| Next changeset 1:9be4beda6482 (2021-03-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8 |
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added:
generate_test_data.sh metaphlan2.xml metaphlan2_macros.xml repository_dependencies.xml test-data/community_profile.tabular test-data/formatted_to_krona.tabular test-data/heatmap.pdf test-data/heatmap.png test-data/heatmap.svg test-data/input_sequences.fasta test-data/marker_metadata.json test-data/marker_sequences.fasta test-data/merged_community_profile.tabular tool-data/metaphlan2_database.loc.sample tool_data_table_conf.xml.sample transform_json_to_pkl.py |
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| diff -r 000000000000 -r 8c82c4d90cc6 generate_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Sat Mar 04 12:23:45 2017 -0500 |
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| @@ -0,0 +1,49 @@ +#/usr/bin/env bash + +metaphlan_hclust_heatmap.py \ + --in test-data/merged_community_profile.tabular \ + --out test-data/heatmap.png \ + -m 'average' \ + -d 'braycurtis' \ + -f 'correlation' \ + --minv '0' \ + --tax_lev 'a' \ + --sdend_h '0.1' \ + --fdend_w '0.1' \ + --cm_h '0.03' \ + --font_size '7' \ + --clust_line_w '1' \ + --perc '90' \ + -c 'jet' + +metaphlan_hclust_heatmap.py \ + --in test-data/merged_community_profile.tabular \ + --out test-data/heatmap.pdf \ + -m 'ward' \ + -d 'euclidean' \ + -f 'euclidean' \ + --minv '0' \ + --tax_lev 'a' \ + --sdend_h '0.1' \ + --fdend_w '0.1' \ + --cm_h '0.03' \ + --font_size '7' \ + --clust_line_w '1' \ + --perc '90' \ + -c 'pink' + +metaphlan_hclust_heatmap.py \ + --in test-data/merged_community_profile.tabular \ + --out test-data/heatmap.svg \ + -m 'complete' \ + -d 'hamming' \ + -f 'matching' \ + --minv '0' \ + --tax_lev 'a' \ + --sdend_h '0.1' \ + --fdend_w '0.1' \ + --cm_h '0.03' \ + --font_size '7' \ + --clust_line_w '1' \ + --perc '90' \ + -c 'pink' \ No newline at end of file |
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| diff -r 000000000000 -r 8c82c4d90cc6 metaphlan2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan2.xml Sat Mar 04 12:23:45 2017 -0500 |
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| b'@@ -0,0 +1,193 @@\n+<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0">\n+\n+ <description>to profile the composition of microbial communities</description>\n+\n+ <macros>\n+ <import>metaphlan2_macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.3.0">bowtie2</requirement>\n+ <requirement type="package" version="2.7.10">python</requirement>\n+ </expand>\n+ \n+ <expand macro="stdio"/>\n+\n+ <version_command>\n+<![CDATA[\n+metaphlan2.py -v\n+]]>\n+ </version_command>\n+\n+ <command>\n+<![CDATA[\n+ #if $db.db_selector == "history"\n+ mkdir ref_db\n+ &&\n+ bowtie2-build \'$db.bowtie2db\' \'ref_db/ref_db\'\n+ &&\n+ python \'$__tool_directory__/transform_json_to_pkl.py\'\n+ --json_input \'$db.mpa_pkl\'\n+ --pkl_output \'ref_db/metadata.pkl\'\n+ &&\n+ #end if\n+\n+ metaphlan2.py\n+ \'$input_file\'\n+ -o \'$output_file\'\n+ --input_type \'${input_file.datatype.file_ext}\'\n+ --bowtie2_exe `which bowtie2`\n+\n+ #if $db.db_selector == "cached"\n+ #set $path = $db.cached_db.fields.path\n+ #set $value = $db.cached_db.fields.value\n+ --bowtie2db $path/$value\n+ --mpa_pkl $path/$value\'.pkl\'\n+ #else\n+ --bowtie2db \'ref_db/ref_db\'\n+ --mpa_pkl \'ref_db/metadata.pkl\'\n+ #end if\n+\n+ --no_map\n+\n+ -t \'$analysis_type.analysis_type_select\'\n+ #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"\n+ --tax_lev \'$analysis_type.tax_lev\'\n+ #else if $analysis_type.analysis_type_select == "marker_ab_table"\n+ --nreads \'$analysis_type.nreads\'\n+ #else if $analysis_type.analysis_type_select == "marker_pres_table"\n+ --pres_th \'$analysis_type.pres_th\'\n+ #end if\n+\n+ --min_cu_len \'$min_cu_len\'\n+ --min_alignment_len \'$min_alignment_len\'\n+\n+ $ignore_viruses\n+ $ignore_eukaryotes\n+ $ignore_bacteria\n+ $ignore_archaea\n+\n+ --stat_q \'$stat_q\'\n+ -s \'$sam_output_file\'\n+ --biom \'$biom_output_file\'\n+]]>\n+ </command>\n+\n+ <inputs>\n+ <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>\n+ <conditional name="db">\n+ <param name="db_selector" type="select" label="Database with clade-specific marker genes">\n+ <option value="cached" selected="true">Locally cached</option>\n+ <option value="history">From history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">\n+ <options from_data_table="metaphlan2_database"/>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>\n+ <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>\n+ </when>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t">\n+ <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>\n+ <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>\n+ <option value="reads_map">Mapping from reads to clade'..b'0" label=" Threshold for calling a marker present"/>\n+ </when>\n+ </conditional>\n+ <param argument="--min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>\n+ <param argument="--min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>\n+ <param argument="--ignore_viruses" type=\'boolean\' checked="true" truevalue=\'\' falsevalue=\'--ignore_viruses\' label="Profile viral organisms?"/>\n+ <param argument="--ignore_eukaryotes" type=\'boolean\' checked="true" truevalue=\'\' falsevalue=\'--ignore_eukaryotes\' label="Profile eukaryotic organisms?"/>\n+ <param argument="--ignore_bacteria" type=\'boolean\' checked="true" truevalue=\'\' falsevalue=\'--ignore_bacteria\' label="Profile bacteria organisms?"/>\n+ <param argument="--ignore_archaea" type=\'boolean\' checked="true" truevalue=\'\' falsevalue=\'--ignore_archaea\' label="Profile archea organisms?"/>\n+ <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>\n+ </inputs>\n+\n+ <outputs>\n+ <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />\n+ <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />\n+ <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" />\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="input_file" value="input_sequences.fasta"/>\n+ <param name="db_selector" value="history" />\n+ <param name="mpa_pkl" value="marker_metadata.json" />\n+ <param name="bowtie2db" value="marker_sequences.fasta" />\n+ <param name="analysis_type_select" value="rel_ab" />\n+ <param name="taxonomic_level" value="a" />\n+ <param name="min_cu_len" value="2000" />\n+ <param name="min_alignment_len" value="0" />\n+ <param name="ignore_viruses" value="" />\n+ <param name="ignore_eukaryotes" value="" />\n+ <param name="ignore_bacteria" value="" />\n+ <param name="ignore_archaea" value="" />\n+ <param name="stat_q" value="0.1" />\n+ <output name="output_file" file="community_profile.tabular"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+**What it does**\n+\n+MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.\n+\n+**Inputs**\n+\n+Metaphlan2 takes as input a sequence file in Fasta, FastQ, a SAM file.\n+\n+It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:\n+\n+::\n+\n+ {\n+ "taxonomy": {\n+ "taxonomy of genome1": genome1_length,\n+ "taxonomy of genome2": genome2_length,\n+ ...\n+ }\n+ "markers": {\n+ "marker1_name": {\n+ "clade": the clade that the marker belongs to,\n+ "ext": [list of external genomes where the marker appears],\n+ "len": length of the marker,\n+ "score": score of the marker,\n+ "taxon": the taxon of the marker\n+ }\n+ ...\n+ }\n+ }\n+\n+The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.\n+\n+**Outputs**\n+\n+The main output file is a tab-separated file with the predicted taxon relative abundances.\n+\n+ ]]></help>\n+\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 8c82c4d90cc6 metaphlan2_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan2_macros.xml Sat Mar 04 12:23:45 2017 -0500 |
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| @@ -0,0 +1,40 @@ +<?xml version="1.0"?> +<macros> + <token name="@WRAPPER_VERSION@">2.6.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">metaphlan2</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="" /> + <regex match="ERROR" + source="stderr" + level="fatal" + description="" /> + <regex match="WARNING" + source="stderr" + level="warning" + description="" /> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.3589</citation> + </citations> + </xml> + <xml name="tax_lev"> + <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output"> + <option value="a" selected="true">All taxonomic levels</option> + <option value="k">Kingdoms (Bacteria and Archaea) only</option> + <option value="p">Phyla only</option> + <option value="c">Classes only</option> + <option value="o">Orders only</option> + <option value="f">Families only</option> + <option value="g">Genera only</option> + <option value="s">Species only</option> + </param> + </xml> +</macros> |
