Mercurial > repos > scisjnu123 > test
changeset 10:24d2dc34dd17 draft
Uploaded
| author | scisjnu123 |
|---|---|
| date | Fri, 13 Sep 2019 02:21:23 -0400 |
| parents | e1ad03534fb2 |
| children | 050856988602 |
| files | GATK/gatk/analyze_covariates.xml GATK/gatk/base_recalibrator.xml GATK/gatk/combine_gvcfs.xml GATK/gatk/combine_variants.xml GATK/gatk/gatk.xml GATK/gatk/gatk_macros.xml GATK/gatk/generation/gatk.xsl GATK/gatk/generation/gatk.xsldb.xml GATK/gatk/genotype_gvcfs.xml GATK/gatk/haplotype_caller.xml GATK/gatk/indel_realigner.xml GATK/gatk/print_reads.xml GATK/gatk/realigner_target_creator.xml GATK/gatk/tool-data/destinations.py GATK/gatk/tool-data/picard_index.loc.sample GATK/gatk/tool_data_table_conf.xml.sample GATK/gatk/tool_dependencies.xml GATK/package_picard_1_135/tool_dependencies.xml GATK/package_r_for_gatk_3_4_0/tool_dependencies.xml Galaxy-Workflow-Haplotypecaller.ga Galaxy-Workflow-SAMTools.ga Galaxy-Workflow-SVDetect.ga Galaxy-Workflow-VARSCAN.ga picard/read_group_macros.xml sr_assembly/velvetg.xml sr_assembly/velvetg_wrapper.py sr_assembly/velveth.xml sr_assembly/velveth_wrapper.py suite_samtools_0_1_19/repository_dependencies.xml svdetect/BAM_preprocessingPairs.pl svdetect/BAM_preprocessingPairs.xml svdetect/SVDetect_compare.pl svdetect/SVDetect_compare.xml svdetect/SVDetect_import.sh svdetect/SVDetect_import.xml svdetect/SVDetect_run_parallel.pl svdetect/SVDetect_run_parallel.xml svdetect/circos_graph.xml varscan/tool_dependencies.xml varscan/varscan_mpileup.pl varscan/varscan_mpileup.xml varscan/varscan_somatic.pl varscan/varscan_somatic.xml |
| diffstat | 43 files changed, 294 insertions(+), 8498 deletions(-) [+] |
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--- a/GATK/gatk/analyze_covariates.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<macros> - <xml name="AnalyzeCovariatesParameters" tokens="tag"> - - <!-- BQSR in main config --> - - <param name="afterReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR second-pass report file" help="-after,‑‑afterReportFile &lt;afterReportFile&gt;" /> - - <param name="beforeReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR first-pass report file" help="-before,‑‑beforeReportFile &lt;beforeReportFile&gt;" /> - - </xml> - - <xml name="AnalyzeCovariatesOutput"> - <data format="pdf" name="ac_plotsReportFile" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (PDF Recalibration Report)"> - <yield /> - </data> - </xml> - - <template name="AnalyzeCovariatesPreprocessing"> -<![CDATA[ -]]> - </template> - - <template name="AnalyzeCovariatesOptions"> -<![CDATA[ - --plotsReportFile ${ac_plotsReportFile} - - #if str($analysis_type.afterReportFile) - --afterReportFile $analysis_type.afterReportFile - #end if - #if str($analysis_type.beforeReportFile) - --beforeReportFile $analysis_type.beforeReportFile - #end if -]]> - </template> -</macros> - -
--- a/GATK/gatk/base_recalibrator.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -<macros> - <xml name="BaseRecalibratorParameters" tokens="tag"> - - <expand macro="macro_bam_input" tag="@TAG@" /> - - <param name="knownSites" type="data" format="vcf,bcf,bed,pileup,tabular,table" label="Database of known Sites (ROD files; e.g. VCF format)" multiple="true" title="A database of known polymorphic sites to skip over in the recalibration algorithm" help="-knownSites,‑‑knownSites &lt;knownSites&gt;" /> - - </xml> - - <xml name="BaseRecalibratorOutput"> - <data format="tabular" name="br_table" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (Table)"> - <yield /> - </data> - </xml> - - <template name="BaseRecalibratorPreprocessing"> -<![CDATA[ - @token_bam_input_pre@ - #for $i, $variant in enumerate($analysis_type.knownSites): - ln -s -f ${variant} variant_${i}.vcf && - #end for -]]> - </template> - - <template name="BaseRecalibratorOptions"> -<![CDATA[ - --out ${br_table} - - @token_bam_input@ - - #for $i, $variant in enumerate($analysis_type.knownSites): - --knownSites variant_${i}.vcf - #end for -]]> - </template> -</macros> - -
--- a/GATK/gatk/combine_gvcfs.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<macros> - <xml name="CombineGVCFsParameters" tokens="tag"> - - <expand macro="macro_gvcf_input" tag="@TAG@" /> - - <expand macro="macro_optional_parameters"> - - <param name="breakBandsAtMultiplesOf" type="integer" value="0" label="If > 0, reference bands will be broken up at genomic positions that are multiples of this number" help="-breakBandsAtMultiplesOf,‑‑breakBandsAtMultiplesOf &lt;breakBandsAtMultiplesOf&gt;" /> - - </expand> - - </xml> - - <xml name="CombineGVCFsOutput"> - <data format="vcf" name="cg_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)"> - <yield /> - </data> - </xml> - - <template name="CombineGVCFsPreprocessing"> -<![CDATA[ - @token_gvcf_input_pre@ -]]> - </template> - - <template name="CombineGVCFsOptions"> -<![CDATA[ - --out ${cg_output_vcf} - - @token_gvcf_input@ - - #set $optionals = $analysis_type.optional_parameters - #if $optionals.optional_parameters_enabled - #if $optionals.breakBandsAtMultiplesOf > 0 - --breakBandsAtMultiplesOf $optionals.breakBandsAtMultiplesOf - #end if - #end if -]]> - </template> - - -</macros> - -
--- a/GATK/gatk/combine_variants.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -<macros> - <xml name="CombineVariantsParameters" tokens="tag"> - - <expand macro="macro_vcf_input" tag="@TAG@" /> - - <expand macro="macro_optional_parameters"> - - <param name="filteredRecordsMergeType" type="select" label="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields" help="-filteredRecordsMergeType,‑‑filteredrecordsmergetype &lt;filteredrecordsmergetype&gt;"> - <option value="">No Selection</option> - <option value="KEEP_IF_ANY_UNFILTERED">KEEP_IF_ANY_UNFILTERED</option> - <option value="KEEP_IF_ALL_UNFILTERED">KEEP_IF_ALL_UNFILTERED</option> - <option value="KEEP_UNCONDITIONAL">KEEP_UNCONDITIONAL</option> - </param> - - <param name="genotypeMergeOptions" type="select" label="Determines how we should merge genotype records for samples shared across the ROD files" help="-genotypeMergeOptions,‑‑genotypemergeoption &lt;genotypemergeoption&gt;"> - <option value="">No Selection</option> - <option value="UNIQUIFY">UNIQUIFY</option> - <option value="PRIORITIZE">PRIORITIZE</option> - <option value="UNSORTED">UNSORTED</option> - <option value="REQUIRE_UNIQUE">REQUIRE_UNIQUE</option> - </param> - - <param name="minimumN" type="integer" value="1" optional="true" label="Combine variants and output site only if the variant is present in at least N input files" help="-minN,‑‑minimumN &lt;minimumN&gt;" /> - - <param name="rod_priority_list" type="text" value="" optional="true" label="A comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted" help="-priority,‑‑rod_priority_list &lt;rod_priority_list&gt;" /> - - <param name="setKey" type="text" value="" optional="true" label="Key used in the INFO key=value tag emitted describing which set the combined VCF record came from" help="-setKey,‑‑setKey &lt;setKey&gt;" /> - - <param name="assumeIdenticalSamples" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls" help="-assumeIdenticalSamples,‑‑assumeIdenticalSamples" /> - - <param name="excludeNonVariants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the combining procedure" help="-env,‑‑excludeNonVariants" /> - - <param name="filteredAreUncalled" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotations don't appear in the combined VCF" help="-filteredAreUncalled,‑‑filteredAreUncalled" /> - - <param name="mergeInfoWithMaxAC" type="boolean" truevalue="--mergeInfoWithMaxAC" falsevalue="" label="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records." help="-mergeInfoWithMaxAC,‑‑mergeInfoWithMaxAC" /> - - <param name="minimalVCF" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype FORMAT fields" help="-minimalVCF,‑‑minimalVCF" /> - - <param name="printComplexMerges" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,‑‑printComplexMerges" /> - - <param name="suppressCommandLineHeader" type="boolean" truevalue="--suppressCommandLineHeader" falsevalue="" label="If true, do not output the header containing the command line used" help="-suppressCommandLineHeader,‑‑suppressCommandLineHeader" /> - - </expand> - - </xml> - - <xml name="CombineVariantsOutput"> - <data format="vcf" name="cv_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)"> - <yield /> - </data> - </xml> - - <template name="CombineVariantsPreprocessing"> -<![CDATA[ - @token_vcf_input_pre@ -]]> - </template> - - <template name="CombineVariantsOptions"> -<![CDATA[ - --out ${cv_output_vcf} - - @token_vcf_input@ - - #set $optionals = $analysis_type.optional_parameters - #if $optionals.optional_parameters_enabled - - #if $optionals.filteredRecordsMergeType - --filteredRecordsMergeType $optionals.filteredRecordsMergeType - #end if - #if $optionals.genotypeMergeOptions - --genotypeMergeOptions $optionals.genotypeMergeOptions - #end if - #if $optionals.minimumN != 1 - --minimumN $optionals.minimumN - #end if - #if $optionals.rod_priority_list - --rod_priority_list $optionals.rod_priority_list - #end if - - $optionals.assumeIdenticalSamples - $optionals.excludeNonVariants - $optionals.filteredAreUncalled - $optionals.mergeInfoWithMaxAC - $optionals.minimalVCF - $optionals.printComplexMerges - $optionals.suppressCommandLineHeader - - #end if -]]> - </template> - - -</macros> - -
