| Next changeset 1:95ab864b281a (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f" |
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added:
kma_index.loc.sample kma_map.xml macros.xml test-data/ERR884056.aln test-data/ERR884056.frag test-data/ERR884056.fsa test-data/ERR884056.mat test-data/ERR884056.res test-data/ERR884056_ecoli_b0842.mapped_R1.fastq test-data/ecoli_cgMLST/ecoli_b0842_1to5.comp.b test-data/ecoli_cgMLST/ecoli_b0842_1to5.fasta test-data/ecoli_cgMLST/ecoli_b0842_1to5.index.b test-data/ecoli_cgMLST/ecoli_b0842_1to5.length.b test-data/ecoli_cgMLST/ecoli_b0842_1to5.name test-data/ecoli_cgMLST/ecoli_b0842_1to5.seq.b test-data/generate_test_data.sh test-data/test_database.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 2595c27071c2 kma_index.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kma_index.loc.sample Sat Feb 15 15:32:58 2020 -0500 |
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| @@ -0,0 +1,7 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the KMA index) +# +# e.g. +# senterica_cgmlst<tab>Salmonella cgMLST<tab>/path/to/kma_index/senterica |
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| diff -r 000000000000 -r 2595c27071c2 kma_map.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kma_map.xml Sat Feb 15 15:32:58 2020 -0500 |
| [ |
| b'@@ -0,0 +1,179 @@\n+<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0">\n+ <description></description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">kma</requirement>\n+ </requirements>\n+ <version_command>kma -v</version_command>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ kma\n+ -t \\${GALAXY_SLOTS:-1}\n+\t -t_db \'${kma_index.fields.path}\'\n+ #if $single_paired.single_paired_selector == \'paired\'\n+ -ipe \'${single_paired.forward_input}\' \'${single_paired.reverse_input}\'\n+ #elif $single_paired.single_paired_selector == "paired_collection":\n+ -ipe \'${single_paired.input_pair.forward}\' \'${single_paired.input_pair.reverse}\'\n+ #else:\n+ -i \'${single_paired.input_sequences}\'\n+ #end if\n+ #if str($settings.advanced) == "advanced"\n+ #if str($settings.kmer_size)\n+ -k \'${settings.kmer_size}\'\n+ #end if\n+ #if str($settings.p_value)\n+ -p \'${settings.p_value}\'\n+ #end if\n+ ${settings.decontaminate}\n+ ${settings.dense}\n+ ${settings.ref_fsa}\n+ ${settings.matrix}\n+ ${settings.all_best_mappings}\n+ #if str($settings.minimum_phred_score)\n+ -mp \'${settings.minimum_phred_score}\'\n+ #end if\n+ #if str($settings.cut_5_prime)\n+ -5p \'${settings.cut_5_prime}\'\n+ #end if\n+ ${settings.only_count_kmers}\n+ #if str($settings.min_id)\n+ -ID \'${settings.min_id}\'\n+ #end if\n+ #if str($settings.base_call_depth)\n+ -bcd \'${settings.base_call_depth}\'\n+ #end if\n+ #if str($settings.minimum_mapping_quality)\n+ -mq \'${settings.minimum_mapping_quality}\'\n+ #end if\n+ #if str($settings.reward)\n+ -reward \'${settings.reward}\'\n+ #end if\n+ #if str($settings.penalty)\n+ -penalty \'${settings.penalty}\'\n+ #end if\n+ #if str($settings.gapopen)\n+ -gapopen \'${settings.gapopen}\'\n+ #end if\n+ #if str($settings.gapextend)\n+ -gapextend \'${settings.gapextend}\'\n+ #end if\n+ ${settings.force_end_to_end}\n+ ${settings.set_cge_penalties_and_rewards}\n+ #end if\n+ -o output\n+\t \n+ #if str($settings.advanced) == "advanced" and $settings.matrix\n+ && gunzip output.mat.gz\n+ #end if\n+ && gunzip output.frag.gz\n+\t]]>\n+ </command>\n+ <inputs>\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">\n+ <option value="paired_collection">Paired collection</option>\n+ <option value="paired">Paired-end data</option>\n+ <option selected="True" value="single">Single-end data</option>\n+ </param>\n+ <when value="paired_collection">\n+ <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />\n+ </when>\n+ <when value="paired">\n+ <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>\n+ <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>\n+ </when>\n+ <when value="single">\n+ <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>\n+ </when>\n+ </conditi'..b'="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />\n+ <param name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>\n+ <param name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />\n+ <param name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />\n+ <param name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />\n+ <param name="reward" type="integer" min="1" value="1" max="100" label="Score for match" />\n+ <param name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />\n+ <param name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />\n+ <param name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />\n+ <param name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />\n+ <param name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />\n+ <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" />\n+ <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" />\n+ <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" />\n+ <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat">\n+ <filter>settings[\'matrix\']</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="single_paired_selector" value="single"/>\n+ <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>\n+ <param name="advanced" value="advanced"/>\n+ <param name="kmer_size" value="8"/>\n+ <param name="kma_index" value="test_index"/>\n+ <output name="result_overview" file="ERR884056.res" ftype="tabular"/>\n+ <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/>\n+ <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/>\n+ <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/>\n+ </test>\n+ <test>\n+ <param name="single_paired_selector" value="single"/>\n+ <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>\n+ <param name="advanced" value="advanced"/>\n+ <param name="kmer_size" value="8"/>\n+ <param name="matrix" value="true"/>\n+ <param name="kma_index" value="test_index"/>\n+ <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+When the mapping is done KMA will produce the following files:\n+\n+ *.res A result overview giving the most common statistics for each mapped template.\n+ *.fsa The consensus sequences drawn from the alignments.\n+ *.aln The consensus alignment of the reads against their template.\n+ *.frag Mapping information on each mapped read, columns are: \n+ 1. read\n+ 2. number of equally well mapping templates\n+ 3. mapping score\n+ 4. start position\n+ 5. end position (w.r.t. template)\n+ 6. the choosen template.\n+ *.mat Base counts on each position in each template, (only if \xe2\x80\x9c-matrix\xe2\x80\x9d is enabled)\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 2595c27071c2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Feb 15 15:32:58 2020 -0500 |
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| @@ -0,0 +1,18 @@ +<macros> + <token name="@TOOL_VERSION@">1.2.21</token> + <token name="@INTYPES@"> + fastq,fastq.gz,fastqsanger,fastqsanger.gz + </token> + <xml name="kma_index"> + <param label="Select a KMA index" name="kma_index" type="select"> + <options from_data_table="kma_index"> + <validator message="No KMA index available" type="no_options" /> + </options> + </param> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s12859-018-2336-6</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 2595c27071c2 test-data/ERR884056.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR884056.aln Sat Feb 15 15:32:58 2020 -0500 |
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| b'@@ -0,0 +1,170 @@\n+# b0842_1\n+template: \tATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTC\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCTGTCGGATCGTATTGGT\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tCGCCGTCCGGTGATGCTGGCGGGAGTGGTGTGGTTTATCGTCACCTGTCTGGCAATATTG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tCTGGCGCAAAACATTGAACAATTCACCCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGT\n+ \t______________________________________________||||||||||||||\n+query: \t----------------------------------------------gcataagcctctgt\n+\n+template: \tTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATC\n+ \t||||||||||||||||||||||||||||||||||||||||||||_|||||||||||||||\n+query: \tttcattggcgctgtgggatacgccgcaattcaggaatccttcgatgaggcggtttgtatc\n+\n+template: \tAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTG\n+ \t||||||||____________________________________________________\n+query: \taagatcac----------------------------------------------------\n+\n+template: \tGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAGGGGATGTTTGTTTTGTTTGCCGCATTG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGC\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGC\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCC\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATGATTGGTCTATTG\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACTGCCGGGTTA\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tAGTATTTATGCTTTCGGTATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTT\n+ \t____________________________________________________________\n+query: \t------------------------------------------------------------\n+\n+template: \tGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATC\n+ \t__________________________||||||_|||||||||||||||||||||||||||\n+query: \t--------------------------ttctgCgGcGATGGGAATGCTGCAAATGC'..b'||||||||||||||||||||||||||\n+query: \tTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCAATGACCGCA\n+\n+template: \tTATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tTATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGT\n+\n+template: \tCGCCGTCCGGTGATGCTGGCGGGGGTGGTGTGGTTTATCATCACCTGTCTGGCAATATTA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCGCCGTCCGGTGATGCTGGCGGGGGTGGTGTGGTTTATCATCACCTGTCTGGCAATATTA\n+\n+template: \tCTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGT\n+\n+template: \tTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATC\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATC\n+\n+template: \tAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTG\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTG\n+\n+template: \tGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAAGGGATGTTTGTCTTGTTTGCCGCATTG\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAAGGGATGTTTGTCTTGTTTGCCGCATTG\n+\n+template: \tGCAGCGATCTCCTTTTTCGGTCTGCAACAAGCCATGCCTGAAACCGCCACGCGTATAGGC\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGCAGCGATCTCCTTTTTCGGTCTGCAACAAGCCATGCCTGAAACCGCCACGCGTATAGGC\n+\n+template: \tGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGC\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGC\n+\n+template: \tTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGCCTGCCATTGCTGGCGTGGATCGCC\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGCCTGCCATTGCTGGCGTGGATCGCC\n+\n+template: \tCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTG\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTG\n+\n+template: \tCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCG\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCG\n+\n+template: \tCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTGGTCTGTTG\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTGGTCTGTTG\n+\n+template: \tGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACCGCCGGGTTA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACCGCCGGGTTA\n+\n+template: \tAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTT\n+\n+template: \tGCCAGCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGAATGCTGCAAATGCTGATC\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGCCAGCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGAATGCTGCAAATGCTGATC\n+\n+template: \tTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTT\n+ \t||||||||_||||||||||||||||||||||||||||||||||||||||||||||_||||\n+query: \tTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTT\n+\n+template: \tAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAA\n+\n+template: \tGATAAACAGATGGGAAATTCTCACGAAGGGTAA\n+ \t|||||||||||||||||||||||||||||||||\n+query: \tGATAAACAGATGGGAAATTCTCACGAAGGGTAA\n+\n' |
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| diff -r 000000000000 -r 2595c27071c2 test-data/ERR884056.frag --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR884056.frag Sat Feb 15 15:32:58 2020 -0500 |
| b |
| b'@@ -0,0 +1,506 @@\n+TGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCAACGGAATTTT\t1\t94\t1072\t1169\tb0842_1\tERR884056.2834864\t0\t97\n+GATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAATGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTG\t1\t94\t1076\t1176\tb0842_1\tERR884056.2647297\t0\t100\n+AAGAGACAGGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCT\t1\t77\t1050\t1145\tb0842_1\tERR884056.2441237\t0\t99\n+TGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGATTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGCTGT\t1\t50\t1183\t1233\tb0842_1\tERR884056.2335253\t0\t101\n+GGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCA\t1\t89\t1058\t1150\tb0842_1\tERR884056.2321059\t0\t92\n+GCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAAC\t1\t96\t1053\t1152\tb0842_1\tERR884056.2143874\t0\t99\n+GATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCT\t1\t96\t1076\t1175\tb0842_1\tERR884056.2103308\t0\t99\n+GCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCT\t1\t98\t1053\t1154\tb0842_1\tERR884056.1887994\t0\t101\n+CGGCGATTGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATC\t1\t84\t1051\t1144\tb0842_1\tERR884056.1872018\t0\t93\n+TCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTG\t1\t95\t1078\t1176\tb0842_1\tERR884056.1857520\t0\t98\n+CTGCGGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGC\t1\t77\t1048\t1128\tb0842_1\tERR884056.1732986\t0\t80\n+GCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCT\t1\t98\t1053\t1154\tb0842_1\tERR884056.1622292\t0\t101\n+GAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAAC\t1\t89\t1060\t1152\tb0842_1\tERR884056.1533035\t0\t92\n+TGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCA\t1\t84\t1072\t1159\tb0842_1\tERR884056.1246840\t0\t87\n+TGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGATTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGCTGT\t1\t50\t1183\t1233\tb0842_1\tERR884056.1091687\t0\t101\n+TTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCT\t1\t85\t1087\t1175\tb0842_1\tERR884056.960542\t0\t88\n+GATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGC\t1\t41\t1076\t1117\tb0842_1\tERR