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| diff -r 000000000000 -r 8c82c4d90cc6 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat Mar 04 12:23:45 2017 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases."> + <repository changeset_revision="9c4ad82be5bd" name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r 8c82c4d90cc6 test-data/community_profile.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/community_profile.tabular Sat Mar 04 12:23:45 2017 -0500 |
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| @@ -0,0 +1,11 @@ +#SampleID Metaphlan2_Analysis +k__Bacteria 100.0 +k__Bacteria|p__Bacteroidetes 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris 68.05418 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron 31.94582 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris|t__Bacteroides_stercoris_unclassified 68.05418 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified 31.94582 |
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| diff -r 000000000000 -r 8c82c4d90cc6 test-data/formatted_to_krona.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatted_to_krona.tabular Sat Mar 04 12:23:45 2017 -0500 |
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| @@ -0,0 +1,4 @@ +68.05418 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_stercoris +31.94582 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_thetaiotaomicron +68.05418 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_stercoris Bacteroides_stercoris_unclassified +31.94582 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_thetaiotaomicron Bacteroides_thetaiotaomicron_unclassified |
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| diff -r 000000000000 -r 8c82c4d90cc6 test-data/heatmap.pdf |
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| Binary file test-data/heatmap.pdf has changed |
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| diff -r 000000000000 -r 8c82c4d90cc6 test-data/heatmap.png |
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| Binary file test-data/heatmap.png has changed |
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| diff -r 000000000000 -r 8c82c4d90cc6 test-data/heatmap.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmap.svg Sat Mar 04 12:23:45 2017 -0500 |
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| diff -r 000000000000 -r 8c82c4d90cc6 test-data/input_sequences.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_sequences.fasta Sat Mar 04 12:23:45 2017 -0500 |
| b |
| b'@@ -0,0 +1,2260 @@\n+>r2|637000026.fna|5753889|5754040|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln383_#0/1\n+CTCCGTCCGCTGGTAGAACGTCTGGTAGAAGCTCAAAAAGCATTGGCAACCAAATACCTTTCCGAAGCCAAACGACTGATTGCCTCCAACGACAAGAAGGAAGTGGAAGAAGGATTCCTTGCCCTTTATCGTAGCCACAAGTGTCTTCCGA\n+>r3|637000026.fna|1749333|1749484|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln165_#0/1\n+AAGTAAAAGTCTACACACAGGAAGGAACGATAATGGAAAGTACGATTGAAGTAAATCGTCCGATGGAGATAGCAGGATGGAAAATTTATCAGCTTAGTTATGATGAGTCGAAAGGTCGCTGGAGCGATATCAGTGTCTTTGAGCTGGTTCG\n+>r8|637000026.fna|2991814|2991965|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln402_#0/1\n+AGAAAGTTTTGATCAAAGCATGGGATGCTGAAAACGGACCGGTAATTATCGACTCAGGAGAAAGTACCTACAACACAACCGCCAAAAAGTTCAGCCTCAAATATACGATCGGTAACACGCTATATGAAGAGCAACTGACCAAAGAAAAAGA\n+>r24|641736196.fna|214158|214309|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln388_#0/1\n+CAGATACGAGTACCAATTGGCCGTCAACGACTATTGGAAGGAAGTCGGCGGATTGCAGATGCTGCCCGGAACCAACCGCTCCAGCGACCGCTTTGTACGCGCGTCATTCTACATTCATGCCATTCCGCAGACAGCAGACGCGGCGATTGCA\n+>r32|637000026.fna|4140951|4141102|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln422_#0/1\n+TATTCTCAGGGGACTAATTGGTGATATAGTGCTCGATTATGATAGAGGTGAAGGAATTATGTCCTTTAAGACTCAAAAGGTAGGTTATATATCAGGATATTATTTGGGATGTACTACATATTGTTATGCCATGGGATTTTATCCTACATAT\n+>r55|637000026.fna|6212867|6213018|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln342_#0/1\n+CAGGCGTCGGGTGAGCTGGACTTTGAAGAGTTGTGCGAAGCGATCACCAGTCGTTCTACTTGTACGGAAACGGATGTACGTGCGGCTATTTCGGGTATTCTTTACGAAGTGAAGCGTGCGTTGAAGGCAGGAAGAATTGCGAGACTGGGTG\n+>r94|641736196.fna|124792|124943|_from_ |NZ_ABFZ02000020_Bacteroides_stercoris_ATCC_43183,|_ln396_#0/1\n+AATCAGTTTCATACGCTATCAATATCCGGGGTCAATAGTTTCCATTTGTTGCTCGCTTGACACGCTTTCAAAGCTAACATCTTCCGCATCAATCAACTGTTTGTTTGCGTAATTGTCGGTCAATATTTCACGCTGTGAAGTTTCGTCACCC\n+>r115|641736196.fna|175677|175828|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln360_#0/1\n+CTGTCAGATACGTGAAAGATTACATTCGATACGTGAGTATGTAATGAAATATCCTGAGTTTGACGATAGAAACGATATTGACCCGTCAATGCGAATGTTCTATATCCAGTCTGTTGAAGCACAAGCAAAAAATCGAAGTTATTCAGATGCA\n+>r121|641736196.fna|7934|8085|_from_ |NZ_ABFZ02000017_Bacteroides_stercoris_ATCC_43183,|_ln383_#0/1\n+TGAGCGGTTCGGTCTATACCCTTATGAATAAAATCTTCAGGGATTCAAAAGAACCGCTGTATGGCCGTGCTGACAATATCATGAAGTTAGCTCCTTTTACTACTTCCGTATTGAAAGAAATCATATCGGATCATAAGGCCGACTATACTAA\n+>r145|637000026.fna|1378791|1378942|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln396_#0/1\n+TCCGTCTGATTCGTAGTGTACCAGCATATCCGCCATGACATCGCTCACTGTAGCGCTGAAATCTTTCAGAAGTTTATGGCTGCCCACCCAGTAAGTCTTGCCTTGATAAGACACCTTTATACCTTTGCCTGTGATGCTCTCAAAACTGCTC\n+>r158|637000026.fna|3242194|3242345|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln388_#0/1\n+GGACAGCAGTATCAAACGGTTAAAATACGTGAGATACGCAGATGACTTTCTGATTGGAATTACCGGTAATCTTGAAGACTGCAAAACAGTAAAAGAGGATATTAAGAATTATTTGAATGAAGCTCTTAAACTGGAACTGTCAGACGAAAAG\n+>r160|637000026.fna|3948359|3948510|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln347_#0/1\n+CGGAAGTGACTCATACATATCAGGTGGTTCTTCCAGTTATAAGAACCTGTCTGCAAGTGAAATGAAGAACACATCTTCATTCACAAACTGGAATTTCAGTACGGTTTGGGAAATGGGAAGTGAATACCCGACATTACAGGGCTTATTAAAA\n+>r187|637000026.fna|5220534|5220685|_from_ 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|NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln407_#0/1\n+GAATGTTTTTCCATGAATATTTATGTTTTCTGACCGGGAGTCTTTCATGGAATTAATCAATAAATCATACATATGTTCCATTGCTCCCTTAGAAGGAGCTTTGATGTAGCTAACGGTTAAACTGCTGACACCATGTCCTCGAAGTTGCAAT\n+>r12072|637000026.fna|2532372|2532523|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln392_#0/1\n+GGCTCCGGGATTGATGTGCAGCATGTCCAACGTTTTGTCGTATTTCACCTTTAATATATGGGAGTGTCCGCTGATGAAAAGTTTCGGCGGACGGGCCATCAAACTGCCGATAACCGAAGGGTCGTACTTGCCCGGATACCCGCCGATATGC\n+>r12073|637000026.fna|6194446|6194597|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln420_#0/1\n+CTGAATATTATAGTCATATCCCTTCACCGGTTCTTCCAGCTCTTTGAATATCACAAAGGCGCGTTGCCCGTCTTTATTCTTGTCACTGATCCATCCGTTTCCATTGCTCGGGAACATTGTTTTTCCATCATCCAGAGTGAAATAGAAATCC\n+>r12077|641736196.fna|245225|245376|_from_ 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|NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln262_#0/1\n+ACGGGCTTCTTCGCCAATGCTCTTCCCATAAAGATAAGACATTTCGGGATTCCATGTTGCAGAAAGGCAAGTCAATGCAGGATAGGCTATACAGGAATCGTTTGTCCATCCTGCCTGATCCCACTCATCCCATAATACTTCGGGACGGATG\n+>r12152|637000026.fna|2685134|2685285|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln353_#0/1\n+CACTCAAATCATCAATCAAGCTGACTTTCTTTAATGTATCCTTCTTAGCATCATAATATTTCATCTCCAGATTATTAGCAATCGAGAAACTAACCGTTCCCGAACCCTCACGTGAAGGGACTCCAAAAGGCTGTCCCGTATAGGGTGAATA\n+>r12163|637000026.fna|5651468|5651619|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln367_#0/1\n+AATGAACAACACCATTAAAAACGGTTGGCTATTCGACTGTGATGATGAGAGCTTCGAGCAAGTAAGCAAGCGCATTGAAGATGCTGTATATGTATATAATCATGTGCGGCCTCATCAAGGGATAAACATGAGGACACCTATGGAAGTGGTC\n+>r12201|641736196.fna|253613|253764|_from_ |NZ_ABFZ02000023_Bacteroides_stercoris_ATCC_43183,|_ln348_#0/1\n+CCACTCCGGAAGGTATTATTGGCAATGAAGACTGCGGGCAGATGTCGGCATGGTATATTCTTTCAAGTATGGGACTTTATTCGGTTTGTCCTGGTAGCAACGAATATGTTCTTACTACTCCCTTGTTCGAGAAAGTTGTAGTGCATTTGGC\n+>r12208|637000026.fna|1887139|1887290|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln435_#0/1\n+ACATCGCGGTTGCTTTTCGCTACCCGTACCTTTCCGCGTCTCTTTCCCCAGTCCAGAATCGGAATCTGAACGCCTACCTGCACAATCTGATTATCCTGCAAGTTCCTGTAGACACTGGAAAGTTCACGACTCTCTCCCGTATATCCTACAC\n+>r12218|641736196.fna|422226|422377|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln296_#0/1\n+GTCCAATTGCGCACGTGCCAGCCGGGTGGCATTAACCAGTTTTGTACCGTTGAAGAGTGTCCAACTGAGGCTTGGCGCTATTTCAAACGTCATACTGTTCCGTTTGGTGAAATCTTTCAGGTCATGGGAAGAATATCCTACGGAACCTTTT\n+>r12223|637000026.fna|4646221|4646372|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln436_#0/1\n+CGGTACTGCTTTTAGAAAGGAACGGATACGGGGTTGAGTCCATTTCTTTTTGTCATAGAAGAACATCCAGGTCATTTGTAACCATTGGGCTGCTGAGTCTACCTGATGAATCGACTCGTAAATCTTGCTTGAAACATTGGCTAAAAAATCC\n+>r12228|641736196.fna|168782|168933|_from_ |NZ_ABFZ02000023_Bacteroides_stercoris_ATCC_43183,|_ln401_#0/1\n+GGTCTCTACCATTTCCGAAATGTTACCTTTCTCTACACGGAACATTTTATAATCACTGCCCACCTTATGCAGAATACGATCCAAATGTTCACGATTGGTATCTGTTATAAAGATCTGTCCAAAGTTATCACCTGCCACCAGTTTAATTATC\n+>r12236|637000026.fna|5656063|5656214|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln344_#0/1\n+TTCAGTGAGACAGATGTGCGGACCATGTTTCAGTACTATAAAGACGCCGGACAACTGCCGGCAGATACAGACATAGATGCACTGATTCGGGAAATAAAACCGTGGTATGACAATTATTGCTTTGCCAAAGAAAGTCTGGAACGTGATCCGA\n' |
| b |
| diff -r 000000000000 -r 8c82c4d90cc6 test-data/marker_metadata.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/marker_metadata.json Sat Mar 04 12:23:45 2017 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"taxonomy": {"k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Micromonosporaceae|g__Salinispora|s__Salinispora_pacifica|t__GCF_000374725": 5438612, "k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Mononegavirales|f__Rhabdoviridae|g__Nucleorhabdovirus|s__Maize_mosaic_virus|t__PRJNA14920": 12133, "k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae|g__Halorubrum|s__Halorubrum_sp_T3|t__GCF_000296615": 3168011, "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes|t__GCF_000145075": 2614131, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__GCF_000485655": 5022965, "k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia_trachomatis|t__GCF_000304515": 1042736, "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Leuconostocaceae|g__Weissella|s__Weissella_koreensis|t__GCF_000277645": 1728940, "k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Leptospiraceae|g__Leptospira|s__Leptospira_interrogans|t__GCF_000244635": 4459519, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Buchnera|s__Buchnera_aphidicola|t__GCF_000007365": 641454, "k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_sp|t__GCF_000209835": 3545606, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii|t__GCF_000302035": 3973165, "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mitis_oralis_pneumoniae|t__GCF_000495335": 2144825, 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"k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Caudovirales|f__Siphoviridae|g__Siphoviridae_noname|s__Bacillus_phage_Fah|t__PRJNA16382": 37974, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_johnsonii|t__GCF_000162055": 3690010, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella_pneumoniae|t__GCF_000409125": 5671251, "k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Viruses_noname|f__Viruses_noname|g__Viruses_noname|s__Geobacillus_virus_E2|t__PRJNA19797": 40863, "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinobacteria_noname|f__Actinobacteria_noname|g__Actinobacteria_noname|s__actinobacterium_SCGC_AAA278_O22|t__GCF_000372185": 1138490, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas_sp_BSi20429|t__GCF_000238895": 4495777, "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae|t__GCF_000427035": 2138694, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__P'..b'teria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|514974163|ref|NZ_KE340313.1|:332123-333478": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 1356, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|384096987|ref|NZ_JH636042.1|:382588-383040": {"ext": ["GCF_000162515", "GCF_000159875"], "score": 2.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 453, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|514974745|ref|NZ_KE340318.1|:c38550-38392": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 159, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|512436172|ref|NZ_KE159460.1|:c349752-348871": {"ext": ["GCF_000159875"], "score": 1.