--- a/GATK/gatk/gatk.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,179 +0,0 @@ -<?xml version="1.0" encoding="utf-8"?> -<tool id="gatk" name="GATK" version="@VERSION@.d9"> - <description>tool collection Version @VERSION@</description> - <macros> - <import>gatk_macros.xml</import> - <import>realigner_target_creator.xml</import> - <import>indel_realigner.xml</import> - <import>base_recalibrator.xml</import> - <import>analyze_covariates.xml</import> - <import>print_reads.xml</import> - <import>haplotype_caller.xml</import> - <import>genotype_gvcfs.xml</import> - <import>combine_gvcfs.xml</import> - <import>combine_variants.xml</import> - </macros> - <expand macro="requirements"/> - <stdio> - <regex match="^INFO" level="log"/> - <regex match="^WARN" level="warning"/> - <regex match="Using .* implementation of PairHMM" level="warning"/> - <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal"/> - <regex match="^##### ERROR" level="fatal"/> - <exit_code range="1:" level="fatal"/> - </stdio> - <command><![CDATA[ - ############################ - ## import analysis specific preprocessings by using cheetahs internal searchList - ## if not defined, ignore - ############################ - #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2] - #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"] - #include source=$analysisPreprocessing - #end if - - ############################ - ## GATK tool unspecific options - ############################ - @GATK_EXEC@ - - --analysis_type ${analysis_type.analysis_type_selector} - --reference_sequence ${ref_file.fields.path} - - --log_to_file ${output_log} - - #if $cond_intervals.cond_intervals_enabled - #for $interval in $cond_intervals.intervals: - --intervals ${interval.L} - #end for - #end if - - #if $cond_BQSR.cond_BQSR_enabled - --BQSR $cond_BQSR.BQSR - #end if - - ############################ - ## import analysis specific options by using cheetahs internal searchList - ## if not defined throw raw python error until better idea - ############################ - #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2] - #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"] - #include source=$analysisOptions - #else - #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"] - #end if - - ############################ - ## only put ERROR or FATAL log messages into stderr - ## but keep full log for printing into log file - ############################ - 2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2 -]]></command> - <inputs> - <param name="ref_file" type="select" label="Using reference genome" help="-R,‑‑reference_sequence &lt;reference_sequence&gt;"> - <options from_data_table="picard_indexes"/> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - <conditional name="cond_intervals"> - <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?"/> - <when value="true"> - <repeat name="intervals" title="genomic interval over which to operate" help="-L,‑‑intervals &lt;intervals&gt;"> - <param name="L" type="text" value=""/> - </repeat> - </when> - <when value="false"/> - </conditional> - <conditional name="cond_BQSR"> - <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?"/> - <when value="true"> - <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,‑‑BQSR &lt;BQSR&gt; intended primarily for use with BaseRecalibrator and PrintReads"/> - </when> - <when value="false"/> - </conditional> - <conditional name="cond_threads"> - <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?"/> - <when value="true"> - <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool"/> - <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool"/> - <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread"/> - </when> - <when value="false"/> - </conditional> - <conditional name="analysis_type"> - <param name="analysis_type_selector" type="select" label="Analysis Type"> - <option value="RealignerTargetCreator">RealignerTargetCreator</option> - <option value="IndelRealigner">IndelRealigner</option> - <option value="BaseRecalibrator">BaseRecalibrator</option> - <option value="AnalyzeCovariates">AnalyzeCovariates</option> - <option value="PrintReads">PrintReads</option> - <option value="HaplotypeCaller">HaplotypeCaller</option> - <option value="GenotypeGVCFs">GenotypeGVCFs</option> - <option value="CombineGVCFs">CombineGVCFs</option> - <option value="CombineVariants">CombineVariants</option> - </param> - <when value="RealignerTargetCreator"> - <expand macro="RealignerTargetCreatorParameters" tag="rtc"/> - </when> - <when value="IndelRealigner"> - <expand macro="IndelRealignerParameters" tag="ir"/> - </when> - <when value="BaseRecalibrator"> - <expand macro="BaseRecalibratorParameters" tag="br"/> - </when> - <when value="AnalyzeCovariates"> - <expand macro="AnalyzeCovariatesParameters" tag="ac"/> - </when> - <when value="PrintReads"> - <expand macro="PrintReadsParameters" tag="pr"/> - </when> - <when value="HaplotypeCaller"> - <expand macro="HaplotypeCallerParameters" tag="hc"/> - </when> - <when value="GenotypeGVCFs"> - <expand macro="GenotypeGVCFsParameters" tag="gg"/> - </when> - <when value="CombineGVCFs"> - <expand macro="CombineGVCFsParameters" tag="cg"/> - </when> - <when value="CombineVariants"> - <expand macro="CombineVariantsParameters" tag="cv"/> - </when> - </conditional> - </inputs> - <outputs> - <expand macro="RealignerTargetCreatorOutput" tag="rtc"> - <filter>analysis_type['analysis_type_selector'] == 'RealignerTargetCreator'</filter> - </expand> - <expand macro="IndelRealignerOutput" tag="ir"> - <filter>analysis_type['analysis_type_selector'] == 'IndelRealigner'</filter> - </expand> - <expand macro="BaseRecalibratorOutput" tag="br"> - <filter>analysis_type['analysis_type_selector'] == 'BaseRecalibrator'</filter> - </expand> - <expand macro="AnalyzeCovariatesOutput" tag="ac"> - <filter>analysis_type['analysis_type_selector'] == 'AnalyzeCovariates'</filter> - </expand> - <expand macro="PrintReadsOutput" tag="pr"> - <filter>analysis_type['analysis_type_selector'] == 'PrintReads'</filter> - </expand> - <expand macro="HaplotypeCallerOutput" tag="hc"> - <filter>analysis_type['analysis_type_selector'] == 'HaplotypeCaller'</filter> - </expand> - <expand macro="GenotypeGVCFsOutput" tag="gg"> - <filter>analysis_type['analysis_type_selector'] == 'GenotypeGVCFs'</filter> - </expand> - <expand macro="CombineGVCFsOutput" tag="cg"> - <filter>analysis_type['analysis_type_selector'] == 'CombineGVCFs'</filter> - </expand> - <expand macro="CombineVariantsOutput" tag="cv"> - <filter>analysis_type['analysis_type_selector'] == 'CombineVariants'</filter> - </expand> - <data format="txt" name="output_log" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (log)"/> - </outputs> - <expand macro="macro_tests"/> - <citations> - <citation type="doi">10.1101/gr.107524.110</citation> - <citation type="doi">10.1038/ng.806</citation> - <citation type="doi">10.1002/0471250953.bi1110s43</citation> - </citations> -</tool>
--- a/GATK/gatk/gatk_macros.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ -<macros> - - <xml name="requirements"> - <requirements> - <requirement type="package">gatk</requirement> - <requirement type="set_environment">GATK_PATH</requirement> - <requirement type="set_environment">GATK_SITE_OPTIONS</requirement> - <requirement type="package" version="3.1.2.1">package_r_for_gatk_3_4_0</requirement> - </requirements> - </xml> - - <xml name="version_command"> - <version_command><![CDATA[ @GATK_EXEC@ --help|grep '^The Genome' ]]></version_command> - </xml> - - <token name="@VERSION@">3.4-0</token> - <token name="@OUTPUT_NAME_PREFIX@">${tool.name} - ${analysis_type.analysis_type_selector}</token> - <token name="@GATK_EXEC@"> -<![CDATA[ - #if $cond_threads.cond_threads_enabled: - #if int($cond_threads.nct) > 1: - THREAD_STRING="-nct $cond_threads.nct" && - #end if - #if int($cond_threads.nt) > 1: - THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" && - #end if - #if int($cond_threads.mem) > 0: - GATK_MEM=$cond_threads.mem && - #end if - #end if - java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-} -]]> - </token> - - <xml name="macro_vcf_input" tokens="tag"> - <param name="input" type="data" format="vcf" multiple="true" label="Variant files (VCF format)" help="-V, ‑‑variant"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> - </param> - </xml> - <token name="@token_vcf_input_pre@" tokens="tag"> -<![CDATA[ - ############################ - ## create links to gVCF input files with correct extensions - ############################ - #for $i, $variant in enumerate($analysis_type.input): - ln -s -f ${variant} variant_${i}.vcf && - #end for -]]> - </token> - <token name="@token_vcf_input@"> -<![CDATA[ - #for $i, $variant in enumerate($analysis_type.input): - --variant variant_${i}.vcf - #end for - @token_reference_input@ -]]> - </token> - - - <xml name="macro_gvcf_input" tokens="tag"> - <param name="input" type="data" format="vcf" multiple="true" label="Variant files (gVCF format)" help="-V, ‑‑variant"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> - </param> - </xml> - <token name="@token_gvcf_input_pre@" tokens="tag"> -<![CDATA[ - ############################ - ## create links to gVCF input files with correct extensions - ############################ - #for $i, $variant in enumerate($analysis_type.input): - ln -s -f ${variant} variant_${i}.g.vcf && - #end for -]]> - </token> - <token name="@token_gvcf_input@"> -<![CDATA[ - #for $i, $variant in enumerate($analysis_type.input): - --variant variant_${i}.g.vcf - #end for - @token_reference_input@ -]]> - </token> - - <xml name="macro_bam_input"> - <conditional name="cond_bam_input"> - <param name="all_in_one" type="boolean" value="false" label="Input all BAM files in a single command" /> - <when value="true"> - <param name="input" type="data" format="bam" multiple="true" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file"> - <validator type="unspecified_build"/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/> - </param> - </when> - <when value="false"> - <param name="input" type="data" format="bam" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file"> - <validator type="unspecified_build"/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/> - </param> - </when> - </conditional> - </xml> - <token name="@token_bam_input_pre@"> -<![CDATA[ - ############################ - ## create links to bam input files with correct extensions - ############################ - #if $analysis_type.cond_bam_input.all_in_one - #for $i, $bam in enumerate($analysis_type.cond_bam_input.input): - ln -s -f ${bam} input_${i}.bam && - ln -s -f ${bam.metadata.bam_index} input_${i}.bam.bai && - #end for - #else - ln -s -f ${analysis_type.cond_bam_input.input} input.bam && - ln -s -f ${analysis_type.cond_bam_input.input.metadata.bam_index} input.bam.bai && - #end if -]]> - </token> - <token name="@token_bam_input@"> -<![CDATA[ - #if $analysis_type.cond_bam_input.all_in_one - #for $i, $bam in enumerate($analysis_type.cond_bam_input.input): - --input_file input_${i}.bam - #end for - #else - --input_file input.bam - #end if - @token_reference_input@ -]]> - </token> - - <token name="@token_reference_input@"> -<![CDATA[ -]]> - </token> - <xml name="macro_input" tokens="tag"> - <yield /> - </xml> - - <xml name="macro_optional_parameters"> - <conditional name="optional_parameters"> - <param name="optional_parameters_enabled" type="boolean" label="Configure Optional Parameters" /> - <when value="true"> - <yield /> - </when> - <when value="false" /> - </conditional> - </xml> - - <xml name="macro_advanced_parameters"> - <conditional name="advanced_parameters"> - <param name="advanced_parameters_enabled" type="boolean" label="Configure Advanced Parameters" /> - <when value="true"> - <yield /> - </when> - <when value="false" /> - </conditional> - </xml> - - <xml name="macro_tests"> - <tests> - - </tests> - </xml> - -</macros>
