| Next changeset 1:a09398bc953a (2023-07-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73 |
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added:
freyja_boot.xml macros.xml test-data/NC_045512_Hu-1.fasta test-data/abundances.tsv test-data/abundances2.tsv test-data/abundances3.tsv test-data/abundances4.tsv test-data/bunch_of_files.tsv test-data/csv_sample_meta.csv test-data/csv_sample_meta2.csv test-data/depths.tsv test-data/test.bam test-data/test.vcf test-data/times_metadata.csv test-data/variants.tsv |
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| diff -r 000000000000 -r dda5772507b2 freyja_boot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/freyja_boot.xml Thu Jul 28 09:25:33 2022 +0000 |
| [ |
| @@ -0,0 +1,122 @@ +<tool id="freyja_boot" name="Freyja: Bootstrapping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + profile="@PROFILE@"> + <description> + method + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="biotools"/> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ +@RUN_FREYJA_UPDATE_COMMAND@ +@PREPROCESS_VCF_INPUT@ +freyja boot + @STANDARD_INPUT_FOR_BOOT@ + --nt \${GALAXY_SLOTS:-4} + #if $nb + --nb $nb + #end if + --output_base 'boot_output' + @CUSTOM_BARCODES_COMMAND@ + $boxplot_pdf + ]]></command> + <inputs> + <param name="variants_file" type="data" format="tabular" label="Variants file"/> + <expand macro="demixing_common_options"/> + <param argument="--nb" type="integer" optional="true" label="Number of bootstraps"/> + <param name="boxplot_pdf" argument="--boxplot pdf" type="boolean" truevalue="--boxplot pdf" + falsevalue="" + checked="false" label="Generate boxplot"/> + </inputs> + <outputs> + <data name="boot_lineages" format="csv" label="${tool.name} on ${on_string}: Lineages" + from_work_dir="boot_output_lineages.csv"/> + <data name="boot_summarized" format="csv" label="${tool.name} on ${on_string}: Summarized" + from_work_dir="boot_output_summarized.csv"> + </data> + <data name="boot_lineages_plot" format="pdf" + label="${tool.name} on ${on_string}: Lineages boxplot" + from_work_dir="boot_output_lineages.pdf"> + <filter>boxplot_pdf</filter> + </data> + <data name="boot_summarized_plot" format="pdf" + label="${tool.name} on ${on_string}: Summarized boxplot" + from_work_dir="boot_output_summarized.pdf"> + <filter>boxplot_pdf</filter> + </data> + </outputs> + <tests> + <!-- Test 01: test tsv input files and plots --> + <test expect_num_outputs="4"> + <conditional name="usher_update_option"> + <param name="choice" value="repo"/> + </conditional> + <param name="variants_file" value="variants.tsv"/> + <param name="depth_file" value="depths.tsv"/> + <param name="confirmedonly" value="false"/> + <param name="nb" value="10"/> + <param name="boxplot_pdf" value="true"/> + <output name="boot_lineages" ftype="csv"> + <assert_contents> + <has_text text="B.1.617.2"/> + </assert_contents> + </output> + <output name="boot_summarized" ftype="csv"> + <assert_contents> + <has_text text="Delta"/> + </assert_contents> + </output> + <output name="boot_lineages_plot" ftype="pdf"> + <assert_contents> + <has_text text="Matplotlib"/> + </assert_contents> + </output> + <output name="boot_summarized_plot" ftype="pdf"> + <assert_contents> + <has_text text="Matplotlib"/> + </assert_contents> + </output> + </test> + <!-- Test 02: test VCF input file --> + <test expect_num_outputs="2"> + <conditional name="usher_update_option"> + <param name="choice" value="repo"/> + </conditional> + <param name="variants_file" value="test.vcf"/> + <param name="depth_file" value="depths.tsv"/> + <param name="confirmedonly" value="false"/> + <param name="nb" value="10"/> + <param name="boxplot_pdf" value="false"/> + <output name="boot_lineages" ftype="csv"> + <assert_contents> + <has_text text="B.1.617.2"/> + </assert_contents> + </output> + <output name="boot_summarized" ftype="csv"> + <assert_contents> + <has_text text="Delta"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +Information about **freyja boot** method +======================================== + +A fast bootstrapping method for freyja. + +Outputs +======= + +Bootstrapping method results: + +1. Bootstrap lineages: the 0.025, 0.05,0.25,0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage; +2. Bootstrap summarized: WHO designated VOI/VOC + + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r dda5772507b2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 28 09:25:33 2022 +0000 |