884056.917207\t0\t41\n+GGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACTGGGGCAA\t1\t69\t1058\t1130\tb0842_1\tERR884056.791515\t0\t72\n+GCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGATGAGGCGGTTTGTATCAAGATCAC\t1\t79\t346\t428\tb0842_1\tERR884056.731782\t0\t82\n+TTCTGCGGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTT\t1\t88\t1046\t1140\tb0842_1\tERR884056.552530\t0\t94\n+TCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATCTCTTCAACCTTGTCAACGGAGTTTTGTG\t1\t88\t1078\t1172\tb0842_1\tERR884056.307281\t0\t94\n+CCTGCCATTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAAT\t1\t74\t695\t769\tb0842_3\tERR884056.2922822\t0\t74\n+GAAGAGCGGCCGCTTTGTGGCGGGGGCGCTGCCGCTGGGATTCGTTAGCCTGCCATTGCTGGCGTGGAT\t1\t63\t647\t716\tb0842_3\tERR884056.2921952\t0\t69\n+TTAGCCTGCCATTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAAT\t1\t78\t691\t769\tb0842_3\tERR884056.2909363\t0\t78\n+TTACCGGCGAGCAGTTGAGCAGCTCTGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATT\t2\t65\t739\t807\tb0842_3\tERR884056.2901629\t0\t68\n+GCGTATTTATGGATGACCGCCGGGTTAAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAG\t1\t101\t933\t1034\tb0842_3\tERR884056.2898975\t0\t101\n+GATCACCGCGCTGATGGCGAACGTGGCGCTG\t3\t31\t422\t453\tb0842_3\tERR884056.2895985\t0\t31\n+GATCGTATTGGTCGCCGTCCGGTGATGCTGGCGGGGGTGGTGTGGTTTATCATCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCT\t1\t101\t228\t329\tb0842_3\tERR884056.2892663\t0\t101\n+CAAAATAAATTAGCTTCCGGTGCCAGTCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACC\t4\t81\t3\t87\tb0842_3\tERR884056.2892595\t0\t84\n+GGTTTATCATCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTG'..b'56.154502\t0\t35\n+AGAGACAGCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAA\t2\t83\t1140\t1233\tb0842_3\tERR884056.149198\t0\t101\n+TGGATGACCGCCGGGTTAAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGG\t1\t98\t942\t1040\tb0842_3\tERR884056.148041\t0\t98\n+CTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTGGTCTGTTGGTCGCTGCTGCGG\t1\t98\t815\t913\tb0842_3\tERR884056.146603\t0\t98\n+CGCAAAACATTGAACACTTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAA\t1\t98\t304\t405\tb0842_3\tERR884056.141798\t0\t101\n+GGATGTTTGTCTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACAAGCCATGCCTGAAACCGCCACGCGTATA\t1\t83\t514\t597\tb0842_3\tERR884056.132716\t0\t83\n+GCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGA\t1\t101\t303\t404\tb0842_3\tERR884056.130233\t0\t101\n+ATTGGCGAAGAAATTGCATGCAAAATAAATTAGCTTACGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGG\t4\t64\t0\t67\tb0842_3\tERR884056.128819\t0\t84\n+ATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGATTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGGTCGTCAATCTGGTGT\t2\t32\t1201\t1233\tb0842_3\tERR884056.125093\t0\t100\n+TGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGTCGCCGTCCGGTGATGCTGGCGGGGGTGGTGTGGTTTATCATCACC\t1\t89\t196\t285\tb0842_3\tERR884056.124429\t0\t89\n+GTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTG\t2\t97\t372\t469\tb0842_3\tERR884056.111065\t0\t97\n+ATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGATTGCTTTGTGCGATCAGGCATTCTCGAA\t2\t45\t1188\t1233\tb0842_3\tERR884056.108798\t0\t85\n+GGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCC\t2\t72\t1161\t1233\tb0842_3\tERR884056.98521\t0\t81\n+ATTATTGGTCTGTTGGTCGCTGCTGCGGCAACGGTTATCTCATCGC\t1\t46\t885\t931\tb0842_3\tERR884056.96205\t0\t46\n+CTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGG\t4\t100\t48\t148\tb0842_3\tERR884056.90492\t0\t100\n+TAGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAAGGGATGTT\t1\t82\t436\t521\tb0842_3\tERR884056.87557\t0\t85\n+CAGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAA\t2\t63\t1134\t1200\tb0842_3\tERR884056.87421\t0\t66\n+GGCATTGATTGGGTTCCTACTTCAATGACCGCATATCTGGCGGGCGGGATGTTTTTACAAT\t1\t61\t147\t208\tb0842_3\tERR884056.82382\t0\t61\n+AGAGACAGGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGT\t4\t88\t21\t121\tb0842_3\tERR884056.68978\t0\t101\n+CGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCT\t2\t52\t589\t641\tb0842_3\tERR884056.57400\t0\t52\n+CATTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGC\t1\t74\t700\t774\tb0842_3\tERR884056.51896\t0\t74\n+TATTTATGGATGACCGCCGGGTTAAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGC\t1\t90\t936\t1026\tb0842_3\tERR884056.49971\t0\t90\n+GTTTGTATCAAGATCGCCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCTGGGA\t3\t98\t411\t512\tb0842_3\tERR884056.45596\t0\t101\n+CGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCG\t2\t101\t727\t828\tb0842_3\tERR884056.44406\t0\t101\n+GTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCA\t1\t101\t286\t387\tb0842_3\tERR884056.35909\t0\t101\n+TCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTAT\t1\t60\t830\t890\tb0842_3\tERR884056.28618\t0\t60\n+CCGCTGGTGGGCGCGGCG\t4\t18\t471\t489\tb0842_3\tERR884056.25879\t0\t18\n+CAATGACCGCATATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGTCGCCGTCCGGTGATGCTGGCGGGGGT\t1\t97\t169\t266\tb0842_3\tERR884056.18517\t0\t97\n+GGAGATGTGTATAAGAGACAGCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTT\t1\t73\t263\t361\tb0842_3\tERR884056.13376\t0\t101\n+AGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGC\t2\t71\t569\t640\tb0842_3\tERR884056.12478\t0\t71\n+CCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACT\t2\t51\t583\t634\tb0842_3\tERR884056.2831\t0\t51\n+CCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGC\t2\t96\t353\t449\tb0842_3\tERR884056.1120\t0\t96\n' |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ERR884056.