--- a/GATK/gatk/generation/gatk.xsl Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,162 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"> -<xsl:output - method="xml" - encoding="utf-8" - indent="yes" - cdata-section-elements="script style" /> - -<xsl:template match="/"> - -<tool id="gatk" name="GATK" version="@VERSION@.d9"> - <description>tool collection Version @VERSION@</description> - - <macros> - <import>gatk_macros.xml</import> - <xsl:for-each select="analyses/analysis"> - <import><xsl:value-of select="macro_file" /></import> - </xsl:for-each> - </macros> - - <expand macro="requirements" /> - - <stdio> - <regex match="^INFO" level="log" /> - <regex match="^WARN" level="warning" /> - <regex match="Using .* implementation of PairHMM" level="warning" /> - <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal" /> - <regex match="^##### ERROR" level="fatal" /> - <exit_code range="1:" level="fatal"/> - </stdio> - - <command> -<xsl:text disable-output-escaping="yes"><![CDATA[ - ############################ - ## import analysis specific preprocessings by using cheetahs internal searchList - ## if not defined, ignore - ############################ - #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2] - #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"] - #include source=$analysisPreprocessing - #end if - - ############################ - ## GATK tool unspecific options - ############################ - @GATK_EXEC@ - - --analysis_type ${analysis_type.analysis_type_selector} - --reference_sequence ${ref_file.fields.path} - - --log_to_file ${output_log} - - #if $cond_intervals.cond_intervals_enabled - #for $interval in $cond_intervals.intervals: - --intervals ${interval.L} - #end for - #end if - - #if $cond_BQSR.cond_BQSR_enabled - --BQSR $cond_BQSR.BQSR - #end if - - ############################ - ## import analysis specific options by using cheetahs internal searchList - ## if not defined throw raw python error until better idea - ############################ - #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2] - #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"] - #include source=$analysisOptions - #else - #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"] - #end if - - ############################ - ## only put ERROR or FATAL log messages into stderr - ## but keep full log for printing into log file - ############################ - 2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2 -]]></xsl:text> - </command> - - <inputs> - - <param name="ref_file" type="select" label="Using reference genome" help="-R,‑‑reference_sequence &lt;reference_sequence&gt;" > - <options from_data_table="picard_indexes"> - <!--filter type="data_meta" key="dbkey" ref="@TAG@_input" column="dbkey" /--> - </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - - <conditional name="cond_intervals"> - <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?" /> - <when value="true"> - <repeat name="intervals" title="genomic interval over which to operate" help="-L,‑‑intervals &lt;intervals&gt;"> - <param name="L" type="text" value="" /> - </repeat> - </when> - <when value="false" /> - </conditional> - - <conditional name="cond_BQSR"> - <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?" /> - <when value="true"> - <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,‑‑BQSR &lt;BQSR&gt; intended primarily for use with BaseRecalibrator and PrintReads" /> - </when> - <when value="false" /> - </conditional> - - <conditional name="cond_threads"> - <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?" /> - <when value="true"> - <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool" /> - <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool" /> - <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread" /> - </when> - <when value="false" /> - </conditional> - - <conditional name="analysis_type"> - <param name="analysis_type_selector" type="select" label="Analysis Type"> - <xsl:for-each select="analyses/analysis"> - <option value="{name}"><xsl:value-of select="name" /></option> - </xsl:for-each> - </param> - <xsl:for-each select="analyses/analysis"> - <when value="{name}"> - <!--xsl:choose> - <xsl:when test="input_type = 'bam'"> - <expand macro="macro_bam_input" tag="{tag}" /> - </xsl:when> - <xsl:when test="input_type = 'gvcf'"> - <expand macro="macro_gvcf_input" tag="{tag}" /> - </xsl:when> - </xsl:choose--> - <expand macro="{name}Parameters" tag="{tag}" /> - </when> - </xsl:for-each> - </conditional> - </inputs> - - <outputs> - <xsl:for-each select="analyses/analysis"> - <expand macro="{name}Output" tag="{tag}"> - <filter>analysis_type['analysis_type_selector'] == '<xsl:value-of select="name" />'</filter> - </expand> - </xsl:for-each> - <data format="txt" name="output_log" label="${{tool.name}} - ${{analysis_type.analysis_type_selector}} on ${{on_string}} (log)" /> - </outputs> - - <expand macro="macro_tests" /> - - <citations> - <citation type="doi">10.1101/gr.107524.110</citation> - <citation type="doi">10.1038/ng.806</citation> - <citation type="doi">10.1002/0471250953.bi1110s43</citation> - </citations> -</tool> - -</xsl:template> -</xsl:stylesheet> - -
--- a/GATK/gatk/generation/gatk.xsldb.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<analyses> - <analysis> - <name>RealignerTargetCreator</name> - <input_type>bam</input_type> - <tag>rtc</tag> - <macro_file>realigner_target_creator.xml</macro_file> - </analysis> - <analysis> - <name>IndelRealigner</name> - <input_type>bam</input_type> - <tag>ir</tag> - <macro_file>indel_realigner.xml</macro_file> - </analysis> - <analysis> - <name>BaseRecalibrator</name> - <input_type>bam</input_type> - <tag>br</tag> - <macro_file>base_recalibrator.xml</macro_file> - </analysis> - <analysis> - <name>AnalyzeCovariates</name> - <input_type>bam</input_type> - <tag>ac</tag> - <macro_file>analyze_covariates.xml</macro_file> - </analysis> - <analysis> - <name>PrintReads</name> - <input_type>bam</input_type> - <tag>pr</tag> - <macro_file>print_reads.xml</macro_file> - </analysis> - <analysis> - <name>HaplotypeCaller</name> - <input_type>bam</input_type> - <tag>hc</tag> - <macro_file>haplotype_caller.xml</macro_file> - </analysis> - <analysis> - <name>GenotypeGVCFs</name> - <input_type>gvcf</input_type> - <tag>gg</tag> - <macro_file>genotype_gvcfs.xml</macro_file> - </analysis> - <analysis> - <name>CombineGVCFs</name> - <input_type>gvcf</input_type> - <tag>cg</tag> - <macro_file>combine_gvcfs.xml</macro_file> - </analysis> - <analysis> - <name>CombineVariants</name> - <input_type>vcf</input_type> - <tag>cv</tag> - <macro_file>combine_variants.xml</macro_file> - </analysis> -</analyses>
--- a/GATK/gatk/genotype_gvcfs.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -<macros> - <xml name="GenotypeGVCFsParameters" tokens="tag"> - - <expand macro="macro_gvcf_input" tag="@TAG@" /> - - <expand macro="macro_optional_parameters"> - - - <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,‑‑sample_ploidy &lt;sample_ploidy&gt;" /> - - </expand> - - </xml> - - <xml name="GenotypeGVCFsOutput"> - <data format="vcf" name="gg_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (gVCF)"> - <yield /> - </data> - </xml> - - <template name="GenotypeGVCFsPreprocessing"> -<![CDATA[ - @token_gvcf_input_pre@ -]]> - </template> - - <template name="GenotypeGVCFsOptions"> -<![CDATA[ - --out output.g.vcf - - @token_gvcf_input@ - - #set $optionals = $analysis_type.optional_parameters - #if $optionals.optional_parameters_enabled - --sample_ploidy $optionals.sample_ploidy - #end if -]]> - </template> - - -</macros> - -
--- a/GATK/gatk/haplotype_caller.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<macros> - <xml name="HaplotypeCallerParameters" tokens="tag"> - - <expand macro="macro_bam_input" tag="@TAG@" /> - - <conditional name="cond_usage"> - <param name="cond_usage_selector" type="select" label="Select usage"> - <option value="GVCF">Single-sample all-sites calling on DNAseq (GVCF mode)</option> - </param> - <when value="GVCF"> - <expand macro="HaplotypeCallerGVCF" /> - </when> - </conditional> - - <expand macro="macro_optional_parameters"> - - <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,‑‑sample_ploidy &lt;sample_ploidy&gt;" /> - - </expand> - - </xml> - - <xml name="HaplotypeCallerOutput"> - <data format="vcf" name="hc_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string} (gVCF)"> - <yield /> - </data> - </xml> - - <template name="HaplotypeCallerPreprocessing"> -<![CDATA[ - @token_bam_input_pre@ -]]> - </template> - - <template name="HaplotypeCallerOptions"> -<![CDATA[ - --out output.g.vcf - - @token_bam_input@ - - #set $optionals = $analysis_type.optional_parameters - #if $optionals.optional_parameters_enabled - --sample_ploidy $optionals.sample_ploidy - #end if - - #set $usage_selector = $analysis_type.cond_usage.cond_usage_selector - #set $usage = $analysis_type.cond_usage - - #if str($usage_selector) == 'GVCF' - --emitRefConfidence "GVCF" - #end if -]]> - </template> - - - - <xml name="HaplotypeCallerGVCF"> - <param name="emitRefConfidence" type="select" optional="true" label="Mode for emitting reference confidence scores" help="-ERC,‑‑emitRefConfidence &lt;emitRefConfidence&gt;"> - <option value="GVCF">GVCF (Reference model emitted with condensed non-variant blocks)</option> - </param> - </xml> - -</macros> - -