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| @@ -0,0 +1,151 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.3.8</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">freyja</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">freyja</requirement> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command>freyja --version</version_command> + </xml> + <token name="@RUN_FREYJA_UPDATE_COMMAND@"><![CDATA[ +#if $usher_update_option.choice == 'update' + freyja update && +#end if +]]></token> + <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[ +ln -s '$variants_file' 'variants_file.vcf' && +]]></token> + <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[ +#if $variants_file.ext == 'vcf' + 'variants_file.vcf' +#else + '$variants_file' +#end if +'$depth_file' +#if $eps + --eps '${eps}' +#end if +#if $meta + --meta '${meta}' +#end if +$confirmedonly +]]></token> + <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[ +#if $usher_update_option.choice == 'custom' + --barcodes '${usher_update_option.usher_barcodes}' +#end if +]]></token> + <token name="@DASH_COMMAND@"><![CDATA[ +echo '${plot_format.plot_title}' > plot_title.txt && +echo '${plot_format.plot_intro}' > plot_intro.txt && +freyja dash + #if $need_aggregation.choice == 'no' + '$tsv_aggregated' + #else + 'aggregated.tsv' + #end if + '$plot_format.csv_meta' + plot_title.txt + plot_intro.txt + --output abundances_dashboard.html +]]></token> + <token name="@PLOT_COMMAND@"><![CDATA[ +freyja plot + #if $need_aggregation.choice == 'no' + '$tsv_aggregated' + #else + 'aggregated.tsv' + #end if + --output abundances_plot.pdf + #if $plot_format.csv_meta + --times '${plot_format.csv_meta}' + #end if + #if $plot_format.interval == 'MS' + --interval MS + #else + --interval D + --windowsize 70 + #end if +]]></token> + <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[ +#if $plot_format.choice == 'dash' + @DASH_COMMAND@ +#else if $plot_format.choice == 'plot' + freyja plot + #if $need_aggregation.choice == 'no' + $tsv_aggregated + #else + aggregated.tsv + #end if + --output abundances_plot.pdf + #if $plot_format.need_metadata.choice == 'yes' + --times '${plot_format.need_metadata.csv_meta}' + #if $plot_format.need_metadata.interval == 'MS' + --interval MS + #else + --interval D + --windowsize 70 + #end if + #end if +#else if $plot_format.choice == 'plot_and_dash' + @DASH_COMMAND@ && + @PLOT_COMMAND@ +#end if +]]></token> + <xml name="demixing_common_options"> + <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/> + <conditional name="usher_update_option"> + <param name="choice" type="select" label="Source of UShER barcodes data" + help="Freyja ships with an usher_barcodes.csv file, which the tool can access internally. Since this file gets updated rather frequently, you can also download the latest version of the file from https://github.com/andersen-lab/Freyja/raw/main/freyja/data/usher_barcodes.csv, set the dataset's datatype to csv and use it as a custom barcodes file."> + <option value="repo" selected="true">Use data shipped with the tool (can be + outdated) + </option> + <option value="custom">Provide a custom barcodes file</option> + <!--<option value="update">Get updated versions of the curated lineage file as well as the UShER global phylogenetic tree (can cause tool to run slowly)</option>--> + </param> + <when value="repo"/> + <when value="custom"> + <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/> + </when> + <!--<when value="update" />--> + </conditional> + <param argument="--meta" type="data" format="json" optional="true" + label="Custom lineage metadata file" + help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/> + <param argument="--eps" type="float" optional="true" + label="Minimum lineage abundance tp include" + help="e.g. 0.0001."/> + <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue="" + checked="false" + label="Remove unconfirmed lineages from the analysis" + help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/> + </xml> + <token name="@HELP_HEADER@"><![CDATA[ +What it does +============ + +Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). + +General information +=================== + +Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem. + +Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample. +]]></token> + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.6585067</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r dda5772507b2 test-data/NC_045512_Hu-1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_045512_Hu-1.fasta Thu Jul 28 09:25:33 2022 +0000 |
