-7</citation>\r\n+ </citations>\r\n+ </xml>\r\n+</macros>\r\n' |
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| diff -r 000000000000 -r 6ee7eb5821f0 necat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/necat.xml Fri Nov 25 14:24:27 2022 +0000 |
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| b'@@ -0,0 +1,440 @@\n+<tool id="necat" name="necat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">\r\n+ <description>Error correction and de-novo assembly for ONT Nanopore reads</description>\r\n+ <macros>\r\n+ <import>macros.xml</import>\r\n+ </macros>\r\n+ <xrefs> \r\n+ <xref type="bio.tools">necat</xref>\r\n+ </xrefs>\r\n+ <requirements>\r\n+ <requirement type="package" version="@TOOL_VERSION@">necat</requirement>\r\n+ </requirements>\r\n+ <command detect_errors="exit_code"><![CDATA[\r\n+ ## helper function\r\n+ #def make_filename($i, $input_param)\r\n+ #set ext = $input_param.extension\r\n+ #if $ext == "fastqsanger"\r\n+ #set $ext = "fastq"\r\n+ #end if\r\n+ #set filename = "reads_" + str($i) + "." + $ext\r\n+ #return $filename\r\n+ #end def\r\n+\r\n+ ## push each input file and everything in input collections into read_list.txt\r\n+ #set i = 1\r\n+ #for input in $input_fastqs\r\n+ #set filename = $make_filename($i, $input)\r\n+ cp \'$input\' $filename \r\n+ && echo $filename >> read_list.txt &&\r\n+ #set i = $i + 1\r\n+ #end for\r\n+\r\n+ ## #for $i, $input in enumerate($input_fastqs):\r\n+ ## #set filename = \'reads_${i}.$input.ext\'\r\n+ ## ln -s \'$input\' $filename &&\r\n+ ## echo $filename >> read_list.txt &&\r\n+ ## #end for\r\n+ \r\n+ ## necat commands\r\n+ necat correct \'${job_configfile}\' \r\n+ #if $assembly.should_assemble == "yes":\r\n+ && necat assemble \'${job_configfile}\'\r\n+ && necat bridge \'${job_configfile}\' \r\n+ #end if\r\n+ ]]></command>\r\n+ <configfiles> \r\n+ <expand macro="job_conf" />\r\n+ </configfiles>\r\n+ <inputs>\r\n+ <param name="input_fastqs" type="data" format="fastq,fastq.gz,fasta,fasta.gz" multiple="true" label="Input reads" help="Input read files (FASTQ or FASTA). To select more than one file or collection from your history, use the \'ctrl\' key" />\r\n+\r\n+ <param name="genome_size" type="integer" value="" min="1" max="100000000000" label="Genome size" help="Estimated size of genome (bp)" />\r\n+ <param name="min_read_length" type="integer" value="1000" min="1" max="10000000" label="Min read length" help="Minimum length for input reads" />\r\n+ <param name="correction_coverage" type="integer" value="40" min="1" max="10000" label="Correction coverage" help="Number of reads to correct in terms of genome coverage. For a 4Gb genome, setting correction coverage = 10 will correct the longest 40Gb worth of reads from the input fastq. " />\r\n+ <conditional name="assembly">\r\n+ <param name="should_assemble" type="select" label="Assembly">\r\n+ <option value="no" selected="true">Don\'t perform assembly</option>\r\n+ <option value="yes">Perform assembly on corrected reads</option>\r\n+ </param>\r\n+ <when value="no" />\r\n+ <when value="yes">\r\n+ <param name="assembly_coverage" type="integer" value="30" min="1" max="10000" label="Assembly coverage" help="Number of reads to use in genome assembly in terms of genome coverage" />\r\n+ <param name="polish_contigs" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Polish contigs" help="Polish contigs as final step after briding" />\r\n+ </when>\r\n+ </conditional>\r\n+\r\n+ <section name="adv" title="Advanced options" expanded="false" help="Warning: only change these if you really know what you are doing">\r\n+ <expand macro="overlap_sensitive_options" />\r\n+ <expand macro="consensus_sensitive_options" />\r\n+ <expand macro="overlap_fast_options" />\r\n+ <expand macro="consensus_fast_options" />\r\n+ <expand macro="trimming_overlap_options" />\r\n+ <expand macro="assembly_overlap_opt'..b'scard=DOUBLE discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100-coverage_discard)th percentile. default: 0.01\r\n+--bestn=INT output best n overlaps on 5\' or 3\' end for each read. default: 10\r\n+--genome_size=INT genome size. It determines the maximum length of reads with coverage together default: 0\r\n+--coverage=INT coverage. It determines the maximum length of reads with genome_size together default: 40\r\n+--identity_global_deviation1=DOUBLE If min_identity < 0, min_identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 98\r\n+--identity_global_deviation2=DOUBLE If min_identity < 0, min_identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 6\r\n+--overhang_global_deviation1=DOUBLE If max_overhang < 0, max_overhang is set to max(m, deviation1) + 1.4826*mad*deviation2 default: 30\r\n+--overhang_global_deviation2=DOUBLE If max_overhang < 0, max_overhang is set to max(m, deviation1) + 1.4826*mad*deviation2 default: 6\r\n+--identity_local_deviation1=DOUBLE The local threshold of identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 99\r\n+--identity_local_deviation2=DOUBLE The local threshold of identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 6\r\n+--overhang_local_deviation1=DOUBLE The local threshold of overhang is set to max(m, deviation1) + 1.253*mad*deviation2 default: 10\r\n+--overhang_local_deviation2=DOUBLE The local threshold of overhang is set to max(m, deviation1) + 1.253*mad*deviation2 default: 6\r\n+--identity_local_condition=INT Local filtering conditions. 