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR884056.fsa Sat Feb 15 15:32:58 2020 -0500 |
| b |
| @@ -0,0 +1,28 @@ +>b0842_1 +gcataagcctctgtttcattggcgctgtgggatacgccgcaattcaggaatccttcgatg +aggcggtttgtatcaagatcacttctgCgGcGATGGGAATGCTGCAAATGCTGATCTTTA +CCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTTAATC +TCTTCAACCTTGTCAACGGAaTTTTGTGGCTgtggttatctttttaaaagataaacagat +gggaaattctcacgaagggtaa +>b0842_3 +ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTC +TGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATG +TTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCAATGACCGCA +TATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGT +CGCCGTCCGGTGATGCTGGCGGGGGTGGTGTGGTTTATCATCACCTGTCTGGCAATATTA +CTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGT +TTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATC +AAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTG +GGCGCGGCGTGGATCCATGTGCTGCCCTGGGAAGGGATGTTTGTCTTGTTTGCCGCATTG +GCAGCGATCTCCTTTTTCGGTCTGCAACAAGCCATGCCTGAAACCGCCACGCGTATAGGC +GAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGC +TTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGCCTGCCATTGCTGGCGTGGATCGCC +CAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTG +CAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCG +CGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTGGTCTGTTG +GTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACCGCCGGGTTA +AGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTT +GCCAGCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGAATGCTGCAAATGCTGATC +TTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGTTT +AATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAA +GATAAACAGATGGGAAATTCTCACGAAGGGTAA |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ERR884056.mat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR884056.mat Sat Feb 15 15:32:58 2020 -0500 |
| b |
| b'@@ -0,0 +1,2542 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|
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ERR884056.res --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR884056.res Sat Feb 15 15:32:58 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +#Template Score Expected Template_length Template_Identity Template_Coverage Query_Identity Query_Coverage Depth q_value p_value +b0842_1 1721 9112 1233 21.01 21.25 98.85 470.61 1.46 5042.64 1.0e-26 +b0842_3 36074 523 1233 99.84 100.00 99.84 100.00 29.95 34532.73 1.0e-26 |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ERR884056_ecoli_b0842.mapped_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR884056_ecoli_b0842.mapped_R1.fastq Sat Feb 15 15:32:58 2020 -0500 |
| b |
| b"@@ -0,0 +1,2176 @@\n+@ERR884056.1120\n+CCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGA\n++\n+BCCFFFDDHHHHHIIJJIIJGHGHIIIJIIJJIGHIJGIJJJIJJG@G>EDA=EEDDDBDBDDACDDDC@CC>CC?@BD@@BBDD+(0999@88?B#####\n+@ERR884056.2831\n+AGTCACGACCGAGTTCTTTCAGTGACAGTTTCTCGCCTATACGCGTGGCGGTTTTAGGCATGGCTTGTTGCAGACCCGAAAAAGAGATCTCTGCCACTGCG\n++\n+@@@DFAA?FHF:?FGEFGHAGI??<9CH<D@B@<D@0D6CFGGAHGF>DFA##################################################\n+@ERR884056.12478\n+GCTTATAGTCACGACCGAGTTCTTTCAGTGACAGTTTCTCGCCTATACGCGTGGCGGTTTCAGGCATGGCTTTTTTCAAACCGAAAAAGAGGATCGCTGGC\n++\n+@BBFFFFDHHHHHJJIHGHEGHHIJJJJJJJJIEDDHIHFAFFABC@CFHHHHDBCD,8?>CC:<B><?<A##############################\n+@ERR884056.13376\n+AACAGAGGCTTATGCCCTGCAAGAAGCGCAACAGAGTGAATTGTTCAATGTTTTGCGCCAGTAATATTGCCAGACAGGTGCTGTCTCTTATACACATCTCC\n++\n+@@@FFDD?DHHADCFHIIIIIII<D?EE8CFH@GGGFDDFFDF8BFGGGEBBFC@@8BHBHE;CCCA@3?;>36;?CB-(;@>AA>>@::>@C>ACC:>@>\n+@ERR884056.18517\n+ACCCCCGCCAGCATCACCGGACGGCGACCAATACGATCCGACAGCGGCCCCAGGAGCCATTGTAAAAACATCCCGCCCGCCAGATATGCGGTCATTGAAGT\n++\n+CCCFFFFFHFHHHJJJJJJJHGIHIJJGHFFFFEDDDDBA?BBDD@BD7B78?BDDA?ACDDDDC>C@;<@CC?2<BB@BD59AC>@AC35)9>>>@####\n+@ERR884056.25879\n+CCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCCTGGAAGGGATGTTTATCTTGTTTGACGCAGTGGAAGCCGTCCTGTCTCTTATTCACATCCACCA\n++\n+???DDDD+ADDBD8DE0@###################################################################################\n+@ERR884056.27378\n+GTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTTGGGGCGTTTATTGCGGGGGAATTTCTGTTTGCGCGTCTGACCTCGCGCCGCACCGCAC\n++\n+@@@FDFFDHFHHHJJJIIIIJEGI)+++22:1111:4*:CDG<0)?