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| b'@@ -0,0 +1,430 @@\n+>NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA\n+CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC\n+TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG\n+TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC\n+CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC\n+GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT\n+GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC\n+GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT\n+TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA\n+GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG\n+TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG\n+TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG\n+CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA\n+ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA\n+CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC\n+CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT\n+ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG\n+GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG\n+CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA\n+CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA\n+ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT\n+TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG\n+GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG\n+TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC\n+GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG\n+ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n+GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT\n+AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA\n+TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT\n+AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA\n+GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC\n+TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA\n+GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT\n+ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA\n+GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT\n+GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA\n+ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n+ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA\n+TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG\n+AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT\n+TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA\n+CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC\n+AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n+AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA\n+GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA\n+CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG\n+TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT\n+GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT\n+TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCA'..b'GACTATTACCAGCTGTACTCA\n+ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC\n+CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT\n+TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC\n+TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT\n+TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT\n+GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n+CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA\n+TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC\n+CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA\n+AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT\n+AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC\n+ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n+TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT\n+GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA\n+GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG\n+ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG\n+CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC\n+TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n+AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC\n+CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA\n+GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA\n+TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT\n+TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT\n+GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG\n+CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA\n+GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG\n+TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC\n+GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA\n+TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n+GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA\n+AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG\n+ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG\n+TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT\n+GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC\n+CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n+TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT\n+GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA\n+AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC\n+ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT\n+AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA\n+ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n+TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG\n+CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC\n+AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA\n+ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG\n+TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC\n+TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n+TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT\n+TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG\n+CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT\n+GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT\n+TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC\n+GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n+TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAA\n+\n' |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/abundances.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances.tsv Thu Jul 28 09:25:33 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ + variants.tsv +summarized [('A', 0.5789470000000878), ('Delta', 0.4188134220012827)] +lineages A AY.48 B.1.617.2 A.4 A.2 +abundances 0.57475400 0.37892715 0.03988627 0.00313480 0.00105820 +resid 3.5081238846264213 +coverage 99.73246831421596 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/abundances2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances2.tsv Thu Jul 28 09:25:33 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ + test_freyja.vcf.tsv +summarized [('A', 0.5789470000000878), ('Delta', 0.4188134220012827)] +lineages A AY.48 B.1.617.2 A.4 A.2 +abundances 0.57475400 0.37892715 0.03988627 0.00313480 0.00105820 +resid 3.5081238846264213 +coverage 99.73246831421596 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/abundances3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances3.tsv Thu Jul 28 09:25:33 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ + test.vcf.tsv +summarized [('Other', 0.9999999999997052)] +lineages B.1.177.48 B.1.177.58 B.1.177.6 +abundances 0.99556910 0.00225225 0.00217865 +resid 1.2661104938044003 +coverage 99.00678861652678 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/abundances4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances4.tsv Thu Jul 28 09:25:33 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ + test_freyja.vcf.tsv +summarized [('A', 0.5789470000000366), ('Delta', 0.4188134220003692)] +lineages A AY.48 B.1.617.2 A.4 A.2 +abundances 0.57475400 0.37892715 0.03988627 0.00313480 0.00105820 +resid 3.4923565864521677 +coverage 99.73246831421596 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/bunch_of_files.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bunch_of_files.tsv Thu Jul 28 09:25:33 2022 +0000 |