0 = overlap idenitity < threshold, 1 = overlap idenitity < threshold and query identity >= target identity default: 0\r\n+--local_low_coverage=INT If the coverage of reads is less than local_low_coverage, min_identity and max_overhang are used to filter out low-quality overlaps. Otherwise, the local threshold is used. default: 25\r\n+\r\n+|\r\n+|\r\n+\r\n+*fsa_assemble*\r\n+\r\n+| Constructs contigs from filtered overlaps\r\n+| *Contig Assembly Options*\r\n+| \r\n+\r\n+--min_length=INT minimum length of reads default: 0\r\n+--min_identity=DOUBLE minimum identity of overlaps default: 0\r\n+--min_aligned_length=INT minimum aligned length of overlaps default: 0\r\n+--min_contig_length=INT minimum length of contigs default: 500\r\n+--select_branch=BOOL select the most probable branch default: "no"\r\n+--max_spur_length=INT branches less the threshod are treated as spurs default: 50000\r\n+\r\n+|\r\n+|\r\n+\r\n+*fsa_ctg_bridge*\r\n+\r\n+| Bridges contigs using input long raw-reads\r\n+| *Contig Bridging Options*\r\n+| \r\n+\r\n+--read_min_length=INT minimum rawread length default: 5000\r\n+--ctg_min_length=INT minimum contig length default: 500\r\n+--ctg2ctg_min_identity=DOUBLE minimum identity of overlaps between contigs default: 95\r\n+--ctg2ctg_max_overhang=INT maximum overhang of overlaps between contigs default: 100\r\n+--ctg2ctg_min_aligned_length=INT minimum aligned length of overlaps between contigs default: 2000\r\n+--read2ctg_min_identity=DOUBLE minimum identity of overlaps between rawreads and contigs default: 80\r\n+--read2ctg_max_overhang=INT maximum overhang of overlaps between rawreads and contigs default: 500\r\n+--read2ctg_min_aligned_length=INT minimum aligned length of overlaps between rawreads and contigs default: 5000\r\n+--read2ctg_min_coverage=INT minimum coverage of links between rawreads and contigs default: 3\r\n+--min_contig_length=INT minimum length of bridged contig default: 500\r\n+--select_branch=BOOL select the most probable branch default: "no"\r\n+--window_size=INT threshold is used to group rawreads that bridge contigs default: 1000\r\n+\r\n+|\r\n+\r\n+\r\n+ ]]></help>\r\n+ <expand macro="citations" />\r\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 6ee7eb5821f0 test-data/test1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fa Fri Nov 25 14:24:27 2022 +0000 |
| b |
| b'@@ -0,0 +1,164 @@\n+>SRR7477814.1.32925 1aa2d72-91ef-48d9-950c-cb47fa132b5d_Basecall_1D length=542\n+TTGGTACTTCGTTCAGTTACGTATTGCGGGTCTTGTGTCCCCACTTGGGGTTTCGCATTTATCGTCGCGAAACGCTTTTCGCGTTTTTCGTGCGCCCACTTCATTGGCACCAGTCGGTATTGGTAGTCGTGAATATGACATTTGTGCAGGGCTATCGATAAAACTCGAGTGAACTCAAAATTCCGGTGCAAACAGACGGGCGAAACACTGAAGATCAACATTCTGATCACGAGCATTCCGGAAGATCGGCAGAAGAATGGCTGGGATCATTGGATTAATTTACTCAAATAAAGTATATACAGATCGATTGCGATCACTGTGGATAACTTTATCGGGAAGCTTGGATCAACCGGTAGTTATCAAAGAACAACCGTTGTTCAGTTTTGAGTTGTGTATAACCCCTCATTCTGATCCAACGCGGTCGGGGATCACCGATCATTCTGATTGATCCTTTCCGGGTTGTTGATCTTAAAACCCGGATCCTTGGTATCCACAGGGCAGTACGATCTAATAAGAGATAACAATAGAACAGATCTCTACCA\n+>SRR7477814.1.22516 