@######################################################\n+@ERR884056.28618\n+TCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTCGTCTGTTGGTCGCTGCTGCGGCAACGGTTATCTCATTCC\n++\n+???DDBDDDB1CDEE8CDDADD@?0?BDIIIAC@ADE@EI36?<9=?8;<=78<=<>BAB#########################################\n+@ERR884056.35909\n+GTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCA\n++\n+CCCFFFFFHHGHHFGHEHGHHJJJJJJIJGIIJJHGIJJJHI*?BBBFGIAAHIFCCEEH=EFDFFF7>A@CCCCDDDDDC@:;?@;&999?@CCB9B@B<\n+@ERR884056.37433\n+CTGCAAATGCTGATCTTTACCGGTGGGATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACAGGTTAATCTCTTAAACCTAGTCAACGGAAT\n++\n+???A:=BD?4A22<CDB:<?F8)31@)11?D3?@B><**090)00?B**988BCCAC@@##########################################\n+@ERR884056.44406\n+CGCTAACAGCAAGTTACCCGCAATTAACGCCCCGAAAATAGGCACTTGCAGCAAGCCATATTCATAGCTGCTCAACTGCTCGCCGGTAATGATGATAATCG\n++\n+@@@DDDDDHFHHHJJFHIJIIEIIJHJGJIFHFGD@EIFFGIIGGCCH)==EBFDDDCCCEEEDECCDDDDDCC3?CCDDDDD9<05<<>@>@C:@:>@:<\n+@ERR884056.45596\n+TCCCAGGGCAGCACATGGATCCACGCCGCGCCCACCAGCGGACCAAGTAGCGGAGCAATCAGCGCCACGTTCGCCATCAGCGCGGCGATCTTGATACAAAC\n++\n+;?@FFFFDHFHHHJJJJHIGGIIIIIIJJGBFGHGJIIGIHHFCCDD;>@>BB=?BBCDDCDABDD;5;<?<;>DD@A:>+)5<9&5<B?BACC@:@CCDA\n+@ERR884056.49971\n+TATTTATGGATGACCGCCGGGTTAAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAA\n++\n+@@@FFFFFHHHHHJJFHGHJH?GHIHEHIIIJJFHHIIGIJJJJJJI=CGDEHHFBC>CC8?8?BBDCC@@52<?C>ABBDC>CCDAA:?###########\n+@ERR884056.51896\n+GCCATATTCATAGCTGCTCAACTGCTCGCCGGTAATGATGATAATCGGCGACTGGGCGATCCACGCCAGCAATGGAAGGGTAAAGAACACCAGCGCCGTGG\n++\n+@CCFFDFDHHHHGJJIGBCHHHGIJ<DHGI8F@GGGIDDDGGHCHIJGGB<BDF;;69>;88@:@@BBBBC9>A###########################\n+@ERR884056.57400\n+AGCTTATAGTCACGACCGAGTTCTTTCAGTGACAGTTTCTCGCCTATACGCGCGGCGGTTTCACGCATGGCTTGTTGCAGATCGACAAAGGAAGGAGCCTC\n++\n+@78BDDDDFFDFD?EF<FFF)?DFFF*CGF99D<FB?9BBF(7@'@F4)=5@#################################################\n+@ERR884056.68978\n+ACATACCGGGTTGAATCATATCGTTGCCGATATAGGTTGAAAATTCGTAAAGCACCAGACAGAGAGGGAAAAGTAACGCCTGACGTCCAAGCCCTGTCTCT\n++\n+@CCFFFFFHHHHHJJJJJJIJGFHIGIJJIGIIJIHFGHIJJIJIGGHIIEHIJIHFGHFFDDF>?CDDBBDD,5>C<?8?<9>3<><8::??B<84::>C\n+@ERR884056.82382\n+GGCATTGATTGGGTTCCTACTTCAATGACCGCATATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTAGGATCGGTTTGGTCCGCCGCG\n++\n+BB@DDFF?FFHHHJGJIJGIJJIJGIICHDFEHGGFHCGGFGHB<A@@5509CDCB03>CC########################################\n+@ERR884056.87421\n+CAGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGGTAAACAGATGGGAAATTCTCCCGAAGGGAAAAA\n++"..b"++\n+BB@FFFFFHHHHHJJJHHHIHIJJIJJIJI?FGIIJJJJHDGHHDFHGFGHGIJI@GGIIGCACEHHDBB??6;.6>A>AC@C;<?A?59?@BDD######\n+@ERR884056.2859125\n+CGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGAACCGTTTCCGCCGCGATGCGCACGCCGCCACTAC\n++\n+???DDAD3+<A:A3CEE1<2CC1)0?D)8/?D0:=.5=@ADAAA;))7AC###################################################\n+@ERR884056.2867288\n+CGCCAGATATGCGGTCATTGAAGTAGGAACCCAATCAATGACCGCCTGATATTGTTCCACCAAGGCCAACATACCGGGTTGAATCATCTCGTATGCCGTCT\n++\n+CCCDFFFFHHHGHIGFHIJJIJJFFGHIIJJJJIIJJICEGHIIJJJJIIFFFHHEHIIEHF=EDFFD?CCCDDD:@@2<'5:>>:44>@A<BC?CD####\n+@ERR884056.2868977\n+CGGTGATCTTGATACAAACCGCCTCTTCGAAGGATTCCTGAATTGCGGCGTATCCCACAGCGCCAATGAAACAGAGGCTTATGCCTGTCTCTTATACACAT\n++\n+@@@DDDBDFHDHDGHEHIJFGHGIFFIIF9FG@DAGBGHG@GDF?DFGAA8=BEB>>>?5;@B8=8ACC@CD#############################\n+@ERR884056.2875483\n+TTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAAAGCCTAATTTCGGGGCGTTAATTCGGGGTGAACTTCTGTTATCGGGGCTTCACTCC\n++\n+@@CFADDFHDFFFGHGCGGIJIIIDFIHCIIIE?FHI'.=)73@C########################################################\n+@ERR884056.2878314\n+TTTTTTTACCCTTCGTGAGAATTTCCCATCTGTTTATCTTTTAAAAAGATAACCATCAGCGACAGCCACAAAATTCCGTTGACAAGGTTGAAGAGATTAAA\n++\n+@BCDFFFFDHHHHIGHGGHIIJJJJJJ@GHIIIHIJJHJIIGGHH@GE?G=BF=;C@>@7;=EDFEAEEABA?>5>@>5:19A>(92@@9>>A>?CCC###\n+@ERR884056.2889097\n+CCTGAATTGCGGCGTATCCCACAGCGCCAATGAAACAGAGGCTTATGCCCTGCAAGAAGCGCAACAGAGTGAATTGTTCAATGTTTTGCGCCAGTAATATT\n++\n+CCCFFFFFHHHGGJJJIGGHIIIHGFHHGIJHGC=FGHGIIFCCEECFFFCCBEC;CCC?>BDDBBBCC>AADDAACC>ADDCD@@98:9555>CC:3>CC\n+@ERR884056.2890162\n+CTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAACAGGCGGTTTGTATCAAGATCAC\n++\n+BC@FFFFFHHHHHJFIGIJJJJJIJJIIIJJJHHIJIIJIJJJIJJJJIGAEGGCFHBCA?BCCAC>CADC>ACD??8()<AB>9<B<@############\n+@ERR884056.2890892\n+GCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTGGCTGTCTCTTTTACACATCTCCGACCCCACGAGACTAAGGCGAAACTC\n++\n+BBBDDDDDHHHHHJIIIBGGHHHIGIIHIGIIIJIGD@CDB=338?