| [ |
| @@ -0,0 +1,4 @@ + summarized lineages abundances resid coverage +sample1 [('Other', 0.9999999999997052)] B.1.177.48 B.1.177.58 B.1.177.6 0.99556910 0.00225225 0.00217865 1.2661104938044003 99.00678861652678 +sample2 [('A', 0.333333333333333), ('Delta', 0.333333333333333), ('Omicron', 0.333333333333333)] A AY.48 B.1.617.2 A.4 A.2 0.57475400 0.37892715 0.03988627 0.00313480 0.00105820 3.4923565864521677 99.73246831421596 +sample3 [('A', 0.5789470000000878), ('Delta', 0.4188134220012827)] A AY.48 B.1.617.2 A.4 A.2 0.57475400 0.37892715 0.03988627 0.00313480 0.00105820 3.5081238846264213 99.73246831421596 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/csv_sample_meta.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv_sample_meta.csv Thu Jul 28 09:25:33 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Sample,sample_collection_datetime,viral_load +sample1,03/01/21,460326 +sample2,03/03/21,176645.1 +sample3,03/08/21,449891.7 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/csv_sample_meta2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv_sample_meta2.csv Thu Jul 28 09:25:33 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Sample,sample_collection_datetime,viral_load +variants.tsv,03/01/21,460326 +test_freyja.vcf.tsv,03/03/21,176645.1 +test.vcf.tsv,03/08/21,449891.7 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/depths.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/depths.tsv Thu Jul 28 09:25:33 2022 +0000 |
| b |
| b'@@ -0,0 +1,29903 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|
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/test.bam |
| b |
| Binary file test-data/test.bam has changed |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/test.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.vcf Thu Jul 28 09:25:33 2022 +0000 |
| b |
| @@ -0,0 +1,89 @@ +##fileformat=VCFv4.0 +##fileDate=20220125 +##source=lofreq call -f freyja/data/NC_045512_Hu-1.fasta -o test.vcf freyja/data/test.bam +##reference=freyja/data/NC_045512_Hu-1.fasta +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##FILTER=<ID=min_snvqual_64,Description="Minimum SNV Quality (Phred) 64"> +##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 210 . G T 48519 PASS DP=3206;AF=0.500312;SB=13;DP4=585,1012,533,1071 +NC_045512.2 241 . C T 49314 PASS DP=3610;AF=0.497230;SB=9;DP4=580,1229,530,1265 +NC_045512.2 372 . A C 110 PASS DP=1369;AF=0.008766;SB=1;DP4=568,789,4,8 +NC_045512.2 441 . G A 105 PASS DP=2250;AF=0.007111;SB=2;DP4=893,1338,5,11 +NC_045512.2 1055 . G A 1592 PASS DP=300;AF=0.220000;SB=1;DP4=127,106,34,32 +NC_045512.2 1191 . C T 11391 PASS DP=850;AF=0.450588;SB=1;DP4=215,252,181,202 +NC_045512.2 1267 . C T 9741 PASS DP=577;AF=0.549393;SB=1;DP4=144,116,170,147 +NC_045512.2 2184 . A C 154 PASS DP=888;AF=0.014640;SB=1;DP4=768,107,11,2 +NC_045512.2 2973 . C T 1395 PASS DP=1368;AF=0.057749;SB=20;DP4=862,427,41,38 +NC_045512.2 3037 . C T 13537 PASS DP=1209;AF=0.401158;SB=0;DP4=209,511,139,346 +NC_045512.2 4897 . C T 159 PASS DP=431;AF=0.027842;SB=1;DP4=235,184,6,6 +NC_045512.2 5184 . C T 3943 PASS DP=347;AF=0.409222;SB=1;DP4=197,8,135,7 +NC_045512.2 5457 . C T 949 PASS DP=1254;AF=0.044657;SB=1;DP4=722,476,35,21 +NC_045512.2 6996 . T C 80 PASS DP=98;AF=0.040816;SB=0;DP4=48,46,2,2 +NC_045512.2 8782 . C T 32957 PASS DP=1458;AF=0.693416;SB=8;DP4=170,277,344,667 +NC_045512.2 8883 . T C 72 PASS DP=506;AF=0.015810;SB=6;DP4=113,384,0,8 +NC_045512.2 9203 . G A 10829 PASS DP=1088;AF=0.351103;SB=8;DP4=307,398,185,197 +NC_045512.2 9678 . T C 1593 PASS DP=109;AF=0.486239;SB=5;DP4=11,45,16,37 +NC_045512.2 11005 . C A 4808 PASS DP=467;AF=0.368308;SB=0;DP4=191,103,112,60 +NC_045512.2 11414 . C T 246 PASS DP=529;AF=0.030246;SB=6;DP4=398,115,10,6 +NC_045512.2 12235 . A C 117 PASS DP=603;AF=0.018242;SB=5;DP4=60,532,2,9 +NC_045512.2 12583 . T A 67 PASS DP=1093;AF=0.006404;SB=0;DP4=588,498,4,3 +NC_045512.2 14256 . A C 75 PASS DP=1404;AF=0.010684;SB=0;DP4=689,697,7,8 +NC_045512.2 14408 . C T 1357 PASS DP=108;AF=0.472222;SB=2;DP4=18,39,19,32 +NC_045512.2 16247 . C T 99 PASS