| Previous changeset 2:76e69de726b2 (2019-11-28) Next changeset 4:91a1ed0b486f (2024-03-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd" |
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modified:
macros.xml ngsfilter.xml test-data/output_ngsfilter_error_3.fastq test-data/output_ngsfilter_unidentified.fastq test-data/output_obisort.fastq |
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added:
test-data/illuminapairedend.output.fastq.gz test-data/output_ngsfilter_error_3.fastq.gz test-data/output_obiannotate.fasta.gz test-data/output_obiclean_advanced.fasta.gz test-data/output_obigrep_predicat.fasta.gz test-data/output_obiuniq.fasta.gz test-data/output_obiuniq_family.fasta.gz test-data/wolf_small.F.fastq.gz test-data/wolf_small.R.fastq.gz |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd macros.xml --- a/macros.xml Thu Nov 28 15:52:43 2019 -0500 +++ b/macros.xml Mon May 10 19:34:54 2021 +0000 |
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| @@ -6,7 +6,8 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">1.2.11</token> + <token name="@TOOL_VERSION@">1.2.13</token> + <token name="@PROFILE@">21.01</token> <xml name="stdio"> <stdio> @@ -14,6 +15,80 @@ </stdio> </xml> + <token name="@INPUT_FORMATS@">fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz</token> + <token name="@GUNZIP_INPUT@"><![CDATA[ + #if $input.ext.endswith(".gz") + gunzip -c '$input' > input && + #else + ln -s '$input' input && + #end if + ]]></token> + <token name="@GZIP_OUTPUT@"><![CDATA[ + #if $input.ext.endswith(".gz") + | gzip -c + #end if + ]]></token> + + <!-- generate galaxy.json to determine output format + - by default same as input + - if out_format can be specified + - fasta/fastq depending on $out_format (if != "") + - or fasta if the tool does not support choosing the output format, e.g. obiuniq which always outputs fasta + - gz if $input is zipped + + A list of outputs to include in the json can be given by + setting a variable $outputs = [...] listing pairs of output names and the actual output + (defaults to [("output", $output)]) + --> + <token name="@GENERATE_GALAXY_JSON@"><![CDATA[ + #import json + + #try: + #silent $outputs[0] + #except + #set outputs = [("output", $output)] + #end try + + #if $input.ext.startswith("fastq") + #set ext = "fastqsanger" + #else if $input.ext.startswith("fasta") + #set ext = "fasta" + #end if + + #try + #if $out_format == "fasta" + #set ext = "fasta" + #else if $out_format == "fastq" + #set ext = "fastqsanger" + #end if + #except + #set ext = "fasta" + #end try + + #if $input.ext.endswith(".gz") + #set ext = ext + ".gz" + #end if + + #set gxy_json = {} + #for oname, o in $outputs + #silent gxy_json[oname] = {"ext": ext} + #end for + && echo '${json.dumps(gxy_json)}' >> galaxy.json + ]]></token> + + <token name="@OUT_FORMAT@"><![CDATA[ + #if $out_format + --${out_format}-output + #end if + ]]></token> + + <xml name="out_format_macro"> + <param name="out_format" type="select" optional="true" label="Output data type" help="For FASTA/Q the the default output type is the same as the input type"> + <option value="fasta">fasta</option> + <option value="fastq">fastq</option> + </param> + </xml> + <token name="@OBITOOLS_LINK@"> <![CDATA[ -------- @@ -105,15 +180,43 @@ <option value="taxid">taxid</option> </xml> - <xml name="inputtype"> - <option value="--genbank">genbank</option> - <option value="--embl">embl</option> - <option value="--sanger">sanger</option> - <option value="--solexa">solexa</option> - <option value="--ecopcr">ecopcr</option> - <option value="--ecopcrdb">ecopcrdb</option> - <option value="--fasta" selected="true">fasta</option> + <xml name="input_format_options_macro"> + <section name="input_format_options" title="Input format options" expanded="false"> + <param name="options_inputtype" type="select" optional="true" label="Specify the input datatype" help="default: determine automatically (should only be necessay for non FASTA/FASTQ datasets)"> + <option value="--genbank">genbank</option> + <option value="--embl">embl</option> + <option value="--sanger">sanger</option> + <option value="--solexa">solexa</option> + <option value="--ecopcr">ecopcr</option> + <option value="--ecopcrdb">ecopcrdb</option> + <option value="--fasta">fasta (including obitools fasta extentions)</option> + <option value="--raw-fasta">raw fasta (more tolerant format variant)</option> + </param> + <param name="options_seqtype" type="select" optional="true" label="Specify the sequence