<:5;@C>>CCB8>@::3(+(4++4@@>4:<5&&08@<9-&&5::@AD########\n+@ERR884056.2892198\n+GGTTTATCATCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCT\n++\n+@B@DFFDFHHFFHIGGIGIJJJJJJJJGJIJIIJGIEGDGIIGICGFHH;EBFHIIIGGGHEFHIHBFF;>CCAC<=5ACA3:?AC@:>;:5;@CCCCB##\n+@ERR884056.2892595\n+GGTTGAAAATTCGTAAAGCACCAGACAGAGAGGGAAAAGTAACGCCTGACGTCCAAGACTGGCACCGGAAGCTAATTTATTTTGCATGCAATTTCTTCGCA\n++\n+@@BDDFEFHHHHHIIIJIJJIHGJIIJJHIHIIIJIJGF9?FGHIIEHGGA@;@;C7(.7AA?CF;ABBBB?:>5AA>CD@CAC#################\n+@ERR884056.2892663\n+AGAGTGAATTGTTCAATGTTTTGCGCCAGTAATATTGCCAGACAGGTGATGATAAACCACACCACCCCCGCCAGCATCACCGGACGGCGACCAATACGATC\n++\n+@@CF=BDEHHGHHIHIGDCJHJEHIJIIJFHIBIJJDHIGFHIGFH?FHGDEEFGGIH;B@CFHHIIHHBADDDDDDDDCC?55@@BBD30<9?3>>8<<A\n+@ERR884056.2895985\n+GATCACCGCGCTGATGGCGAACGTGGCGCTGGTTTCTCCGCTACTTGGTCCGCTGGTTCGCGCGTCGTGGATCCCTGTGCTGCCCTGGGAAGGCATGCTTG\n++\n+??@7=+=AC18@D@F4C9E10@DG9BB@A:F######################################################################\n+@ERR884056.2898975\n+CTCATATCGCTGGCAAACAGGGTTAATCGCACCAGTCCCGCATTCGCCAGACCAATGCCGAAAGCATAAATACTTAACCCGGCGGTCATCCATAAATACGC\n++\n+@BCDDDFFCFHHHJHJJJIIHIFHHGIHIIIJJEHIJJJJIIHFFGIGGHHFHHGFFFCBABB;ACCCA>@CCC(;,,+85>>B<>@9AACCDCAA>>A?5\n+@ERR884056.2901629\n+TTACCGGCGAGCAGTTGAGCAGCTCTGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGGAACTTGCTTGTTGGGGGTTCGACCTCC\n++\n+@@@DFFFFHHHHFHDHGDFHGEHI3?DHGIIGG88BG@6C;=)=7).=@9)..7=749AC3)07)<@@#################################\n+@ERR884056.2909363\n+ATTCATAGCTGCTCAACTGCTCGCCGGTAATGATGATAATCGGCGACTGGGCGATCCACGCCAGCAATGGCAGGCTAACGAATCCCAGACACAGCGCACCC\n++\n+<@@DFFFDFFFFH4EHIEHGHGDAFHFC@DGGICHCFIJJJ<:@@;:5=?B9<;>??AC8=@:/+<?CC(2><5)2@C#######################\n+@ERR884056.2921952\n+ATCCACGCCAGCAATGGCAGGCTAACGAATCCCAGCGGCAGCGCCCCCGCCACAAAGCGGCCGCTCTTCAGCACCAGCTTATAGTCACGACCGAGTTACTT\n++\n+@@@DDDDDHHHHHIIIIHHII68CC?::?)6BHEBDG(;45;@AEBB>/;8=@(9A>9;;7<@&082>@################################\n+@ERR884056.2922822\n+ATTCATAGCTGCTCAACTGCTCGCCGGTAATGATGATAATCGGCGACTGGGCGATCCACGCCAGCAATGGCAGGCCAACGAATCCCAGCCCCCGCGCGCCC\n++\n+@CCFFFFFHHHHGJJIJJJJJJJJJJEHHIJJJJIIJJGIGGHIJIHFDDDDDB@DDDDDDDDBDDAAC:ACDB###########################\n" |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ecoli_cgMLST/ecoli_b0842_1to5.comp.b |
| b |
| Binary file test-data/ecoli_cgMLST/ecoli_b0842_1to5.comp.b has changed |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ecoli_cgMLST/ecoli_b0842_1to5.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_cgMLST/ecoli_b0842_1to5.fasta Sat Feb 15 15:32:58 2020 -0500 |
| b |
| @@ -0,0 +1,10 @@ +>b0842_1 +ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCTGTCGGATCGTATTGGTCGCCGTCCGGTGATGCTGGCGGGAGTGGTGTGGTTTATCGTCACCTGTCTGGCAATATTGCTGGCGCAAAACATTGAACAATTCACCCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAGGGGATGTTTGTTTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATGATTGGTCTATTGGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACTGCCGGGTTAAGTATTTATGCTTTCGGTATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAA +>b0842_2 +ATGCAAAACCGATTACAAACCGGCGCACGACTGGGGCGTTCGGCGTTACTTTTTCCTCTTTGTCTGGTCCTGTACGAATTCTCGACATATATCGCTAACGATATGATTCAGCCCGGCATGTTGGCTGTAGTGGAGCAATATCAGGCTGGAATTGACTGGGTGCCAACGTCCATGACTGCCTATCTGGCAGGTGGCATGTTCTTACAATGGTTACTTGGGCCGTTGTCGGATCGTGTTGGTCGCCGTCCGGTGATGCTGGTGGGGGTGGTGTGGTTTATCGTCACCTGTCTCGCCACGTTACTGGCACAAAATATTGAACAATTTACGGTGTTACGTTTTTTACAAGGAATTAGCCTCTGTTTTATTGGTGCTGTGGGCTATGCTGCAATTCAGGAGTCTTTCGAAGAGTCGGTATGTATTAAAATTACAGCGCTTATGGCGAACGTCGCTCTGATTGCTCCTCTCCTTGGCCCTTTAGTAGGGGCCGCCTGGGTGCATATGCTGCCCTGGGAGGGGATGTTTATCCTCTTTGCAGTGCTGGCGGCCATTTCCTTTGTGGGCCTGCAGCGAGCAATGCCAGAAACAGCAACCCGTATCGGTGAAAAGCTCTCTTTAAAAGAGTTAGGTCGTGACTACAAACAGGTATTAAAGAATGGTCGCTTTGTAGCCGGAGCTCTGGCCCTGGGATTTGTTAGCTTGCCATTACTGGCGTGGATTGCCCAATCACCCATTATCATTATCACGGGCGAGAAATTAAGCAGCTATGAATATGGCCTGTTACAGGTGCCTGTTTTTGGCGCACTGATTGCTGGCAACCTGGTACTGGCACGGTTAACTGCACGGCGCACAGTACGTTCGTTGATCATTATGGGTGGCTGGCCGATTGTTATCGGGCTGGTCGTTGCTGCGATCGCGACGGCTTTCTCCTCACATGCCTATTTATGGATGACAGCGGGATTAAGTATCTATGCTTTTGGTATTGGCCTGGCCAATGCCGGATTGGTTCGTTTGACCTTGTTTGCCAGTGATATGAGTAAAGGTACAGTGTCGGCGGCCATGGGAATGGTACAGATGCTGATCTTTACGGTGGGAATTGAAGTCAGTAAACACGCATGGTTAGGGGGTGGTAATGGCATGTTTAACCTGTTCAATCTGGCGAATGGTGTTATCTGGCTGCTGTTGATGGTGATTTTTTTACGTGATAAAAGCGTTGGAAATTCACAGAAAGCTTAA +>b0842_3 +ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCAATGACCGCATATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGTCGCCGTCCGGTGATGCTGGCGGGGGTGGTGTGGTTTATCATCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACTCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAAGGGATGTTTGTCTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACAAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGCCTGCCATTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATTATTGGTCTGTTGGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACCGCCGGGTTAAGTATTTATGCTTTCGGCATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAA +>b0842_4 +ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACTGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGTTGTCGGATCGTATTGGCCGCCGTCCGGTGATGTTGGCGGGAGTGGTGTGGTTTATCGTCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACCCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAATCCTTCGAAGAGGCCGTTTGTATCAAGATCACCGCGCTAATGGCGAACGTGGCGCTGATTGCTCCACTACTTGGTCCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAAGGGATGTTTGTCTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCTATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCGCTGAAAGAACTCGGTCGTGACTATAAGTTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGCCTGCCGTTGTTGGCGTGGATCGCCCAGTCGCCGATTATCATTATTACCGGTGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATGATTGGTCTGTTGGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACCGCCGGGTTAAGTATTTATGCTTTCGGTATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGCATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCGCACGAAGGGTAA +>b0842_5 +ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTCCTGGGGCCGCTGTCGGATCGTATTGGTCGCCGTCCGGTGATGCTGGCGGGAGTGGTGTGGTTTATCGTCACCTGTCTGGCAATATTACTGGCGCAAAACATTGAACAATTCACCCTGTTGCGCTTCTTGCAGGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGCCGCAATTCAGGAGTCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGGCGTGGATCCATGTGCTGCCCTGGGAGGGGATGTTTGTCTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCGCTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGTCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGCCTGCCGTTGTTGGCGTGGATCGCCCAGTCGCCGATTATCATTATTACCGGTGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTTGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATGATTGGTCTGTTGGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACCGCCGGGTTAAGTCTTTATGCTTTCGGTATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGCATTTTGTGGCTGTTGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCGCACGAAGGGTAA |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ecoli_cgMLST/ecoli_b0842_1to5.index.b |
| b |
| Binary file test-data/ecoli_cgMLST/ecoli_b0842_1to5.index.b has changed |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ecoli_cgMLST/ecoli_b0842_1to5.length.b |
| b |
| Binary file test-data/ecoli_cgMLST/ecoli_b0842_1to5.length.b has changed |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ecoli_cgMLST/ecoli_b0842_1to5.name --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_cgMLST/ecoli_b0842_1to5.name Sat Feb 15 15:32:58 2020 -0500 |
| b |
| @@ -0,0 +1,5 @@ +b0842_1 +b0842_2 +b0842_3 +b0842_4 +b0842_5 |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/ecoli_cgMLST/ecoli_b0842_1to5.seq.b |
| b |
| Binary file test-data/ecoli_cgMLST/ecoli_b0842_1to5.seq.b has changed |
| b |
| diff -r 000000000000 -r 2595c27071c2 test-data/generate_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate_test_data.sh Sat Feb 15 15:32:58 2020 -0500 |
| b |
| @@ -0,0 +1,30 @@ +#!/usr/bin/bash + +# E. coli locus b0842 (b0842.fasta.gz) downloaded from Enterobase E. coli cgMLST scheme +# requires: wget, kma, bwa, samtools, bedtools + +gunzip b0842.fasta.gz + +# Take first 5 alleles to reduce size of test data +mkdir ecoli_cgMLST +head -n 10 b0842.fasta > ecoli_cgMLST/ecoli_b0842_1to5.fasta + +kma index -k 8 -i ecoli_cgMLST/ecoli_b0842_1to5.fasta -o ecoli_cgMLST/ecoli_b0842_1to5 + +wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR884/ERR884056/ERR884056_1.fastq.gz + +# Use bwa to map reads to reduced E. coli locus b0842 +# and extract only mapped reads (to reduce size of test dataset) +bwa index ecoli_cgMLST/ecoli_b0842_1to5.fasta + +bwa mem ecoli_cgMLST/ecoli_b0842_1to5.fasta ERR884056_1.fastq.gz -o ERR884056_1_ecoli_b0842_1to5.sam + +samtools view ERR884056_1_ecoli_b0842_1to5.sam -bo ERR884056_1_ecoli_b0842_1to5.bam + +# Select mapped reads +samtools view -b -F 4 ERR884056_1_ecoli_b0842_1to5.bam > ERR884056_1_ecoli_b0842_1to5.mapped.bam + +samtools sort -n ERR884056_1_ecoli_b0842_1to5.mapped.bam -o ERR884056_1_ecoli_b0842_1to5.mapped.sort.bam + +bedtools bamtofastq -i ERR884056_1_ecoli_b0842_1to5.mapped.sort.bam -fq ERR884056_ecoli_b0842.mapped_R1.fastq + |
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| diff -r 000000000000 -r 2595c27071c2 test-data/test_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database.loc Sat Feb 15 15:32:58 2020 -0500 |
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| @@ -0,0 +1,7 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the KMA index) +# +# +test_index "Test Index" ${__HERE__}/ecoli_cgMLST/ecoli_b0842_1to5 |
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| diff -r 000000000000 -r 2595c27071c2 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Feb 15 15:32:58 2020 -0500 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of KMA index in the required format --> + <table name="kma_index" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kma_index.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 2595c27071c2 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sat Feb 15 15:32:58 2020 -0500 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of KMA index in the required format --> + <table name="kma_index" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/test_database.loc" /> + </table> +</tables> |