--- a/GATK/gatk/indel_realigner.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -<macros> - <xml name="IndelRealignerParameters" tokens="tag"> - - <expand macro="macro_bam_input" tag="@TAG@" /> - - <param name="targetIntervals" type="data" format="gatk_interval" label="Intervals file output from RealignerTargetCreator" help="-targetIntervals,--targetIntervals &lt;targetIntervals&gt;" /> - - <expand macro="macro_optional_parameters"> - <repeat name="knownAlleles" title="Input VCF file(s) with known indels" help="-known,‑‑knownAlleles &lt;knownAlleles&gt;"> - <param name="knownAllele" type="data" format="vcf" label="Variant file (VCF format)" /> - </repeat> - - <param name="consensusDeterminationModel" type="select" label="minimum reads at a locus to enable using the entropy calculation" help="-model,‑‑consensusDeterminationModel &lt;consensusDeterminationModel&gt;"> - <option value="USE_READS">USE_READS - Additionally uses indels already present in the original alignments of the reads</option> - <option value="KNOWNS_ONLY">KNOWNS_ONLYS - Uses only indels from a provided ROD of known indels</option> - <option value="USE_SW">USE_SW - Additionally uses 'Smith-Waterman' to generate alternate consenses</option> - </param> - <param name="LODThresholdForCleaning" type="float" value="5.0" label="LOD threshold above which the cleaner will clean" help="-LOD,‑‑LODThresholdForCleaning &lt;LODThresholdForCleaning&gt;" /> - <!--param name="nWayOut" type="float" value="5.0" label="Generate one output file for each input (-I) bam file (not compatible with -output)" help="-nWayOut,--nWayOut &lt;nWayOut&gt;" /--> - </expand> - - - <expand macro="macro_advanced_parameters"> - <param name="entropyThreshold" type="float" value="0.15" label="Percentage of mismatches at a locus to be considered having high entropy (0.0 < entropy <= 1.0)" help="-entropy,‑‑entropyThreshold &lt;entropyThreshold&gt;" /> - - <param name="maxConsensuses" type="integer" value="30" label="Max alternate consensuses to try (necessary to improve performance in deep coverage)" help="-maxConsensuses,‑‑maxConsensuses &lt;maxConsensuses&gt;" /> - - <param name="maxIsizeForMovement" type="integer" value="3000" label="maximum insert size of read pairs that we attempt to realign" help="-maxIsize,‑‑maxIsizeForMovement &lt;maxIsizeForMovement&gt;" /> - - <param name="maxPositionalMoveAllowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,‑‑maxPositionalMoveAllowed &lt;maxPositionalMoveAllowed&gt;" /> - - <param name="maxReadsForConsensuses" type="integer" value="120" label="Max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)" help="-greedy,‑‑maxReadsForConsensuses &lt;maxReadsForConsensuses&gt;" /> - - <param name="maxReadsForRealignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,‑‑maxReadsForRealignment &lt;maxReadsForRealignment&gt;" /> - - <param name="maxReadsInMemory" type="integer" value="150000" label="max reads allowed to be kept in memory at a time by the SAMFileWriter" help="-maxInMemory,‑‑maxReadsInMemory &lt;maxReadsInMemory&gt;" /> - - <param name="noOriginalAlignmentTags" type="boolean" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,‑‑noOriginalAlignmentTags" /> - </expand> - - </xml> - - <xml name="IndelRealignerOutput"> - <data format="bam" name="ir_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)"> - <yield /> - </data> - </xml> - - <template name="IndelRealignerPreprocessing"> -<![CDATA[ - @token_bam_input_pre@ - - ln -s -f ${analysis_type.targetIntervals} target.intervals && - - #if $analysis_type.optional_parameters.optional_parameters_enabled - #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles): - ln -s -f ${knownAllele.knownAllele} knownAllele_${i}.vcf && - #end for - #end if -]]> - </template> - - <template name="IndelRealignerOptions"> -<![CDATA[ - --out ${ir_output_bam} - - @token_bam_input@ - --targetIntervals target.intervals - - #if $analysis_type.optional_parameters.optional_parameters_enabled - #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles): - --knownAlleles knownAllele_${i}.vcf - #end for - --consensusDeterminationModel ${analysis_type.consensusDeterminationModel} - --LODThresholdForCleaning ${analysis_type.LODThresholdForCleaning} - #end if - - #if $analysis_type.advanced_parameters.advanced_parameters_enabled - --entropyThreshold ${analysis_type.advanced_parameters.entropyThreshold} - --maxConsensuses ${analysis_type.advanced_parameters.maxConsensuses} - --maxIsizeForMovement ${analysis_type.advanced_parameters.maxIsizeForMovement} - --maxPositionalMoveAllowed ${analysis_type.advanced_parameters.maxPositionalMoveAllowed} - --maxReadsForConsensuses ${analysis_type.advanced_parameters.maxReadsForConsensuses} - --maxReadsForRealignment ${analysis_type.advanced_parameters.maxReadsForRealignment} - --maxReadsInMemory ${analysis_type.advanced_parameters.maxReadsInMemory} - ${analysis_type.advanced_parameters.noOriginalAlignmentTags} - #end if -]]> - </template> -</macros>
--- a/GATK/gatk/print_reads.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -<macros> - <xml name="PrintReadsParameters" tokens="tag"> - - <expand macro="macro_bam_input" tag="@TAG@" /> - - <!-- BQSR in main config --> - - <expand macro="macro_optional_parameters"> - - <param name="number" type="integer" value="" optional="true" label="Print the first n reads from the file, discarding the rest" help="-n,‑‑number &lt;number&gt;" /> - - <param name="platform" type="text" value="" optional="true" label="Exclude all reads with this platform from the output" help="-platform,‑‑platform &lt;platform&gt;" /> - - <param name="readGroup" type="text" value="" optional="true" label="Exclude all reads with this read group from the output" help="-readGroup,‑‑readGroup &lt;readGroup&gt;" /> - - <param name="sample_file" type="data" format="txt" optional="true" label="File containing a list of samples (one per line). Can be specified multiple times" help="-sf,‑‑sample_file &lt;sample_file&gt;" /> - - <repeat name="sample_names" title="Sample names to be included in the analysis" help="-sn,‑‑sample_name &lt;sample_name&gt;"> - <param name="sample_name" type="text" value="" title="Sample name to be included in the analysis" /> - </repeat> - - <param name="simplify" type="text" truevalue="-s" falsevalue="" label="Erase all extra attributes in the read but keep the read group information" help="-s,‑‑simplify" /> - - </expand> - - </xml> - - <xml name="PrintReadsOutput"> - <data format="bam" name="pr_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)"> - <yield /> - </data> - </xml> - - <template name="PrintReadsPreprocessing"> -<![CDATA[ - @token_bam_input_pre@ -]]> - </template> - - <template name="PrintReadsOptions"> -<![CDATA[ - --out ${pr_output_bam} - - @token_bam_input@ - - #set $optionals = $analysis_type.optional_parameters - #if $optionals.optional_parameters_enabled - #if int($optionals.number) > 0 - --number $optionals.number - #end if - #if str($optionals.platform) - --platform $optionals.platform - #end if - #if str($optionals.readGroup) - --readGroup $optionals.readGroup - #end if - #if $optionals.sample_file - --sample_file $optionals.sample_file - #end if - #if $optionals.sample_names - #for $sample in $optionals.sample_names: - --intervals ${sample.sample_name} - #end for - #end if - $optionals.simplify - #end if -]]> - </template> -</macros> - -
--- a/GATK/gatk/realigner_target_creator.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -<macros> - <xml name="RealignerTargetCreatorParameters" tokens="tag"> - - <expand macro="macro_bam_input" tag="@TAG@" /> - - <expand macro="macro_optional_parameters"> - <param name="maxIntervalSize" type="integer" value="500" label="maximum interval size; any intervals larger than this value will be dropped" help="-maxInterval,‑‑maxIntervalSize &lt;maxIntervalSize&gt;" /> - <param name="minReadsAtLocus" type="integer" value="4" label="minimum reads at a locus to enable using the entropy calculation" help="-minReads,‑‑minReadsAtLocus &lt;minReadsAtLocus&gt;" /> - <param name="windowSize" type="integer" value="10" label="window size for calculating entropy or SNP clusters" help="-window,‑‑windowSize &lt;windowSize&gt;" /> - - <param name="mismatchFraction" type="float" value="0.0" label="fraction of base qualities needing to mismatch for a position to have high entropy" help="-mismatch,‑‑mismatchFraction &lt;mismatchFraction&gt;" /> - <repeat name="rod_bindings" title="Input VCF files with known indels" help="-known,‑‑known &lt;known&gt;"> - <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> - </repeat> - </expand> - - </xml> - - <xml name="RealignerTargetCreatorOutput"> - <data format="gatk_interval" name="rtc_output_intervals" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (GATK intervals)"> - <yield /> - </data> - </xml> - - <template name="RealignerTargetCreatorPreprocessing"> -<![CDATA[ - @token_bam_input_pre@ - - #if $analysis_type.optional_parameters.optional_parameters_enabled - #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings): - ln -s -f ${rod_binding.input_rod} rod_binding_${i}.vcf && - #end for - #end if -]]> - </template> - - <template name="RealignerTargetCreatorOptions"> -<![CDATA[ - --out ${rtc_output_intervals} - - @token_bam_input@ - - #if $analysis_type.optional_parameters.optional_parameters_enabled - --maxIntervalSize ${analysis_type.optional_parameters.maxIntervalSize} - --minReadsAtLocus ${analysis_type.optional_parameters.minReadsAtLocus} - --windowSize ${analysis_type.optional_parameters.windowSize} - --mismatchFraction ${analysis_type.optional_parameters.mismatchFraction} - - #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings): - --known rod_binding_${i}.vcf - #end for - #end if -]]> - </template> -</macros> - -