datatype" > + <option value="--nuc">nucleic</option> + <option value="--prot">protein</option> + </param> + </section> </xml> + + <token name="@INPUT_FORMAT@"><![CDATA[ + #if $input_format_options.options_inputtype + $input_format_options.options_inputtype + #else + #if $input.ext.startswith("fasta") + --fasta + #else if $input.ext.startswith("fastqsolexa") + ## input file is in fastq nucleic format produced by solexa sequencer + --solexa + #else + ## input file is in sanger fastq nucleic format (standard fastq) + --sanger + #end if + #end if + #if $input_format_options.options_seqtype + $input_format_options.options_seqtype + #end if + ]]></token> <xml name="sanitizer"> <sanitizer invalid_char="test"> |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd ngsfilter.xml --- a/ngsfilter.xml Thu Nov 28 15:52:43 2019 -0500 +++ b/ngsfilter.xml Mon May 10 19:34:54 2021 +0000 |
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| b'@@ -1,111 +1,125 @@\n-<tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@">\r\n- <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</description>\r\n- <macros>\r\n- <import>macros.xml</import>\r\n- </macros>\r\n- <expand macro="requirements"/>\r\n- <expand macro="stdio"/>\r\n- <command>\r\n-\r\n- <![CDATA[\r\n-\r\n- ngsfilter\r\n- -t \'$inputextrafile\' \'$inputfastq\'\r\n- #if $bool\r\n- -u \'$unident\'\r\n- #end if\r\n- -e \'$mismatch\' > \'$output\'\r\n-\r\n- ]]>\r\n-\r\n- </command>\r\n-\r\n- <inputs>\r\n- <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample" />\r\n- <param name="inputfastq" type="data" format="fastq" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend" />\r\n- <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)" />\r\n- <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?" />\r\n- </inputs>\r\n- <outputs>\r\n- <data format="fastq" name="unident" label="unidentified.fastq with ${tool.name} on ${on_string}">\r\n- <filter>bool is True</filter>\r\n- </data>\r\n- <data format="fastq" name="output" label="${tool.name} on ${on_string}: Trimmed and annotated" />\r\n- </outputs>\r\n- <tests>\r\n- <test>\r\n- <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />\r\n- <param name="inputfastq" value="illuminapairedend.output.fastq" />\r\n- <param name="mismatch" value="2" />\r\n- <param name="bool" value="False" />\r\n- <output name="output" file="output_ngsfilter.fastq" ftype="fastq"/>\r\n- </test>\r\n- <test>\r\n- <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />\r\n- <param name="inputfastq" value="illuminapairedend.output.fastq" />\r\n- <param name="mismatch" value="3" />\r\n- <param name="bool" value="True" />\r\n- <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastq"/>\r\n- <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastq"/>\r\n- </test>\r\n- </tests>\r\n- <help><![CDATA[\r\n-\r\n-.. class:: infomark\r\n-\r\n-**What it does**\r\n-\r\n-A DNA metabarcoding experiment can be considered as a set a PCR products mixed together and sequenced using a next generation sequencer ({i.e.} a solexa or a 454).\r\n-To distinguish between this different PCR products, pairs of small DNA sequences (call tags, see the oligoTag command and its associated paper for more\r\n-informations on the design of such tags) unique for each PCR products are concatenated to the PCR primers.\r\n-As they are amplified during the PCR, these tags should be recognizable, together with their respective primers, at the beginning and the end of the reads.\r\n-The first step in data analysis is thus to demultiplex the large resulting sequence file by identifying these DNA tags and the primers.\r\n-\r\n-Usually the results of sequencing are stored in one or more files formatted according to the fasta or fastq format. ngsfilter take as input such sequence file and an extra file describing the DNA tags and primers sequences used for each sample.\r\n-\r\n-The results consist of sequences trimmed of the primers and tags and annotated with the corresponding sample (and possibly some extra informations).\r\n-Sequences for which the tags and primers have not been well identified, and which are thus unassigned to any sample, are tagged as erroneous sequences\r\n-by ngsfilter. Such erroneous sequences are not reported by the program unless specified by the appropriate option.\r\n-\r\n---------\r\n-\r\n-**Help**\r\n-Extrafile format:\r\n-\r\n-a tab delimited tabular file with 8 columns.