6931c7d-1ac3-4ddd-b75c-778274821323_Basecall_1D length=5075\n+TTGGTATTACTTCGTTCAGTTACGTATTGCTGGTCTTGTGTCCCAGTTACCGGGTTTTCGCATTTATCGTGAAACGCTTTTCGCGTTTTCGTGCGCCGCTTCAGTGGATTCTGCTCAACTTTGTCGGCGAAAGACACAGGATCACGGGTATTAAAGAAGATCTATTTATTTAGAATCTGTTCTAAACGTTATCTCTTATTAGGATCGCACTTTTAACCCTGTGGATGCTGGGGATCGGCTTTTAAGGATCAACAGCACGGAAAGGATCATTAACTGTGAATGATCGATCTTGGGCCGTATAAGCTGGATCAGAATGAGGGGTTATACGCAACTCAAAAAGCGCTGAACAACAGTTGTTCTTTGGATAACTACCGGTTGATCAAGCTTCTGACAGAGTTATCCACAGTAGATCGCGCGATCTGTATACTTGGTAAATTAATCCACGATCCCAGCCATTCTTCTGCCGGATCTTCCCGGAATGTCGTGATCAGAATGTTGATCTTCAGTGTTTTTCGCCCGTCTGTTTTGCACCGGAATTTTTGAACCGGCCTCGAGTTTATCAGTAGCCCCACAAAATGTGTCATATTCGACTACCAATACCGGTGCGCCAAACGGACCGCCAGAAAGTCGGGCTTCTGTTCCTGCAATAGCCATAGAAAGGAAGGTTGTCGGAATATCTCCGGCACCGTGGGTGGAATGATAACCAGCCCAGATCCCGAGGCAGATAAATCTTCAACAGCGGACCGTGCAGCGTTTCTGGTGGTGGTTCTCTTCAGCTTTCAGCGGGTGTTCTGCTACATGTTGGCACCGCCGAGGTGCTACCGCTGATAAAGTTATATCACCATAAACCGCCACTAACCTTTATTAAGAGTGGCGTATTGTACCTTTAATGAACGTTAGGATACTGTGGAAAATTATGGGATTAAAAAGCCGATCAGAACTGATGAAACGCATGATCAGGTTCTGCAGGACGATCAGTAATCTCGGTGGACTGGTTCATCAATTGTTTTGGATCTTGTTGATAAGTACATGCTGGAGAGCATCGATCGAACAGCACATCACTTTTATAAAGATGCTGTAGTGGCCGGTGGTGTAGTACGCCTCGGTCACTTCATCGAACTTTCCAGCTTTGCCAGCGCGGAAAGGGTAGTCTTTGGCGCTCTTTAATATAATGCCGATAAAGCAGCCTACGTCATAACCGGAAAGCTGCTTCGGGCTGATTTATCAATACGCGCCCGAAGTAATGATCCCCGCCGCAACTTCATTTTTCTCTACTCGAACGTGAATCGTCCCCGGACTGACGCCAAATTGTTTCGCCAGTTCGGCGTAAGCAGTGCGCACGTGCCATTAATGCTTCAGCGGATGCCACGGTCCGTTGTCGATAAAGATAATTTTTCCGCAAGTTTTCTTATGCGGATTGATGATTCATTCTATTTTAGCCTTCTTTTTAATGAATCAAAAGTGAGTTAGGCTTTTATTGAATGATTATTGCATGTGTGTCGGTTTTGTTGTAATCATAACTTATCGGACGCAAGGTATAAAAATGAAAACCGCTTACATTGCCAAACAACGCCAAATTAAGCTTCGGTAATCTCCGCACCGTCAACTGGAAGAACGTCTGGGGCTGATCGAAGTCGGTACCGATTCTTAGCCGTGTGAGGATGGCACGCAGGATAACTGGTCGGGCTGTGAAAAGCGGTACAGGTAAAAGTGAAAAGCTCGCCGCAGTGCCCAGTTCGAAGTGGTTCATTCACTGGCGAAGTGAAACGTCAGACCTTAGAACAACGACTTCAGCGCGGGCGAAGGGCTGTACACGCACGCGAAAAACCCACTTCGCCGATGAAGACCGTCTTTCTCCGTTGCACTCGGTCTATGTTGACCAGTGGGACTGGGAACGCGTAATGGGCGACGGTGAGCGGTAATTCTCGACGCTCTGAAAAGCACAGTAAGAGGCGATTTGGGCGGCGAATTAAAAAGCAACCGAAGCTGCGGTTATGGCGAAGAGTTTGGCTTTGGCACCATTCCTGCCGGATCAGATCCACTTCGTACACTGGCGAGTTACTGTCGTTATCGGATCTTGATGCCAAAGGGCGTGAGCGGGCGATAGCGAAGATCTTGGTGCGGTATTCCTTGTCGGGATTGGCGGCAAGCTGAACGTGGTCATCGCCACGACATTACGCGCACCGGATTATGATGACTGGAGCACCCCGTCAGAGCTGGGCCATTGCGGTCTGAACGGCGATATTCTAGTGTGGAACCTGTACTGGAAGGTGCGTTGGCTTTCTTCCGTAGGGGATCCCGCGTGGATGCCGACACGTTGAAGCATCAGTTGGCGCTGACCGGTAGTGAAAAGATCGTCTGCAGCTGGAATGGCATCAGGCGTTGCTGCGCGGTGAAATGCCGCAGACCATCGGCGGCGGTATCGACCAGTCTCGTTTGACCATGCTGCTGCTGCAACTGCCGCATATCGGCCAGGTCAATTAACTGGGTATGGCCAGCTGCTGTTCGCGAGAGCGTCCTTCTCTGCTGTAATAATTTATCGCCGCCAGCGTCTGAGCGAGCGGCTTCGCATCCGGTATCAAAGCGCCAGATATGATCGAAAATGCGCATGATGCCGGGTTTATAGGTATTACCGACATCGCCACGGCATGAAAGCGATACTGATGTACCCGCTGCAGCTCTTTCACTTTACTCGTCACGTCGTCAAAGGCAACCGCTGGGCGATAAAATCAGAAATCACCACCGCATCGGCATCAAACCATTCCCTGCTTTGCAAGCGTTCCATAATGGCGCGAAAACAACTGGCCAAGATCGGTGCCGCCGCAAGGCGCTGCTGGCAAAAACGGATTGCTTGTTCGATGCCTTGTGGGCGCAAAGCTCATAACGGACGATCTCGGTGGAAAATAGCGCCAATATAACAGCGCCGGTTTTCAGCGAGAGCAATAACATCAAAGCCGGGCAGGTACTTTCGCGCACTGTTCATTAAAGCCGCCCATTGAGCCGGAAGTATCACGCAGACAATAAACGGTCCGCGCGGCTGTTCGTCGTAATCTTTATGCCACCGGGCGTTCGAACTTTTCACCACGACTCACCGTGCAGGCGATGGTGAGCAACTGTTTTCCACCAGCCGACGGTAAAGCTCGCATACTCCAGTTCCGTTATCCTAGTGTCGCCAGTTCTGGCGGCAGAAGACATGAAATATCATCGCTTTGTTGCGGACCATCAGCATCCAGGAACCGTCGCCGGTTCGCGCACCATGGTGCGGAAAGGTTTCC'..b'GGGCAACCCACGCGTTTGGCGATGCGGTCTTCCCGAGGTAAGGGTGCTTATATTCCAGATTACCGTGTGCAGGTGACCAATCTTTGCGCATGGTTTCTGCATAAGGACAGCTGGCCGCCATACGATCCTGCGATTACGCATTTTGGAAGCGGCGACCATCTCCATCGCTTTAGTGATCTTTTGCGTGTTCTGGACACGATCTTACTACGTATCTCTTTTGCGCCGACCAGGCTTCTCCTCAATGCCTTGCGGCCTGCCCTACGAGCAAGCCGCCAGACGTTACCCGGAAGTTGGGTTGCTTTGAAGGAATCGAGGATGCCTTTCAGCTTGCCTTCGATTTCGTCGTTGTAACCACCGGTCTGGACGATCTCTTGCATCAACGGGCGCAGTCACGGTCGACGTAAGCCAGCAGAGCGGCTTCGAAGCTGCCACTTCGACAGTTCAACATCCGCCGGTAACCGTTCTGCTGCGAACAGAGCCAGAGACTGCGCTGCGCAACGGACATCGGCGCATACTGTTTCTGTTTCAACCCAGTTCGGTCACTTTTTGACCGATGGTCAAAGCTGCTTACGTGTTGCATCGTCAAAGGTCCGGATGCAAACTGAGAGAACGCTGCCAGTTCACGTACTGTGCCAGAAACCGGTACGGATACCACCGGACAGTTTTCATGATCGCGGTCTGTGCTGCCGCAACACGGGATACGGAAATGCCCGGGTTAACCCGCAGGACGAATACCGGCGTTGAACAGGTTGGTTTCGAAATCTGACCATCGGTAATGGAGATTACGTTTGGTCCGGAACAGGCAGAAGCGTCACCCAACGAGTTTTCGATAATCGGCGGCGCGGTCAGTGAACCGGTTTCCCTTTCACTTCACCTTTGGTGAAAGCTTCAACGTATTCGGCATTAACACGCGCAACACGCTCCAGCGAACCAGCGAGTGGGCAGAATACGTCGCCAAAGAATGCTTCGTCACGGCGGACGACGGAGCAACAGCGAGATCTGACGGTAGCAACAGCCTGTTGGGCAGATCATCGTAAATGATCGGCGCATCTTCACCGCGGTCACGGAAGTATTCGCCCATTGCGCAACCGGCATACGGTGCCGGGTATTGCAGTGCAGCGGATTCAGACGCGGTTGCTACCACAACGATGGTGTTAGCCAGTGCCATTCTCTTCCAGTTTACGTACCACGTTAGAAATGGTGGACGCTTTCTGGCCGATAGCGACATAGATACATTTGATACCGGAATCGCTGGTTGATGATGGCATCGATAGCCGAATTCTGCAGTTTCTCAGTCTGACGGTCACCGTCGATCAATTCGCTGACCACGACCGGTGGGATCATGGAGTCAACGGCTTTATAACCGGTCTGTACCGGCTGATCTGGGACTGACGTTCGATAACGCCCGGAGCGATTGCTTCTGGCCAGAAGCCGTCGTGATCAGCGGACCTTTACCGTCGATTGGTGCAGGGTGTTTCCACACGGCCCAGCAGGCTGACCTTGAACTTCCGGGGATACGGCCAGTACGCCTTTCATGCCTTCGGCAAAGGTCAGCATCTGGACCCACAACAACCGCACCAACAGAGTCGCTCGAGTTCAATGCGATAGCGTAACAGTTGCCGGCAGGAGATCATTCACCCTCCTGCATACAATCAGCGAGACCGTGAATGCGGATAACACCGTCACTTACAGAAACAATGAGTACCTTCGTTGTGAGAGCTTCACTCACAGCATTGAATGAGCAATGCGCTGCTTGATCAGTTCGCTGATTTTCGGTGGAATTCAGTTGCATGCTCGGTCCCTTAAGACTGCAAGACGTCACTGCAAGGCGCTCAAGACAGCCGCGTACGCTGCCATCAATGACCATATCACCCGCTCGGATGATAACGCCTGCCATTACAGACTTATCGATTTTACGAATTCAAAGCTGCTTTTGCGTGACCAGACGTTTTCCATCGCAGCAGAATTTTCGCGAGCTGTTGTTCCACTCGGTGCGGCAGCGGAAATGACGTCTACCTCAGCGGTAGCCTCTCACGGCACGAAGGTGAATAAACAGCAAAACCATCCGGGGCGCGTTAGGCGACCATTTTCGTATTGCGAATAGGTTCAATGCGTTTCGTCAGTTGCTCACCACAAGCTGCGATAAACGGCTCGGCAGCGTTTCCACCCGGCGCAAGCGCGCCAGAGAAATCTGCCATTTGTTCGTTTGGTTACCTCGGCGGCAAACGCCAGCATGTCTGCCAGCGTTCTACGCTTTGGTGTTCGACGGCAAAGTCAAAAGCTGCTTTGGCGTAGGGGCGAGCTACCGTAATAAATTCGAGACATCAGCCCCTCCCCTCCTTACAGTTCAGCGACAAGTTTGTACGATGTCGCTGTTGGCAACCTAATCCACGGAACGTTCGAGTGATCTTCTCGGCAACAACAGCGGGGATAGCAACTTTATACACCCAATCTTCCGCGAGCACGTTTACGCTCGGCTAATTTCCGCCTGCGCACGGGCCACGATTTTTAGTACGTTCCTGTTCTGCCTCAGCTTTCGCTTCGTCAGAATCTGCGAGCGGCGTTTGTTCGCCTGCTCGATGATTACACAGATACTTTCGCTTTTTCAGCTGGTCGAGTCGCGCTGGCGCTGCAGGTCAAGGTCATATGTGCTCGTTCTGCGGAAGCAAGGCCGTCAACAATTTCTTTTATCGACGTTTTCGATGGCTGCCAATGGCGGCCATGCGTACTTCATGCCAGAACAGAACAGACAGGGACAAACGCGATGGCGGCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTCGTAAAAGCAACACTGCGACGCGAACATCGCAATACAGACGGGCCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGTCAGATCAGGTTGACGCCTTTCTTCGGTACCCCGGGATGCCATTACCGATCGCAGCACCGGTGCCGCCAGACCCATCATCACAGCGGCAGCCATGTACGAATCCATATTCAGGTTTTCCGCGTGATCTCCAGTTTGTTTCAGTTAAAACGTAGTAGTGTTGGTAAAATTAATGTTCTTCCAGACGCCATCGACAGATAGACGATCGTCAGAACCATGAAGATGAAGGCTTGCAGCGTAATGATCAGGATGTGGAAAATGGCCCACGGCATTCAAGTTTCTTGACCACCACGGCAACAGACCAGCAATCAGAATGAAAATCAGCTCACCGGCATACATGTTGCCGAACAGTCACCAAACCGAGTGAAACTGGTTTGGACAGCGAAACTACCCTTCAAGGATTAAGTTGGCAAGGAATGAACGCGAGTGATTGAACGGCTGCAGCGTCAACTCTTTCATTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCATAGACGGCGTTACGTTTCGTCCGCAGACCGGAGACACACGCAGTGCAGGCGAACCCAGTACATGTTCAGCAATGTGTACGGCAGCAGGTCGATAGGCAGTAAATCCATCAGTTCATCGGAATACCCAGACGAGATCGTCAGGGCCAGCGGAGCAATCAGCTTGCTTTTGCCATGGTACATGTCTTTCACGCTACCATTAACAAAACCGTCCTGTAGCAACGCTCAATCGGTCTGGAAACTTACACGGCACGCTGGTCGCCTTTTTGGCTACCTTACGGAATAAAACCGGGAACAACAGACCCAGCACCGCCGAAGAACATAGATCAATATTGATTGTCCAGAAGGTGGCTGGGGGTTTGTGGATCCACCAGCGAGAATATTACGCAGGTCAGCTGAAGGTTATTCGGGTGGTGTCTATGTAATCCTGCGGCGTCATATTTTCTGAAGCCATGATGCCTTTTACCTTTGTTGTTAATTACAGCCGGTGCCAGTATCTGAACCACCAGCACCAAAACCACGTAACGATCGCG\n' |
| b |
| diff -r 000000000000 -r 6ee7eb5821f0 test-data/test1_head.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_head.fastq Fri Nov 25 14:24:27 2022 +0000 |
| b |
| b"@@ -0,0 +1,200 @@\n+@SRR7477814.1.32925 1aa2d72-91ef-48d9-950c-cb47fa132b5d_Basecall_1D length=542\n+TTGGTACTTCGTTCAGTTACGTATTGCGGGTCTTGTGTCCCCACTTGGGGTTTCGCATTTATCGTCGCGAAACGCTTTTCGCGTTTTTCGTGCGCCCACTTCATTGGCACCAGTCGGTATTGGTAGTCGTGAATATGACATTTGTGCAGGGCTATCGATAAAACTCGAGTGAACTCAAAATTCCGGTGCAAACAGACGGGCGAAACACTGAAGATCAACATTCTGATCACGAGCATTCCGGAAGATCGGCAGAAGAATGGCTGGGATCATTGGATTAATTTACTCAAATAAAGTATATACAGATCGATTGCGATCACTGTGGATAACTTTATCGGGAAGCTTGGATCAACCGGTAGTTATCAAAGAACAACCGTTGTTCAGTTTTGAGTTGTGTATAACCCCTCATTCTGATCCAACGCGGTCGGGGATCACCGATCATTCTGATTGATCCTTTCCGGGTTGTTGATCTTAAAACCCGGATCCTTGGTATCCACAGGGCAGTACGATCTAATAAGAGATAACAATAGAACAGATCTCTACCA\n++SRR7477814.1.32925 