--- a/GATK/gatk/tool-data/destinations.py Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -from galaxy.jobs import JobDestination -import os -import sys -import json -import cStringIO -import logging - -log = logging.getLogger( __name__ ) - - -def dump(obj, nested_level=0, output=sys.stdout): - spacing = ' ' - if type(obj) == dict: - print >> output, '%s{' % ((nested_level) * spacing) - for k, v in obj.items(): - if hasattr(v, '__iter__'): - print >> output, '%s%s:' % ((nested_level + 1) * spacing, k) - dump(v, nested_level + 1, output) - else: - print >> output, '%s%s: %s' % ((nested_level + 1) * spacing, k, v) - print >> output, '%s}' % (nested_level * spacing) - elif type(obj) == list: - print >> output, '%s[' % ((nested_level) * spacing) - for v in obj: - if hasattr(v, '__iter__'): - dump(v, nested_level + 1, output) - else: - print >> output, '%s%s' % ((nested_level + 1) * spacing, v) - print >> output, '%s]' % ((nested_level) * spacing) - else: - print >> output, '%s%s' % (nested_level * spacing, obj) - - -def dynamic_slurm_cluster_gatk(job, tool_id): - # Allocate extra time - inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) - inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) - inp_data.update( [ ( da.name, json.loads(da.value) ) for da in job.parameters ] ) - out = cStringIO.StringIO() - dump(inp_data, 1, out) - log.debug(out.getvalue()) - - nativeSpecs = '--nodes=1 --ntasks=1' - - # runner doesn't allow to specify --cpus-per-task - # thus the mem calculation gets messy with more than 1 node - # --> translate nt ==> nodes, nct ==> ntasks - - if 'cond_threads' not in inp_data: - return JobDestination(runner="slurm") - - if inp_data['cond_threads']['cond_threads_enabled'] == "True": - nNodes = int(inp_data['cond_threads']['nt']) - nCPU = int(inp_data['cond_threads']['nct']) - nMEM = int(inp_data['cond_threads']['mem']) - if nMEM > 0: - nativeSpecs = '--nodes=%d --ntasks=%d --mem=%d' % (nNodes, nCPU*nNodes, nMEM) - else: - nativeSpecs = '--nodes=%d --ntasks=%d' % (nNodes, nCPU*nNodes) - - return JobDestination(runner="slurm", params={"nativeSpecification": nativeSpecs}) -
--- a/GATK/gatk/tool-data/picard_index.loc.sample Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Picard dict and associated files. You will need -#to create these data files and then create a picard_index.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The picard_index.loc -#file has this format (longer white space is the TAB character): -# -#<unique_build_id> <dbkey> <display_name> <fasta_file_path> -# -#So, for example, if you had hg18 indexed and stored in -#/depot/data2/galaxy/srma/hg18/, -#then the srma_index.loc entry would look like this: -# -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa -# -#and your /depot/data2/galaxy/srma/hg18/ directory -#would contain the following three files: -#hg18.fa -#hg18.dict -#hg18.fa.fai -# -#The dictionary file for each reference (ex. hg18.dict) must be -#created via Picard (http://picard.sourceforge.net). Note that -#the dict file does not have the .fa extension although the -#path list in the loc file does include it. -#
--- a/GATK/gatk/tool_data_table_conf.xml.sample Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<tables> - <!-- Location of Picard dict files valid for GATK --> - <table name="picard_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/picard_index.loc" /> - </table> -</tables>
--- a/GATK/gatk/tool_dependencies.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="GATK_PATH">/mnt/galaxy/tools/GATK/3.4-0</environment_variable> - </set_environment> - <!-- - Use GATK_SITE_OPTIONS to set additional parameters that should be inserted in every GATK call. - The intended use case was to prohibit GATK to collect and send data. - For example: - - -et "NO_ET" -K "/data/gatk_key_file" ##ET no phone home - --> - <set_environment version="1.0"> - <environment_variable action="set_to" name="GATK_SITE_OPTIONS"> </environment_variable> - </set_environment> - <package name="package_r_for_gatk_3_4_0" version="3.1.2.1"> - <repository changeset_revision="49c62e9b71ad" name="package_r_for_gatk_3_4_0" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/GATK/package_picard_1_135/tool_dependencies.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="picard" version="1.135"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">https://github.com/broadinstitute/picard/releases/download/1.135/picard-tools-1.135.zip</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> - <readme> -This picard package dependency is retrieved directly from https://github.com/broadinstitute/picard/releases - </readme> - </package> -</tool_dependency>
--- a/GATK/package_r_for_gatk_3_4_0/tool_dependencies.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="3.1.2"> - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="package_r_for_gatk_3_4_0" version="3.1.2.1"> - <install version="1.0"> - <actions> - <action type="setup_r_environment"> - - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="R" version="3.1.2" /> - </repository> - <package>https://github.com/cran/stringi/archive/0.5-5.tar.gz</package> - <package>https://github.com/cran/magrittr/archive/1.5.tar.gz</package> - <package>https://github.com/cran/stringr/archive/1.0.0.tar.gz</package> - <package>https://github.com/cran/RColorBrewer/archive/1.1-2.tar.gz</package> - <package>https://github.com/cran/dichromat/archive/2.0-0.tar.gz</package> - <package>https://github.com/cran/colorspace/archive/1.2-6.tar.gz</package> - <package>https://github.com/cran/munsell/archive/0.4.2.tar.gz</package> - <package>https://github.com/cran/labeling/archive/0.3.tar.gz</package> - <package>https://github.com/cran/Rcpp/archive/0.11.6.tar.gz</package> - <package>https://github.com/cran/digest/archive/0.6.8.tar.gz</package> - <package>https://github.com/cran/gtable/archive/0.1.2.tar.gz</package> - <package>https://github.com/cran/bitops/archive/1.0-6.tar.gz</package> - <package>https://github.com/cran/caTools/archive/1.17.1.tar.gz</package> - <package>https://github.com/cran/gtools/archive/3.5.0.tar.gz</package> - <package>https://github.com/cran/gdata/archive/2.17.0.tar.gz</package> - <package>https://github.com/cran/gsalib/archive/2.1.tar.gz</package> - <package>https://github.com/cran/gplots/archive/2.17.0.tar.gz</package> - <package>https://github.com/cran/plyr/archive/1.8.3.tar.gz</package> - <package>https://github.com/cran/reshape/archive/0.8.5.tar.gz</package> - <package>https://github.com/cran/reshape2/archive/1.4.1.tar.gz</package> - <package>https://github.com/cran/scales/archive/0.2.5.tar.gz</package> - <package>https://github.com/cran/proto/archive/0.3-10.tar.gz</package> - <package>https://github.com/cran/MASS/archive/7.3-43.tar.gz</package> - <package>https://github.com/cran/ggplot2/archive/1.0.1.tar.gz</package> - </action> - </actions> - </install> - <readme> - ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and none of the bad parts. - It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics. - - http://ggplot2.org/ - </readme> - </package> -</tool_dependency>
--- a/Galaxy-Workflow-Haplotypecaller.ga Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "Haplotypecaller", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 175, - "top": 204 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [], - "uuid": "e6bc3c94-7207-4af0-a856-666d00515f57" - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": { - "analysis_type|cond_bam_input|input": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "GATK", - "outputs": [ - { - "name": "rtc_output_intervals", - "type": "gatk_interval" - }, - { - "name": "ir_output_bam", - "type": "bam" - }, - { - "name": "br_table", - "type": "tabular" - }, - { - "name": "ac_plotsReportFile", - "type": "pdf" - }, - { - "name": "pr_output_bam", - "type": "bam" - }, - { - "name": "hc_output_gvcf", - "type": "vcf" - }, - { - "name": "gg_output_gvcf", - "type": "vcf" - }, - { - "name": "cg_output_vcf", - "type": "vcf" - }, - { - "name": "cv_output_vcf", - "type": "vcf" - }, - { - "name": "output_log", - "type": "txt" - } - ], - "position": { - "left": 381, - "top": 196 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/scisjnu123/test/gatk/3.4-0.d9", - "tool_state": "{\"__page__\": 0, \"cond_threads\": \"{\\\"cond_threads_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"ref_file\": \"\\\"ebola\\\"\", \"__rerun_remap_job_id__\": null, \"cond_BQSR\": \"{\\\"cond_BQSR_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"HaplotypeCaller\\\", \\\"cond_usage\\\": {\\\"emitRefConfidence\\\": \\\"GVCF\\\", \\\"__current_case__\\\": 0, \\\"cond_usage_selector\\\": \\\"GVCF\\\"}, \\\"optional_parameters\\\": {\\\"optional_parameters_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"cond_bam_input\\\": {\\\"input\\\": null, \\\"all_in_one\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 5}\", \"cond_intervals\": \"{\\\"cond_intervals_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "3.4-0.d9", - "type": "tool", - "user_outputs": [], - "uuid": "7c602119-d676-4bf2-ac8d-0369e875e5fe" - } - }, - "uuid": "3855b137-2a43-4c8f-80f5-79d820d618ed" -} \ No newline at end of file
--- a/Galaxy-Workflow-SAMTools.ga Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "This workflow uses SAMTools to call SNPs and INDELs.", - "format-version": "0.1", - "name": "SAMTools", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": ".bam file" - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 200, - "top": 156 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \".bam file\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [], - "uuid": "955f71da-3fad-46c4-a1d9-b0b1cb484569" - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Reference genome." - } - ], - "label": null, - "name": "Input dataset", - "outputs": [], - "position": { - "left": 512, - "top": 285 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Reference genome.\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [], - "uuid": "7069b8d2-a89a-472a-8e18-b5b8f076de33" - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "inputFile": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SortSam", - "outputs": [ - { - "name": "outFile", - "type": "bam" - } - ], - "position": { - "left": 436.5, - "top": 121 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_SortSam/1.135", - "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"coordinate\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", - "tool_version": "1.135", - "type": "tool", - "user_outputs": [], - "uuid": "b06955b6-6bba-4aaa-a919-fbb2aba9fdf5" - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "reference_source|input_bams_0|input_bam": { - "id": 2, - "output_name": "outFile" - }, - "reference_source|ref_file": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "MPileup", - "outputs": [ - { - "name": "output_mpileup", - "type": "pileup" - }, - { - "name": "output_log", - "type": "txt" - } - ], - "position": { - "left": 746, - "top": 192 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", - "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", - "tool_version": "0.0.3", - "type": "tool", - "user_outputs": [], - "uuid": "99b58983-e355-4357-b77e-8e29afcdc866" - } - }, - "uuid": "6b217aca-887a-4cca-91e4-446a7cc50726" -} \ No newline at end of file