\r\n-\r\n-experiment'..b'_string}: Unassigned sequences">\n+ <filter>bool is True</filter>\n+ </data>\n+ <data name="output" format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />\n+ <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger" />\n+ <param name="mismatch" value="2" />\n+ <param name="bool" value="False" />\n+ <output name="output" file="output_ngsfilter.fastq" ftype="fastqsanger"/>\n+ </test>\n+ <test>\n+ <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />\n+ <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" />\n+ <param name="mismatch" value="3" />\n+ <param name="bool" value="True" />\n+ <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastqsanger.gz" decompress="true"/>\n+ <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastqsanger.gz" decompress="true"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+A DNA metabarcoding experiment can be considered as a set a PCR products mixed together and sequenced using a next generation sequencer ({i.e.} a solexa or a 454).\n+To distinguish between this different PCR products, pairs of small DNA sequences (call tags, see the oligoTag command and its associated paper for more\n+informations on the design of such tags) unique for each PCR products are concatenated to the PCR primers.\n+As they are amplified during the PCR, these tags should be recognizable, together with their respective primers, at the beginning and the end of the reads.\n+The first step in data analysis is thus to demultiplex the large resulting sequence file by identifying these DNA tags and the primers.\n+\n+Usually the results of sequencing are stored in one or more files formatted according to the fasta or fastq format. ngsfilter take as input such sequence file and an extra file describing the DNA tags and primers sequences used for each sample.\n+\n+The results consist of sequences trimmed of the primers and tags and annotated with the corresponding sample (and possibly some extra informations).\n+Sequences for which the tags and primers have not been well identified, and which are thus unassigned to any sample, are tagged as erroneous sequences\n+by ngsfilter. Such erroneous sequences are not reported by the program unless specified by the appropriate option.\n+\n+--------\n+\n+**Help**\n+Extrafile format:\n+\n+a tab delimited tabular file with 8 columns.\n+\n+experiment_name\tsample_name\toligo_tag(s)\tforward_primer\treverse_primer\tF\t@\textra_information\n+\n+ex:\n+\n+laos_gh LA01E1a agcgacta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01A;\n+\n+laos_gh LA01E1b tcagtgtc:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01B;\n+\n+laos_gh LA01E2a actctgct:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01C;\n+\n+laos_gh LA01E2b atatagcg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01D;\n+\n+laos_gh LA01P1a ctatgcta:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01E;\n+\n+laos_gh LA01P1b tcgcgctg:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01F;\n+\n+laos_gh LA01P2a agcacagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01G;\n+\n+laos_gh LA01P2b tagctagt:acacacac GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_01H;\n+\n+laos_gh LA02E1a agcgacta:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02A;\n+\n+laos_gh LA02E1b tcagtgtc:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02B;\n+\n+laos_gh LA02E2a actctgct:acagcaca GGGCAATCCTGAGCCAA CCATTGAGTCTCTGCACCTATC F @ position=04_02C;\n+\n+@OBITOOLS_LINK@\n+\n+\n+]]>\n+\n+ </help>\n+ <expand macro="citation" />\n+\n+</tool>\n' |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/illuminapairedend.output.fastq.gz |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_ngsfilter_error_3.fastq |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_ngsfilter_error_3.fastq.gz |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_ngsfilter_unidentified.fastq |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_obiannotate.fasta.gz |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_obiclean_advanced.fasta.gz |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_obigrep_predicat.fasta.gz |
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| diff -r 76e69de726b2 -r 3bf57dadf7cd test-data/output_obisort.fastq --- a/test-data/output_obisort.fastq Thu Nov 28 15:52:43 2019 -0500 +++ b/test-data/output_obisort.fastq Mon May 10 19:34:54 2021 +0000 |