1aa2d72-91ef-48d9-950c-cb47fa132b5d_Basecall_1D 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length=5075\n+TTGGTATTACTTCGTTCAGTTACGTATTGCTGGTCTTGTGTCCCAGTTACCGGGTTTTCGCATTTATCGTGAAACGCTTTTCGCGTTTTCGTGCGCCGCTTCAGTGGATTCTGCTCAACTTTGTCGGCGAAAGACACAGGATCACGGGTATTAAAGAAGATCTATTTATTTAGAATCTGTTCTAAACGTTATCTCTTATTAGGATCGCACTTTTAACCCTGTGGATGCTGGGGATCGGCTTTTAAGGATCAACAGCACGGAAAGGATCATTAACTGTGAATGATCGATCTTGGGCCGTATAAGCTGGATCAGAATGAGGGGTTATACGCAACTCAAAAAGCGCTGAACAACAGTTGTTCTTTGGATAACTACCGGTTGATCAAGCTTCTGACAGAGTTATCCACAGTAGATCGCGCGATCTGTATACTTGGTAAATTAATCCACGATCCCAGCCATTCTTCTGCCGGATCTTCCCGGAATGTCGTGATCAGAATGTTGATCTTCAGTGTTTTTCGCCCGTCTGTTTTGCACCGGAATTTTTGAACCGGCCTCGAGTTTATCAGTAGCCCCACAAAATGTGTCATATTCGACTACCAATACCGGTGCGCCAAACGGACCGCCAGAAAGTCGGGCTTCTGTTCCTGCAATAGCCATAGAAAGGAAGGTTGTCGGAATATCTCCGGCACCGTGGGTGGAATGATAACCAGCCCAGATCCCGAGGCAGATAAATCTTCAACAGCGGACCGTGCAGCGTTTCTGGTGGTGGTTCTCTTCAGCTTTCAGCGGGTGTTCTGCTACATGTTGGCACCGCCGAGGTGCTACCGCTGATAAAGTTATATCACCATAAACCGCCACTAACCTTTATTAAGAGTGGCGTATTGTACCTTTAATGAACGTTAGGATACTGTGGAAAATTATGGGATTAAAAAGCCGATCAGAACTGATGAAACGCATGATCAGGTTCTGCAGGACGATCAGTAATCTCGGTGGACTGGTTCATCAATTGTTTTGGATCTTGTTGATAAGTACATGCTGGAGAGCATCGATCGAACAGCACATCACTTTTATAAAGATGCTGTAGTGGCCGGTGGTGTAGTACGCCTCGGTCACTTCATCGAACTTTCCAGCTTTGCCAGCGCGGAAAGGGTAGTCTTTGGCGCTCTTTAATATAATGCCGATAAAGCAGCCTACGTCATAACCGGAAAGCTGCTTCGGGCTGATTTATCAATACGCGCCCGAAGTAATGATCCCCGCCGCAACTTCATTTTTCTCTACTCGAACGTGAATCGTCCCCGGACTGACGCCAAATTGTTTCGCCAGTTCGGCGTAAGCAGTGCGCACGTGCCATTAATGCTTCAGCGGATGCCACGGTCCGTTGTCGATAAAGATAATTTTTCCGCAAGTTTTCTTATGCGGATTGATGATTCATTCTATTTTAGCCTTCTTTTTAATGAATCAAAAGTGAGTTAGGCTTTTATTGAATGATTATTGCATGTGTGTCGGTTTTGTTGTAATCATAACTTATCGGACGCAAGGTATAAAAATGAAAACCGCTTACATTGCCAAACAACGCCAAATTAAGCTTCGGTAATCTCCGCACCGTCAACTGGAAGAACGTCTGGGGCTGATCGAAGTCGGTACCGATTCTTAGCCGTGTGAGGATGGCACGCAGGATAACTGGTCGGGCTGTGAAAAGCGGTACAGGTAAAAGTGAAAAGCTCGCCGCAGTGCCCAGTTCGAAGTGGTTCATTCACTGGCGAAGTGAAACGTCAGACCTTAGAACAACGACTTCAGCGCGGGCGAAGGGCTGTACACGCACGCGAAAAACCCACTTCGCCGATGAAGACCGTCTTTCTCCGTTGCACTCGGTCTATGTTGACCAGTGGGACTGGGAACGCGTAATGGGCGACGGTGAGCGGTAATTCTCGACGCTCTGAAAAGCACAGTAAGAGGCGATTTGGGCGGCGAATTAAAAAGCAACCGAAGCTGCGGTTATGGCGAAGAGTTTGGCTTTGGCACCATTCCTGCCGGATCAGATCCACTTCGTACACTGGCGAGTTACTGTCGTTATCGGATCTTGATGCCAAAGGGCGTGAGCGGGCGATAGCGAAGATCTTGGTGCGGTATTCCTTGTCGGGATTGGCGGCAAGCTGAACGTGGTCATCGCCACGACATTACGCGCACCGGATTATGATGACTGGAGCACCCCGTCAGAGCTGGGCCATTGCGGTCTGAACGGCGATATTCTAGTGTGGAACCTGTACTGGAAGGTGCGTTGGCTTTCTTCCGTAGGGGATCCCGCGTGGATGCCGACACGTTGAAGCATCAGTTGGCGCTGACCGGTAGTGAAAAGATCGTCTGCAGCTGGAATGGCATCAGGCGTTGCTGCGCGGTGAAATGCCGCAGACCATCGGCGGCGGTATCGACCAGTCTCGTTTGACCATGCTGCTGCTGCAACTGCCGCATATCGGCCAGGTCAATTAACTGGGTATGGCCAGCTGCTGTTCGCGAGAGCGTCCTTCTCTGCTGTAATAATTTATCGCCGCCAGCGTCTGAGCGAGCGGCTTCGCATCCGGTATCAAAGCGCCAGATATGATCGAAAATGCGCATGATGCCGGGTTTATAGGTATTACCGACATCGCCACGGCATG"..b'0%6>4/8-*5((-40:8:6=;855.3,+,/1=F>A@2+,44?7,3=@,*,317B431154E618:8,7<,),($*(%..2311564+-+00.,((+,$,%*//?7DE99.,,,//+.0,/68,.74:;6;786:*%\'%*.)00=;5*-.27269-/4;806.