--- a/Galaxy-Workflow-SVDetect.ga Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,163 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "This workflows uses SVDetect to call structural variants.", - "format-version": "0.1", - "name": "SVDetect", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [], - "label": null, - "name": "Import data", - "outputs": [ - { - "name": "outbamfile", - "type": "bam" - }, - { - "name": "outlenfile", - "type": "len" - }, - { - "name": "outsvfile", - "type": "sv" - } - ], - "position": { - "left": 164, - "top": 190 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect/svdetect_import/1.0.0", - "tool_state": "{\"file_name\": \"\\\"file1\\\"\", \"__rerun_remap_job_id__\": null, \"type\": \"{\\\"file_type\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}\", \"file_path\": \"\\\"\\\"\", \"__page__\": 0}", - "tool_version": "1.0.0", - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard/read_group_macros.xml Fri Sep 13 02:21:23 2019 -0400 @@ -0,0 +1,294 @@ +<macros> + <!-- Import this at the top of your command block and then + define rg_auto_name. --> + <token name="@define_read_group_helpers@"> +#def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq') + #end if +#end def + +#def clean(name) + #import re + #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) + #return $name_clean +#end def + +#def read_group_name_default($input1, $input2=None) + #if $input2 is None + #return $clean($identifier_or_name($input1)) + #else + #import itertools + #set $input_name1 = $clean($identifier_or_name($input1)) + #set $input_name2 = $clean($identifier_or_name($input2)) + #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))]) + #if len($common_prefix) > 3 + #return $common_prefix + #else + #return $input_name1 + #end if + #end if +#end def + +#def format_read_group(prefix, value, quote='', arg='') + #if $value + #return $arg + $quote + $prefix + $value + $quote + #else + #return '' + #end if +#end def + +#def rg_param(name) + #if $varExists("rg") + #return $rg.get($name, None) + #else + #return $getVar($name, None) + #end if +#end def + +#set $use_rg = True + </token> + <!-- preconditions use_rg and rg_auto_name have been + defined. + --> + <token name="@set_read_group_vars@"> +#if $use_rg + #if $rg_param('read_group_id_conditional') is None + #set $rg_id = $rg_auto_name + #elif $rg_param('read_group_id_conditional').do_auto_name + #set $rg_id = $rg_auto_name + #else + #set $rg_id = str($rg_param('read_group_id_conditional').ID) + #end if + + #if $rg_param('read_group_sm_conditional') is None + #set $rg_sm = '' + #elif $rg_param('read_group_sm_conditional').do_auto_name + #set $rg_sm = $rg_auto_name + #else + #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) + #end if + + #if $rg_param('PL') + #set $rg_pl = str($rg_param('PL')) + #else + #set $rg_pl = '' + #end if + + #if $rg_param('read_group_lb_conditional') is None + #set $rg_lb = '' + #elif $rg_param('read_group_lb_conditional').do_auto_name + #set $rg_lb = $rg_auto_name + #else + #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) + #end if + + #if $rg_param('CN') + #set $rg_cn = str($rg_param('CN')) + #else + #set $rg_cn = '' + #end if + + #if $rg_param("DS") + #set $rg_ds = str($rg_param("DS")) + #else + #set $rg_ds = '' + #end if + + #if $rg_param("DT") + #set $rg_dt = str($rg_param("DT")) + #else + #set $rg_dt = '' + #end if + + #if $rg_param("FO") + #set $rg_fo = str($rg_param("FO")) + #else + #set $rg_fo = '' + #end if + + #if $rg_param("KS") + #set $rg_ks = str($rg_param("KS")) + #else + #set $rg_ks = '' + #end if + + #if $rg_param("PG") + #set $rg_pg = str($rg_param("PG")) + #else + #set $rg_pg = '' + #end if + + #if str($rg_param("PI")) + #set $rg_pi = str($rg_param("PI")) + #else + #set $rg_pi = '' + #end if + + #if $rg_param("PU") + #set $rg_pu = str($rg_param("PU")) + #else + #set $rg_pu = '' + #end if +#end if + </token> + <token name="@set_use_rg_var@"> +#set $use_rg = str($rg.rg_selector) != "do_not_set" + </token> + <xml name="read_group_auto_name_conditional"> + <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" /> + <when value="true"> + </when> + <when value="false"> + <yield /> + </when> + </xml> + <xml name="read_group_id_param"> + <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> + <validator type="empty_field" /> + </param> + </xml> + <xml name="read_group_id_conditional"> + <conditional name="read_group_id_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_id_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_sm_param"> + <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> + </xml> + <xml name="read_group_sm_conditional"> + <conditional name="read_group_sm_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_sm_param" /> + </expand> + </conditional> + </xml> + <!-- Above SM param is optional (for SAM/BAM spec, this is required + as per Picard. + --> + <xml name="read_group_sm_param_required"> + <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> + <validator type="empty_field" /> + </param> + </xml> + <xml name="read_group_sm_required_conditional"> + <conditional name="read_group_sm_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_sm_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_pl_param"> + <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)"> + <option value="CAPILLARY">CAPILLARY</option> + <option value="LS454">LS454</option> + <option selected="True" value="ILLUMINA">ILLUMINA</option> + <option value="SOLID">SOLID</option> + <option value="HELICOS">HELICOS</option> + <option value="IONTORRENT">IONTORRENT</option> + <option value="PACBIO">PACBIO</option> + </param> + </xml> + <xml name="read_group_lb_param"> + <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" /> + </xml> + <xml name="read_group_lb_conditional"> + <conditional name="read_group_lb_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_lb_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_lb_required_param"> + <param name="LB" type="text" size="25" label="Library name (LB)" optional="false"> + <validator type="empty_field" /> + </param> + </xml> + <xml name="read_group_lb_required_conditional"> + <conditional name="read_group_lb_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_lb_required_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_cn_param"> + <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" /> + </xml> + <xml name="read_group_ds_param"> + <param name="DS" type="text" size="25" label="Description (DS)" /> + </xml> + <xml name="read_group_dt_param"> + <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> + </xml> + <xml name="read_group_fo_param"> + <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> + <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> + </param> + </xml> + <xml name="read_group_ks_param"> + <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> + </xml> + <xml name="read_group_pg_param"> + <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" /> + </xml> + <xml name="read_group_pi_param"> + <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> + </xml> + <xml name="read_group_pu_param"> + <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> + </xml> + <xml name="read_group_pu_required_param"> + <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + </xml> + <!-- Only ID is required - all groups available --> + <xml name="read_group_inputs_spec"> + <expand macro="read_group_id_conditional" /> + <expand macro="read_group_sm_conditional" /> + <expand macro="read_group_pl_param" /> + <expand macro="read_group_lb_conditional" /> + <expand macro="read_group_cn_param" /> + <expand macro="read_group_ds_param" /> + <expand macro="read_group_dt_param" /> + <expand macro="read_group_fo_param" /> + <expand macro="read_group_ks_param" /> + <expand macro="read_group_pg_param" /> + <expand macro="read_group_pi_param" /> + <expand macro="read_group_pu_param" /> + </xml> + <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. --> + <xml name="read_group_inputs_picard"> + <expand macro="read_group_id_conditional" /> + <expand macro="read_group_sm_required_conditional" /> + <expand macro="read_group_lb_required_conditional" /> + <expand macro="read_group_pl_param" /> + <expand macro="read_group_pu_required_param" /> + <expand macro="read_group_cn_param" /> + <expand macro="read_group_ds_param" /> + <expand macro="read_group_pi_param" /> + <expand macro="read_group_dt_param" /> + </xml> + <xml name="read_group_conditional"> + <conditional name="rg"> + <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets."> + <option value="set">Set read groups (SAM/BAM specification)</option> + <option value="set_picard">Set read groups (Picard style)</option> + <option value="set_id_auto">Automatically assign ID</option> + <option value="do_not_set" selected="True">Do not set</option> + </param> + <when value="set_picard"> + <expand macro="read_group_inputs_picard" /> + </when> + <when value="set"> + <expand macro="read_group_inputs_spec" /> + </when> + <when value="set_id_auto"> + </when> + <when value="do_not_set"> + </when> + </conditional> + </xml> +</macros>