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 882, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|514974549|ref|NZ_KE340315.1|:c186066-185032": {"ext": ["GCF_000374365"], "score": 1.0, "clade": "s__Bacteroides_stercoris", "len": 1035, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|384096980|ref|NZ_JH636035.1|:50682-52622": {"ext": ["GCF_000159875"], "score": 1.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 1941, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|223955876|ref|NZ_DS499677.1|:c358511-356622": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 1890, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|223955871|ref|NZ_DS499672.1|:29963-30130": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 168, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|514973000|ref|NZ_KE340309.1|:c227121-226093": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 1029, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|512436172|ref|NZ_KE159460.1|:c266283-265069": {"ext": ["GCF_000159875"], "score": 1.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 1215, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|298384780|ref|NZ_GG774704.1|:496496-497020": {"ext": ["GCF_000162515", "GCF_000159875"], "score": 2.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 525, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|223955871|ref|NZ_DS499672.1|:193538-194158": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 621, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|298385318|ref|NZ_GG774705.1|:324177-324773": {"ext": ["GCF_000162515", "GCF_000159875"], "score": 2.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 597, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|223955873|ref|NZ_DS499674.1|:c270435-267715": {"ext": ["GCF_000243215"], "score": 1.0, "clade": "s__Bacteroides_stercoris", "len": 2721, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}}}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 8c82c4d90cc6 test-data/marker_sequences.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/marker_sequences.fasta Sat Mar 04 12:23:45 2017 -0500 |
| b |
| b'@@ -0,0 +1,7704 @@\n+>gi|223955874|ref|NZ_DS499675.1|:82124-83086\n+ATGAAAAAATCGATACTGTTAATGGGCCTTGCAGCTCTCATAGCAAGCTGTTCGGACGAT\n+GACCGGAACAACGATACTGATAATCAGCATCTTGTCAGTCCCTCAATGGCTGTGAGCATC\n+AGCAACACCGACGGCCGCCAAAGCCCGTTTACCGGCATTCTTACAATTATGCCATGCGAT\n+GCAAACAGTTCCATATACTATGGAAATTATGTAAAAGGGAAACTGTCTCCTTTCTACGGC\n+TATTACCGGGTAAAGGACGGAAGTTTCCATGACAATTCCATCAATAGGGAGATTTCTCTG\n+CCGATAGGCACTTACAATATGATTTATTGGGGAACACCCCAATACCAAACTCCCATTTAT\n+GCCCACCCTGCCATAAAAGAGGCGGCTCACAGCATAGGTGCCGATATGTCCAAACAGTCT\n+CTCGGCTTGTTCAGAATATCAGCCGATACCATTTACTATCCCGTATTCGACCTGGTGTAC\n+GCCACACAGCCGGTAAACATCGGAAGCGAAAGCCTCAGTGGCTCTTTAAAACGAGTGGTA\n+GCCGGAATAAAGGTTGTCCTGAAGGACAAAGACAATGCCGTACTAAGTTCCAGTATAGAC\n+AGTGTGTCCGTACGCATCACCAACATTTACAGCGAACTCAACTATTATACGGGAAAACCG\n+CAAGGTACACCACGTACAATCGCGTTCCCTCTGATTCGTTCGAACGATGGTACTCAGATG\n+AGCAACAGCACCGTTATGCTGTTCCCGTCCGCCGGAAAACCGGAATTCCAACTAGCAATC\n+ATTCTTAAAAACGGTAATGTGAAAAGCTTCAGACAAGCATTGAGCAGCCCGCTCGATGCC\n+AATGCCAAACTGACATTAACGTTAAGTCTGGGTGATATTTTCTCTGAAGAATCCTCCGGT\n+GACTTTACCATCGATGACTGGAACGAGAAAAACGAGAATATTGATATACCGATAATAGAG\n+TAG\n+>gi|29345410|ref|NC_004663.1|:2392014-2392814\n+ATGAAAATTACAATTATAGGAGCCGGAAACATAGGGAGCGCAGTTGCTGCCTGTCTGGCA\n+AAAGGACATCTCTACAACGAAAAAGATATTATCATTTCTACCCCTCATACAGACAAGCTA\n+GAAAATCTGCACAAACAATTTCCTGCGATACGCATAATGACAGAGAATCAGTATGCCATA\n+TCGGAAGCCGACATTATTATTCTGGCTGTCAAACCATGTATAGTAGACGAAGTATTATCT\n+CCGTTACGATTCTCACGCACCCAAATCCTGGTTTCACTGGTAACCGGAATATCCATTTCT\n+CACCTGGCACATTTATCGGAAACCGAAATGCCTATATTCCGGGTTGTTCCAAACATCGCC\n+ATTACGGAACATTCGAGCCTGACCCTGATAACTTCACGCAAAGCCGGCAAAGAACACCAG\n+CAACTCATAAAACAGACATTTGAAGAAGGAGGAAAGTGTTTGTTCGCAGAAGAGAAACAG\n+CTGGATATCATTTCTGCATTAACTTCCAGTGGAATCGCTTTCGCATTAAAATATATTCAT\n+GCAGCCATGCAAGCCGGCATAGAATTGGGTATCTCCGCTGAAGATGCAATGCGAATGACG\n+GCATATAGCATGGAAGGAGCTACAGAACTGATTTTAAATCACGACACCCACCCGCTGTTA\n+GAAATAGAAAAAGCAGCTACTCCCGGTGGAGCCACCATTAAAGGATTGAATGAACTGGAG\n+CACAGGGGATTTACTTCCGCCGTTATTCATGCCATAAAAAGTAGCGCCACAGTATCGACC\n+GATAAAGAGACTGAAGAATAG\n+>gi|298385318|ref|NZ_GG774705.1|:275923-276495\n+ATGATAAATTCAATTAATATACAAATCAGAGAGACCAATACAGATGATTTCGACAGCATA\n+ATGACTGTTGAAAAACAAGCGTTTGGCTATGACAAAGAAGCACAGTTGGTAGCCGATCTG\n+CTGGCTGACAAAACTGCAAAACCAATGGTTTCGTTGCTCGCTTTCTACAAAGGTGAGGCT\n+GTCGGACACATTCTCTTCACCAGAGCCTATTTTGATGGTCAGGGAGCACAACAGATGATG\n+CACATTCTTGCACCTTTAGCTGTCAAGCCGGAATATCAACGGCAGGGTATAGGCGGAATG\n+CTGATACGGGCAGGTATAGAGAGGTTGCAGGAAAAAGGTTCGTGCCTTGTGTTTGTATTG\n+GGGCATAAAGAATATTATCCAAAATATGGTTTTATACCGGATGCAGCCAGGCTGGGTTAT\n+CCTGCTCCTTACCCGATACTGGAACAGTTCTCGGATTATTGGATGGTTCAGGCAATCAGT\n+CCGAAGGGATTTGATGTGGATAAAGGAAAGATCAGGTGTTCGGATGAGTTGAACAAACCT\n+GAACATTGGAGAGATGATGAATCGGACAGATAG\n+>gi|514973850|ref|NZ_KE340312.1|:c10221-7987\n+ATGAAACATTTGTCTGTTATTATATCTGTATTATTTTCAATACTTTGTATCGGATGCTCT\n+AAGGAGGATTTTAACGATGGAAAAACCAATGATGTTCAGAACAAGCATTCTCTCCGGCTT\n+TTGGTCTACACACCGACTTCAGAAACTGTTCTTAGTACGGACCTGCCGGGAAACATAGAG\n+GCTTATCTGTTCAAAGAGGGAGTTCTGTCCGACGTTTACAAAAATCTGACAGTGGATAAG\n+AACGGATACACTACAATCAGCTCGTTAGCCGAAGGAGAGCAAATCTATTTCTTTGTAAAC\n+ACCGGTAATCTGCTGGATGGGATTACACAGGAAATAGGCCGATTGAAAGAGAACGAACTG\n+CTTGCCACTACAATACTCTCTGCCTCTCCTCAAGCAGATGGAGAGAAACCGGTGATGACC\n+GGAAAGGCAGACTTAACCGGAAGCCAGGAGAGTACCACCCAAGTATTGCTTACACGGGCC\n+ATTGCCAGAGTAGACTTAAACATAGCTGACGATGCCGACATACAAATCAATAGGATAAGT\n+ATGGATAACATACATTGTGAAGCATTCCTGCTTCCGCAAAATCCGGTCAGTTCGCCGTCC\n+GGTGCAGCATTGGCAAAAATAGACACTACATTCAATACCCCGTTGAAGCCGGGTGAATAT\n+GCCGGATTGGTCCACCTGTATGAACAAGTGGGGGACGGTATTCCTGTGGAGCTGCATGGC\n+ACCCTTGAAGGCGATCCTGTCACACTTTCACTGGCACTGCCTAACACAATCCATAGAAAC\n+CACATTTATAAAATAAAGTTATTTAGCGGAGACAGTTCTAATTTGCAGGCAAGCATATCC\n+GTGGAAAATGAAAGTTGGGAAGTCGAAGAAACTATCACGGCAAAACCTTCTACCAATATT\n+CTGGTTAATAGTGAACTTTCTACTTTGGCTGAAGGGGCGTATATAAGTGCAACAAAAGAT\n+ACGGTTTACCTCCCAAGCAAGGAGTCAACGTCAATACTTGTATTGGATAAGGTGCCGGAA\n+GATGCGGAATTCACAATTGATGGGACAACAGCCTCCATTACTCCGTATACGGAAACTCGT\n+GCCGACCTTCAAGGGAAAAAGTTCTTGGTACGCAATTCTTGGAAAAAGCCGGGTACTAAG\n+ACGGAATATATGTACCTGAATATGCACAGCAAGAGGCACCCGGACTACTACAGTGGCCGG\n+TTGGTAATTGTTCAGTCCAATGCAACGACCTTCAAGGGAGAATTGTATAATCATCTTACA\n+AACACTCCTCCCTATAACATTCATTTCAATAAATATGTCGACAGTGCTTTAGGCCAGATA\n+GAGGTACCT'..b'CGCTTTTCCTATAGGGGGAATTGGTGCAGGTATGTATTGT\n+CTGGAAGGAACAGGCTATATATCTCATATGTCAGTATGGCATCGACCGGAAGTTTTTCAT\n+GAACCGGGAATGTTTGCTGCTCTGTATGTGAAGGGGGTATGTAATGGGGCTAAGGTACTT\n+GAAGGACCTGTATCTGATTGGAGAAAATTTGGAATGCCCAATTACGGTACAGGAGGCAGT\n+ATGGGATCAATATTAGGACTTCCCCGTTTTGATACGGTTGAATTTGAAGCACGTTTTCCG\n+TTTGCCAAAGTTTCATTAACAGATAAAGATATCCCCGTTAAGGTAACCATTTTGGGGTGG\n+AGTCCTTTTATTCCGGGTGATCCGGATAATTCCAGTTTACCGGTAGGAGGATTGGAATAT\n+AGTTTAGAGAATACTAGCAAAGAGGTTCAGGAAACTATTTTCTCCTACCATGCTCGTAAC\n+TTTCTGAGTTCGGGTAAAGGATTGGATGCTATAAAAACGATGCCTCATGGGTTTATCCTT\n+TCACAGTCAGGTACAGAAACGGAGCCTCATTTGCAGGGTGATTTTGCTATCTTTACGGAT\n+CAGGATTCTTTAAAGATCAATTATTGTTGGTTTCGTGGAGGATGGTTTGATAGTCTTACG\n+ATGGTTTGGAACGCTATTGAGACAGGTTTAATGCCACAATCTCCAGCAATAGAGAAAGGT\n+GCACCAGGAGCTTCTATGTTTGTCCCGGTAACATTGATGCCAGGGGAAAAGAAAACAATC\n+AGAATTTATACGGCGTGGTATGTTCCTAACTCGACTTTAAGGCTTGGAAAGGAACCGGAA\n+GACTGGAATGACAATAATGTCGACTCCGCAAGACTAGCTGTAGAAAAGGCAGATAAGGGT\n+AATTATAAACCTTGGTATAGTAGCCGCTTTACAGGAGTGAATGAGGTTATTGATTATTTT\n+CTGTCTCATTATAAGATTTTGCGCAATCAGACGGAAAGGTTCACAGACTCTTTTTATCGT\n+TCTACCTTACCGCCTGAAGTGATTGAAGCTGTTTCTGCTAACTTAAGTATTTTAAAGTCT\n+CCAACGGTGATGCGGCAATATGATGGACGCTTATGGACTTGGGAAGGATGTGCCGATAAT\n+TGGGGCTCGTGTCATGGCTCATGTACTCATGTCTGGAATTATGCACAAGCTATTCCACAC\n+TTATTTCCTTCCTTGGAACGTTCGTTAAGGCATACTGAATTTGAAGAAGGGCAAGATTTG\n+AAAGGCCATCAAGTGTTTCGTGCCAATTTACCGATTCGTCCTACTCGGCACGACTTTCAC\n+TCAGCTGCTGACGGGCAATTGGGAGGTATAATGAAAGTATATCGTGAGTGGCGAATTTCA\n+GGCGATAATGAGTTCCTTATCTCTATGTATCCAAAAGTAAAAAAGAGTTTGGACTACTGT\n+ATCTCAACTTGGGATCCTCGTAGGGTAGGAAGTATTGAAGAACCACACCATAATACTTAT\n+GATATTGAGTTCTGGGGGCCGGATGGTATGCATAATAGTTTCTATTATGGAGCTTTATCA\n+GCTTTCATTCGTATGAGTGAGTTTCTTGATAAAGACGTTACTGAATATAAGAAACTATTG\n+AAAAAAGGACGAAAATTTACTGAAACAGGCTTGTTTAATGGTGAGTATTTTATCCAAAAG\n+ATAGAGTGGAGGGGATTGAATGCAAAAGATCCGACTGTTGCACAAAGTTTCCATAGTTCT\n+TATTCTCCCGAAGCGAAAGAAATACTGGAGAAGGAAGGTCCTAAATATCAGTATGGGAAC\n+GGTTGTCTGTCTGATGGAGTTTTGGGGTCGTGGCTCTCCCGAATGTGTGGGATGGAAGAA\n+ACTCTGAATACAGAAAAAGTGAAAAGCCATTTATTATCAGTACATCGATATAATTTTAAA\n+AAAGATCTGACTGATCACGCCAATCCTCAACGTTCCCCTTACGCTTTAGGCAAAGAAGGA\n+GGCTTATTATTAGGAAGTTGGCCTAAAGGGAGCAAGTTGTCATTGCCTTTTGTCTATAGT\n+AATGAAGTCTGGACAGGAATAGAATATCAAGTAGCTTCACATTTGATGCTACAGGGAGAG\n+GTAGAAAAAGGCCTTGAGATCGTGCGTGCCTGTAGACAACGTTATGATGGAAGTGTCCGT\n+AACCCTTTTAATGAGTATGAGTGTGGACATTGGTACGGACGAGCGTTATCTAGTTATGGC\n+TTACTTCAAGGATTGACAGGAGTCCGATATGATGCTGTAGATAAAACACTGTATATTAAT\n+TCAAAAATAGGAGACTTTATTAGCTTTATCAGTACGGAGTCTGGATTTGGTAATGTAGAA\n+CTTCGTTCCGGAAAACCTTTTGTAAAAGTAGTATCCGGTCATATAGAGGTCGACAGATTT\n+ATCGTATCAGGGAAAGTAGTTGAATAA\n+>gi|298386634|ref|NZ_GG774708.1|:c143839-142661\n+ATGGAGCAAAAGAAAATCGTGCTATTCATCCTGATCATTCATCTGGCAGCATTTCTAGCA\n+GGATGCAGCGGAAACAAAAATAGCGGAAATAATGACTCCTCTGATCTATGGAATAAGTTA\n+TCGAGCTACTTCCGCACGCCCGCAGAATACGAAAATGTATATGGGAATTTTCGCTCTCCT\n+TTATTATATTATAATGGGGATACAGTCAGAACCGTTGAAGACTGGCAAAGACGACGAACT\n+GAAATCAAGGACAGATGGATGAGCCTGTTAGGACAATGGCCGCCTGTCATTACCGGACAA\n+ACATTTGAAATTCTGGATACTCTCCACCGTGAAAACTTCATGCAATACCGTGTCCGCTTC\n+TACTGGACTCCCAACGAACAGACTGAAGGTTATTTGCTGGTTCCGGACAAAGAAGGCAAA\n+AAGCCTGCCGTTATCACTACCTTTTATGAACCCGAAACGGCTATCGGATTGGGTGGAAAA\n+CCTTATAGAGACTTTGCATATCAATTGACGAAAAGAGGATTTGTCACATTATCAATAGGA\n+ACAACGAAGACCACAGAGAATCAGACATATTCCATTTATTACCCCAGCATTGAAAATGCA\n+ACTCTCCAACCACTTTCAGCATTAGCTTATGCAGCCGCAAATGCATGGGAAGTATTAGCC\n+AAAGTACAGGACGTCGATTCTACAAGAATAGGCATCACAGGGCATTCTTATGGTGGGAAG\n+TGGGCAATGTTTGCCTCATGCCTATACGAAAAGTTCGCTTGTGCGGCATGGGGAGACCCC\n+GGAATTGTATTCGACGAAACAAAAGAGGGATATATCAATTACTGGGAACCCTGGTATTTG\n+GGATATTATCCGCCACCATGGGAAAATACATGGAGTAAAAATGGGCATGATTATGCTAAA\n+GGCATTTATCCGAAGCTCCGCAAAGAAGGATATGATTTGCATGAATTGCATGCGCTGATG\n+GCACCTCGCCCATTTCTTGTTTCCGGAGGATACTCTGACGGAACAGACCGGTGGATAGCG\n+CTAAACCATACAATAGCGGTCAACCGGCTCTTAGGATACCGCAATAATGTCGCGATGAGC\n+AACAGAGTCAATCATGACCCAACCCCTGAATCAAACGAAATTATATATGATTTTTTTAAA\n+TGGTACTTGCATTCAGCAAATAAATCTACCAAAGAGTAG\n+>gi|223955875|ref|NZ_DS499676.1|:c386522-386337\n+TTGGCTTTTAGTTCTGTCCAGTTTTCTTATATTTTTGTAGAAAAAGTATGGGACAGGTAT\n+ATAAAAACAGCCTGGGTTTACGTATTCAACGTAATCCCAGGCTGTTTTTACGGGTATTTG\n+CGGGGGCTTGTTTACCGATTGTTTTTTATTCCGCCAAAGTCGCCCTTCTACTTCAGTCCG\n+AAATAA\n' |
| b |
| diff -r 000000000000 -r 8c82c4d90cc6 test-data/merged_community_profile.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged_community_profile.tabular Sat Mar 04 12:23:45 2017 -0500 |
| b |
| @@ -0,0 +1,11 @@ +ID community_profile community_profile +k__Bacteria 100.0 100.0 +k__Bacteria|p__Bacteroidetes 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris 68.05418 68.05418 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris|t__Bacteroides_stercoris_unclassified 68.05418 68.05418 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron 31.94582 31.94582 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified 31.94582 31.94582 |
| b |
| diff -r 000000000000 -r 8c82c4d90cc6 tool-data/metaphlan2_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan2_database.loc.sample Sat Mar 04 12:23:45 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file |
| b |
| diff -r 000000000000 -r 8c82c4d90cc6 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Mar 04 12:23:45 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="metaphlan2_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/metaphlan2_database.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 8c82c4d90cc6 transform_json_to_pkl.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transform_json_to_pkl.py Sat Mar 04 12:23:45 2017 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import argparse +import bz2 +import cPickle as pickle +import json + + +def transform_json_to_pkl(args): + with open(args.json_input, 'r') as json_file: + json_str = json_file.read() + metadata = json.loads(json_str) + + for marker in metadata["markers"]: + a_set = set(metadata["markers"][marker]["ext"]) + metadata["markers"][marker]["ext"] = a_set + + pkl_output = bz2.BZ2File(args.pkl_output, 'w') + pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL) + pkl_output.close() + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--json_input', required=True) + parser.add_argument('--pkl_output', required=True) + args = parser.parse_args() + + transform_json_to_pkl(args) |