-1622(56*100;78835.2,,-;:3:?@0))(.20,**3*34+-0<5,19+64;3:0;26;IB8B123;FA21,.29<@38)%+((+.4(\',*+*+\'0(,(+\'99+*(*0(.45?/=/A1B//2214A<35@@;<?722B5?4635488;/*+*1=BB>7/8//)0,*%)7\'30.?54*($&)%\'+./,.1=>/\'230<--+441:13,)66&1(*1(/2%\'\'/.8:7./*042=?.*.1667:?D?41,6-,,0/10.2))04.9B:;>35;FB?;..0,*,\'/78@51,,&*+AB<>94%/6)$.(((&((+-;>,%(%,+0;?>H@A9,0/41:FA+124//-.22,@8<0(0+0:B036<55::956@9118>1;47-2*,)*),3A3347//57315425:BA1772.4=,&+&+\'+-*+&).34;471)(\'*,$)2776$+\')\')(&&&+--(-(+1-+/3;>1-%.//7+2A00*>GG7.3*5D.38@F;9;74/3440.+/=0*-).%*,%-\'9?@@5577/+\'9?,*\'(\'&));-++).(,++\'&*(/)\'(*&*6>D-&()-/00-<7=83@E1885221/()\'*(((*&&-4.022;?EB))(2.+)%.+.,)&%$)DC>FA<//..1-7E33?9@=4245-///+(\'&%$()-.-4==@?@A4;50)-,)*276<),+20=306;7523?*.\'\'%%(*.*--3,,%@,D;DG64/3:6AACA3C0%*03249@5374126@::87;40(5123/(,++.26;9;6;HHH=078=@18<8<D;61.<-/8.;;>,)($&65AAH@668,46:>61,-)+5>D*25.*+,11052<1D-6&&\'-126<B*\'\'4,1-<8:8:+37858A))6-@<:+/7-52,1,5-3ADAJ<@*-9:889885)92:04-//01787;/,--5;-1@,(\'\'*)9C</%)*.0.1,00/47:>=?8456:88>-/-3*&(*\'\'(6:0*--08FA9=I831,.268C22#\'+658E<111177<C@32$###$).2;=9@?==>B@;G:9355440/%2.04A66./38469285D=H297056602).40*2).047+)&*++/(1+,),2--\'(\'\'(\'))*-<(8+3.)&*,*+/25415..(&/*).2;6,0.50:45F:35/\')2+/241>@9<@C69+4&&*/-5.,0*)&<8,,/264==<-:-\'*96-28)33->02==257<9<+,5(*&)()*/16511=7-/\')+\'2+2..55,-&\'&,%07<>::/),(&&+,1*+.2DC<A6@<1%,12548/0*3,:-+0/*.77:2666203))*-0?/92,;6.0$&(+-()+;=E96878B=.*./,<90/622/+.&..;2309<.).05A?8-)*-0@(*47051(+++**\'112/++.3<8=;H(7/91FGE.BH>;==7*\'+-,/00.=</-3/((77E<*6,02,*)*)+),)(),11GF7123*(&\'*\'*(*\'*&\'\'57;56;8>31323?<@7..&)&\'+3/7.,)-*&(1;</:(\'.@=D-*..--?G6.>CCA981682>=40/,-146\'1<+8,/1.+-*.15@3-0++,221A2BID8?@+081,*--(\'*()(\'42),&(\'&%#\'%%\'%,\'+)\'*\'((,.)-\',-3=&$##&*)935333=)+(%#,\')(\'+(%(&((*$)\'($*\'\'&)***3,+1,1.79;9=1.\'&&\'$($))1.1316-02A60)-3-+)&%\')\'&*+.(*((($$$(&3:8+0(*./-5/-.1+*(*+%.\'/2400+&%,,)/.-&,-2-&,0\'-(77.%\'&&(%)$(*13)+&7//.()+(++\',\'*#(+&,40*#&*(+(/)7<;600)\'/62?/&$$*.+,)\'*\'&()*$+*61*.)61)\'\'.-)&&$($-,*3,69*%%0.+&*&$&&$)++)%\'(22&4001(5>781(-2/B1?31*)+))\'\'\'(&*-.\'**%.$70>965:,*\'\'&%)+(()*-8@53)0,%%$$)\'))*,2418800*-\'02000/=0/*,+5-*\'$,+/@@@,/\',)(02)+(+*(,+((\')$$++)1//45\'*,,+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| b |
| diff -r 000000000000 -r 6ee7eb5821f0 test-data/test1_tail.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_tail.fasta Fri Nov 25 14:24:27 2022 +0000 |
| b |
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