--- a/sr_assembly/velvetg.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,301 +0,0 @@ -<tool id="velvetg" name="velvetg" version="1.0.0"> - <description>Velvet sequence assembler for very short reads</description> - <version_command>velvetg 2>&1 | grep "Version" | sed -e 's/Version //'</version_command> - <command interpreter="python"> - velvetg_wrapper.py - '$input.extra_files_path' - #if $generate_amos.afg == "yes": - -amos_file $generate_amos.afg - #end if - #if $unused_reads.generate_unused == "yes": - -unused_reads $unused_reads.generate_unused - #end if - $read_trkg - #if $coverage.cutoff == "auto": - -cov_cutoff auto - #elif $coverage.cutoff == "value": - -cov_cutoff $coverage.cov_cutoff - #end if - #if $expected.coverage == "auto": - -exp_cov auto - #elif $expected.coverage == "value": - -exp_cov $expected.exp_cov - #end if - #if $contig_lgth.use_contig_lgth == "yes": - -min_contig_lgth $contig_lgth.min_contig_lgth - #end if - #if $reads.paired == "yes": - #if int($reads.ins_length) > 0: - -ins_length $reads.ins_length - #end if - #if $reads.options.advanced == "yes": - #if int($reads.options.ins_length_sd) > 0: - -ins_length_sd $reads.options.ins_length_sd - #end if - #if int($reads.options.ins_length2) > 0: - -ins_length2 $reads.options.ins_length2 - #end if - #if int($reads.options.ins_length2_sd) > 0: - -ins_length2_sd $reads.options.ins_length2_sd - #end if - #if int($reads.options.ins_length_long) > 0: - -ins_length_long $reads.options.ins_length_long - #end if - #if int($reads.options.ins_length_long_sd) > 0: - -ins_length_long_sd $reads.options.ins_length_long_sd - #end if - #if int($reads.options.max_branch_length) > 0: - -max_branch_length $reads.options.max_branch_length - #end if - #if int($reads.options.max_divergence) > 0: - -max_divergence $reads.options.max_divergence - #end if - #if int($reads.options.max_gap_count) > 0: - -max_gap_count $reads.options.max_gap_count - #end if - #if int($reads.options.min_pair_count) > 0: - -min_pair_count $reads.options.min_pair_count - #end if - #if int($reads.options.max_coverage) > 0: - -max_coverage $reads.options.max_coverage - #end if - #if int($reads.options.long_mult_cutoff) > 0: - -long_mult_cutoff $reads.options.long_mult_cutoff - #end if - $reads.options.scaffolding - #end if - #end if - </command> - <inputs> - <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/> - <conditional name="generate_amos"> - <param name="afg" type="select" label="Generate a AMOS.afg file"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"/> - </conditional> - - <conditional name="unused_reads"> - <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"/> - </conditional> - - <conditional name="last_graph"> - <param name="generate_graph" type="select" label="Generate velvet LastGraph file"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"/> - </conditional> - - <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" /> - - <conditional name="coverage"> - <param name="cutoff" type="select" label="Coverage cutoff" help=""> - <option value="none">None</option> - <option value="auto">Automatically Determined</option> - <option value="value">Specify Cutoff Value</option> - </param> - <when value="none"/> - <when value="auto"/> - <when value="value"> - <param name="cov_cutoff" value = "10.0" label="Remove nodes with coverage below" type="float" /> - </when> - </conditional> - - <conditional name="expected"> - <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help=""> - <option value="none">None</option> - <option value="auto">Automatically Determined</option> - <option value="value">Specify Expected Value</option> - </param> - <when value="none"/> - <when value="auto"/> - <when value="value"> - <param name="exp_cov" value = "10.0" label="Remove nodes with coverage below" type="float" /> - </when> - </conditional> - - <conditional name="contig_lgth"> - <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2)."> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="min_contig_lgth" value = "42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/> - </when> - </conditional> - - <conditional name="reads"> - <param name="paired" type="select" label="Using Paired Reads"> - <option value="no">No</option> - <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="ins_length" value = "-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/> - <conditional name="options"> - <param name="advanced" type="select" label="Velvet Advanced Options"> - <option value="no">Use Defaults</option> - <option value="yes">Set Advanced Option Values</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="ins_length_sd" value = "-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/> - <param name="ins_length2" value = "-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/> - <param name="ins_length2_sd" value = "-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/> - <param name="ins_length_long" value = "-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/> - <param name="ins_length_long_sd" value = "-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/> - <param name="max_branch_length" value = "-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/> - <param name="max_divergence" value = "-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/> - <param name="max_gap_count" value = "-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/> - <param name="min_pair_count" value = "-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/> - <param name="max_coverage" value = "-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/> - <param name="long_mult_cutoff" value = "-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/> - <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/> - - </when> - </conditional> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2"> - <filter>read_trkg is True</filter> - </data> - <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph"> - <filter>last_graph['generate_graph'] == "yes"</filter> - </data> - <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg"> - <filter>generate_amos['afg'] == "yes"</filter> - </data> - <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa"> - <filter>unused_reads['generate_unused'] == "yes"</filter> - </data> - <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" /> - <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" /> - </outputs> - <requirements> - <requirement type="package">velvet</requirement> - </requirements> - <tests> - <test> - <param name="input" value="velveth_test1/output.html" ftype="velvet" > - <composite_data value='velveth_test1/Sequences' ftype="Sequences"/> - <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/> - <composite_data value='velveth_test1/Log'/> - </param> - <param name="afg" value="yes" /> - <param name="generate_unused" value="yes" /> - <param name="generate_graph" value="no" /> - <param name="read_trkg" value="-read_trkg no" /> - <param name="cutoff" value="auto" /> - <param name="coverage" value="auto" /> - <param name="use_contig_lgth" value="no" /> - <param name="paired" value="no" /> - <!-- - <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/> - --> - <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/> - <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/> - <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/> - <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/> - </test> - </tests> - <help> -**Velvet Overview** - -Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. - -Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. - -Read the Velvet `documentation`__ for details on using the Velvet Assembler. - -.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/ - -.. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf - ------- - -**Input formats** - -Velvet can input sequence files in the following formats: fasta fastq fasta.gz fastq.gz eland gerald - -The input files are prepared for the velvet assembler using **velveth**. - ------- - -**Outputs** - -**Contigs** - -The *contigs.fa* file. -This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig length threshold, then the contigs shorter than that value are omitted. -Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively. -The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's. - -**Stats** - -The *stats.txt* file. -This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth. -The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively. -The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1). -Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account. - -**LastGraph** - -The *LastGraph* file. -This file describes in its entirety the graph produced by Velvet. - -**AMOS.afg** - -The *velvet_asm.afg* file. -This file is mainly designed to be read by the open-source AMOS genome assembly package. Nonetheless, a number of programs are available to transform this kind of file into other assembly file formats (namely ACE, TIGR, Arachne and Celera). See http://amos.sourceforge.net/ for more information. -The file describes all the contigs contained in the contigs.fa file (cf 4.2.1). - ------- - -**Velvet parameter list** - -This is a list of implemented Velvetg options:: - - Standard options: - -cov_cutoff floating-point|auto : removal of low coverage nodes AFTER tour bus or allow the system to infer it - (default: no removal) - -ins_length integer : expected distance between two paired end reads (default: no read pairing) - -read_trkg yes|no : tracking of short read positions in assembly (default: no tracking) - -min_contig_lgth integer : minimum contig length exported to contigs.fa file (default: hash length * 2) - -amos_file yes|no : export assembly to AMOS file (default: no export) - -exp_cov floating point|auto : expected coverage of unique regions or allow the system to infer it - (default: no long or paired-end read resolution) - - Advanced options: - -ins_length2 integer : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing) - -ins_length_long integer : expected distance between two long paired-end reads (default: no read pairing) - -ins_length*_sd integer : est. standard deviation of respective dataset (default: 10% of corresponding length) - [replace '*' by nothing, '2' or '_long' as necessary] - -scaffolding yes|no : scaffolding of contigs used paired end information (default: on) - -max_branch_length integer : maximum length in base pair of bubble (default: 100) - -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2) - -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3) - -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10) - -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal) - -long_mult_cutoff int : minimum number of long reads required to merge contigs (default: 2) - -unused_reads yes|no : export unused reads in UnusedReads.fa file (default: no) - - Output: - directory/contigs.fa : fasta file of contigs longer than twice hash length - directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff - directory/LastGraph : special formatted file with all the information on the final graph - directory/velvet_asm.afg : (if requested) AMOS compatible assembly file - - </help> -</tool>