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| b"@@ -1,172 +1,232 @@\n->HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP count=64; merged_sample={'26a_F040644': 64}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=99; obiclean_headcount=1; seq_rank=5; obiclean_samplecount=1; obiclean_status={'26a_F040644': 'h'}; obiclean_head=True; \n-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n-gcctgaaactcaaaggacttggcggtgctttacatccct\n->HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB count=61; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=2; seq_rank=4; obiclean_samplecount=2; obiclean_status={'29a_F260619': 'h', '15a_F730814': 'h'}; obiclean_head=True; \n-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n-agcttaaaactcaaaggacttggcggtgctttataccctt\n->HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB count=46; merged_sample={'13a_F730603': 46}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=1; seq_rank=8; obiclean_samplecount=1; obiclean_status={'13a_F730603': 'h'}; obiclean_head=True; \n-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n-agcttaaaactcaaaggacttggcggtgctttataccctt\n->HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB count=7; merged_sample={'29a_F260619': 7}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=4; obiclean_headcount=0; seq_rank=16; obiclean_samplecount=1; obiclean_status={'29a_F260619': 's'}; obiclean_head=True; \n+@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP count=64; merged_sample={'26a_F040644': 64}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=99; obiclean_headcount=1; seq_rank=5; obiclean_samplecount=1; obiclean_status={'26a_F040644': 'h'}; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB count=61; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=2; seq_rank=4; obiclean_samplecount=2; obiclean_status={'29a_F260619': 'h', '15a_F730814': 'h'}; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB count=46; merged_sample={'13a_F730603': 46}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=1; seq_rank=8; obiclean_samplecount=1; obiclean_status={'13a_F730603': 'h'}; obiclean_head=True; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB count=7; merged_sample={'29a_F260619': 7}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=4; obiclean_headcount=0; seq_rank=16; obiclean_samplecount=1; obiclean_status={'29a_F260619': 's'}; obiclean_head=True; \n tttt\n->HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP count=3; merged_sample={'29a_F260619': 3}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=6; obiclean_samplecount=1; obiclean_status={'29a_F260619': 's'}; obiclean_head=True; \n-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac\n-agcttaaaactcaaaggacttggcggtgctttataccctt\n->HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB count=2; merged_sample={'29a_F260619': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=7; obiclean_sample"..b"M_000100422_612GNAAXX:7:10:9237:10532#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=51; obiclean_samplecount=1; obiclean_status={'29a_F260619': 'i'}; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaataattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:7:11998:4462#0/2_CONS_SUB_SUB count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=52; obiclean_samplecount=1; obiclean_status={'26a_F040644': 'i'}; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtagtactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=53; obiclean_samplecount=1; obiclean_status={'26a_F040644': 's'}; obiclean_head=True; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:3:17077:6562#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=54; obiclean_samplecount=1; obiclean_status={'15a_F730814': 'i'}; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:19:4311:13343#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=55; obiclean_samplecount=1; obiclean_status={'26a_F040644': 'i'}; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactacgagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB count=1; merged_sample={'15a_F730814': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=56; obiclean_samplecount=1; obiclean_status={'15a_F730814': 's'}; obiclean_head=True; \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB count=1; merged_sample={'13a_F730603': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=57; obiclean_samplecount=1; obiclean_status={'13a_F730603': 'i'}; obiclean_head=False; \n+ctagccttaaacacaaatagttatgcagacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=58; obiclean_samplecount=1; obiclean_status={'26a_F040644': 'i'}; obiclean_head=False; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n" |
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