DP=462;AF=0.021645;SB=2;DP4=283,169,5,5 +NC_045512.2 16255 . C T 77 PASS DP=464;AF=0.012931;SB=1;DP4=285,173,3,3 +NC_045512.2 17000 . C T 115 PASS DP=1044;AF=0.010536;SB=0;DP4=501,532,5,6 +NC_045512.2 17474 . C A 106 PASS DP=758;AF=0.015831;SB=1;DP4=405,341,6,6 +NC_045512.2 17496 . A G 6152 PASS DP=504;AF=0.430556;SB=0;DP4=88,199,67,150 +NC_045512.2 18060 . C T 14317 PASS DP=767;AF=0.598435;SB=2;DP4=24,284,41,418 +NC_045512.2 18096 . T C 125 PASS DP=161;AF=0.043478;SB=1;DP4=59,95,2,5 +NC_045512.2 18311 . T C 121 PASS DP=869;AF=0.011507;SB=16;DP4=432,427,1,9 +NC_045512.2 18395 . C T 82 PASS DP=1038;AF=0.009634;SB=1;DP4=568,456,5,5 +NC_045512.2 19547 . C T 851 PASS DP=863;AF=0.054461;SB=0;DP4=409,407,24,23 +NC_045512.2 20396 . A G 489 PASS DP=32;AF=0.500000;SB=0;DP4=14,2,14,2 +NC_045512.2 21618 . C G 375 PASS DP=40;AF=0.375000;SB=1;DP4=15,9,11,4 +NC_045512.2 21792 . A C 4658 PASS DP=477;AF=0.354298;SB=0;DP4=154,154,83,86 +NC_045512.2 21849 . A C 75 PASS DP=288;AF=0.017361;SB=2;DP4=41,239,1,4 +NC_045512.2 21974 . G T 82 PASS DP=168;AF=0.029762;SB=0;DP4=59,104,2,3 +NC_045512.2 21987 . G A 4045 PASS DP=333;AF=0.420420;SB=0;DP4=93,100,68,72 +NC_045512.2 22009 . C A 330 PASS DP=333;AF=0.060060;SB=0;DP4=151,162,10,10 +NC_045512.2 22206 . A G 1045 PASS DP=341;AF=0.131965;SB=0;DP4=142,153,21,24 +NC_045512.2 22296 . A G 103 PASS DP=518;AF=0.015444;SB=3;DP4=340,167,4,4 +NC_045512.2 22482 . C T 79 PASS DP=158;AF=0.031646;SB=0;DP4=51,102,2,3 +NC_045512.2 22995 . C A 3384 PASS DP=222;AF=0.504505;SB=0;DP4=60,50,61,51 +NC_045512.2 23403 . A G 6370 PASS DP=556;AF=0.395683;SB=10;DP4=166,169,126,94 +NC_045512.2 23525 . C T 125 PASS DP=358;AF=0.025140;SB=0;DP4=67,282,1,8 +NC_045512.2 23601 . C T 66 PASS DP=957;AF=0.009404;SB=1;DP4=427,520,5,4 +NC_045512.2 23604 . C G 13373 PASS DP=959;AF=0.488008;SB=0;DP4=220,271,211,257 +NC_045512.2 23607 . G T 532 PASS DP=958;AF=0.037578;SB=0;DP4=412,506,17,19 +NC_045512.2 23618 . A G 83 PASS DP=959;AF=0.011470;SB=0;DP4=424,524,5,6 +NC_045512.2 24410 . G A 267 PASS DP=22;AF=0.409091;SB=0;DP4=4,9,3,6 +NC_045512.2 24780 . A G 84 PASS DP=707;AF=0.012730;SB=2;DP4=316,382,3,6 +NC_045512.2 25469 . C T 10803 PASS DP=1085;AF=0.355760;SB=1;DP4=210,488,111,275 +NC_045512.2 25606 . G A 64 PASS DP=2215;AF=0.005418;SB=0;DP4=1181,1016,6,6 +NC_045512.2 26542 . C T 362 PASS DP=78;AF=0.179487;SB=6;DP4=41,23,6,8 +NC_045512.2 26767 . T C 5916 PASS DP=531;AF=0.384181;SB=3;DP4=219,108,130,74 +NC_045512.2 27752 . C T 2820 PASS DP=415;AF=0.260241;SB=18;DP4=184,123,79,29 +NC_045512.2 27920 . C T 167 PASS DP=2351;AF=0.008932;SB=0;DP4=1543,786,14,7 +NC_045512.2 27924 . A C 1081 PASS DP=2351;AF=0.030200;SB=0;DP4=1511,768,46,25 +NC_045512.2 28144 . T C 17994 PASS DP=669;AF=0.792227;SB=22;DP4=45,94,243,287 +NC_045512.2 28253 . C T 5868 PASS DP=471;AF=0.430998;SB=217;DP4=15,251,86,117 +NC_045512.2 28387 . A C 109 PASS DP=1287;AF=0.012432;SB=6;DP4=1141,129,13,3 +NC_045512.2 28461 . A G 29706 PASS DP=2257;AF=0.443952;SB=1;DP4=688,565,540,462 +NC_045512.2 28698 . C A 7287 PASS DP=544;AF=0.455882;SB=0;DP4=180,114,151,97 +NC_045512.2 28836 . C T 102 PASS DP=815;AF=0.011043;SB=0;DP4=495,310,6,3 +NC_045512.2 28851 . G T 72 PASS DP=815;AF=0.009816;SB=3;DP4=497,310,4,4 +NC_045512.2 28853 . T A 2280 PASS DP=817;AF=0.124847;SB=3;DP4=441,273,59,43 +NC_045512.2 28881 . G T 9326 PASS DP=721;AF=0.443828;SB=2;DP4=221,180,183,137 +NC_045512.2 29402 . G T 30263 PASS DP=1934;AF=0.512410;SB=45;DP4=700,243,814,177 +NC_045512.2 29512 . T C 44232 PASS DP=2655;AF=0.554802;SB=7;DP4=670,511,797,676 +NC_045512.2 29581 . T C 227 PASS DP=2170;AF=0.011982;SB=0;DP4=1905,221,24,2 +NC_045512.2 29742 . G T 1184 PASS DP=60;AF=0.616667;SB=0;DP4=7,16,11,26 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/times_metadata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/times_metadata.csv Thu Jul 28 09:25:33 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Sample,sample_collection_datetime +sample1,2021-05-24 +sample2,2021-06-02 +sample3,2021-07-06 |
| b |
| diff -r 000000000000 -r dda5772507b2 test-data/variants.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants.tsv Thu Jul 28 09:25:33 2022 +0000 |
| b |
| b'@@ -0,0 +1,8194 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