--- a/sr_assembly/velvetg_wrapper.py Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -#!/usr/bin/env python - -""" -Classes encapsulating decypher tool. -James E Johnson - University of Minnesota -""" -import os -import sys -import subprocess - -assert sys.version_info[:2] >= ( 2, 4 ) - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - - -def __main__(): - #Parse Command Line - working_dir = sys.argv[1] - inputs = ' '.join(sys.argv[2:]) - for _ in ('Roadmaps', 'Sequences'): - os.symlink(os.path.join(working_dir, _), _) - cmdline = 'velvetg . %s' % (inputs) - print "Command to be executed: %s" % cmdline - try: - proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) - returncode = proc.wait() - # get stderr, allowing for case where it's very large - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += proc.stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error running velvetg ' + str( e ) ) - - -if __name__ == "__main__": - __main__()
--- a/sr_assembly/velveth.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -<tool id="velveth" name="velveth" version="1.0.0"> - <description>Prepare a dataset for the Velvet velvetg Assembler</description> - <version_command>velveth 2>&1 | grep "Version" | sed -e 's/Version //'</version_command> - <command interpreter="python"> - velveth_wrapper.py - '$out_file1' '$out_file1.extra_files_path' - $hash_length - $strand_specific - #for $i in $inputs - ${i.file_format} - ${i.read_type} - ${i.input} - #end for - </command> - <inputs> - <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed."> - <option value="11">11</option> - <option value="13">13</option> - <option value="15">15</option> - <option value="17">17</option> - <option value="19">19</option> - <option value="21" selected="yes">21</option> - <option value="23">23</option> - <option value="25">25</option> - <option value="27">27</option> - <option value="29">29</option> - </param> - <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/> - <repeat name="inputs" title="Input Files"> - <param label="file format" name="file_format" type="select"> - <option value="-fasta" selected="yes">fasta</option> - <option value="-fastq">fastq</option> - <option value="-eland">eland</option> - <option value="-gerald">gerald</option> - </param> - <param label="read type" name="read_type" type="select"> - <option value="-short" selected="yes">short reads</option> - <option value="-shortPaired">shortPaired reads</option> - <option value="-short2">short2 reads</option> - <option value="-shortPaired2">shortPaired2 reads</option> - <option value="-long">long reads</option> - <option value="-longPaired">longPaired reads</option> - </param> - - <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/> - </repeat> - </inputs> - <outputs> - <data format="velvet" name="out_file1" /> - </outputs> - <requirements> - <requirement type="package">velvet</requirement> - </requirements> - <tests> - <test> - <param name="hash_length" value="21" /> - <param name="read_type" value="-shortPaired" /> - <!-- <repeat name="inputs"> --> - <param name="file_format" value="fasta" /> - <param name="read_type" value="shortPaired reads" /> - <param name="input" value="velvet_test_reads.fa" ftype="fasta" /> - <!-- </repeat> --> - <param name="strand_specific" value="" /> - <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> - <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" /> - <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" /> - </output> - </test> - </tests> - <help> -**Velvet Overview** - -Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. - -Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. - -Read the Velvet `documentation`__ for details on using the Velvet Assembler. - -.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/ - -.. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf - ------- - -**Velveth** - -Velveth takes in a number of sequence files, produces a hashtable, then outputs two files in an output directory (creating it if necessary), Sequences and Roadmaps, which are necessary to velvetg. - ------- - -**Hash Length** - -The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed. - -The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints:: - -# it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed. -# it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits -# it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons. - -Now you still have quite a lot of possibilities. As is often the case, it's a trade- off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below). . . so there's a sweet spot to be found with time and experience. -We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C # (L - k + 1)/L where k is your hash length, and L you read length. -Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! - -**Input Files** - -Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate -read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc. - -Supported file formats are:: - - fasta - fastq - fasta.gz - fastq.gz - eland - gerald - -Read categories are:: - - short (default) - shortPaired - short2 (same as short, but for a separate insert-size library) - shortPaired2 (see above) - long (for Sanger, 454 or even reference sequences) - longPaired - - </help> -</tool>
--- a/sr_assembly/velveth_wrapper.py Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -#!/usr/bin/env python - -""" -Classes encapsulating decypher tool. -James E Johnson - University of Minnesota -""" -import pkg_resources -import logging, os, string, sys, tempfile, glob, shutil, types, urllib -import shlex, subprocess -from optparse import OptionParser, OptionGroup -from stat import * - - -log = logging.getLogger( __name__ ) - -assert sys.version_info[:2] >= ( 2, 4 ) - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def __main__(): - #Parse Command Line - s = 'velveth_wrapper.py: argv = %s\n' % (sys.argv) - argcnt = len(sys.argv) - html_file = sys.argv[1] - working_dir = sys.argv[2] - try: # for test - needs this done - os.makedirs(working_dir) - except Exception, e: - stop_err( 'Error running velveth ' + str( e ) ) - hash_length = sys.argv[3] - inputs = string.join(sys.argv[4:],' ') - cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs) - try: - proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) - returncode = proc.wait() - # get stderr, allowing for case where it's very large - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += proc.stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error running velveth ' + str( e ) ) - sequences_path = os.path.join(working_dir,'Sequences') - roadmaps_path = os.path.join(working_dir,'Roadmaps') - rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>'] - rval.append('<div>%s<p/></div>' % (cmdline) ) - rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') - rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) ) - rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) ) - rval.append( '</ul></div></html>' ) - f = file(html_file,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - -if __name__ == "__main__": __main__()
--- a/suite_samtools_0_1_19/repository_dependencies.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<repositories description="A suite of Galaxy utilities associated with version 0.1.19 of the SAMTools package."> - <repository changeset_revision="cf875cbe2df4" name="data_manager_sam_fasta_index_builder" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="250151b4d934" name="bam_to_sam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="853f787ea759" name="pileup_interval" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="a3dd61e7bec1" name="samtools_flagstat" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="cba1944e3ed0" name="samtools_phase" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="fe83e6f8e65e" name="samtools_rmdup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="973fea5b4bdf" name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="74a8d2d60258" name="samtools_slice_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> -</repositories>
--- a/svdetect/BAM_preprocessingPairs.pl Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,340 +0,0 @@ -#!/usr/bin/perl -w - -use strict; -use warnings; -use Getopt::Std; -my $version = '0.5_galaxy'; - -my $SAMTOOLS_BIN_DIR="/home/cbl/Downloads/samtools-1.9/"; - -my %opts = ( t=>1, p=>1, n=>1000000, f=>3, s=>0, S=>10000, o=>"." ); - -getopts('dt:p:n:f:s:S:o:b:l:x:N:', \%opts); #GALAXY - -my $working_dir=($opts{o} ne ".")? $opts{o}:"working directory"; - -my $pt_bad_mates_file=$opts{b}; #GALAXY -my $pt_log_file=$opts{l}; #GALAXY -my $pt_good_mates_file=$opts{x} if($opts{d}); #GALAXY - - -die(qq/ - -Description: - - Preprocessing of mates to get anomalously mapped mate-pair\/paired-end reads as input - for SVDetect. - - From all pairs mapped onto the reference genome, this script outputs abnormal pairs: - - mapped on two different chromosomes - - with an incorrect strand orientation and\/or pair order - - with an insert size distance +- sigma threshold - into a file <prefix.ab.bam\/sam> - - -BAM\/SAM File input format only, sorted by read names - - Version : $version - SAMtools required for BAM files - - -Usage: BAM_preprocessingPairs.pl [options] <all_mate_file.sorted.bam\/sam> - -Options: -t BOOLEAN read type: =1 (Illumina), =0 (SOLiD) [$opts{t}] - -p BOOLEAN pair type: =1 (paired-end), =0 (mate-pair) [$opts{p}] - -n INTEGER number of pairs for calculating mu and sigma lengths [$opts{n}] - -s INTEGER minimum value of ISIZE for calculating mu and sigma lengths [$opts{s}] - -S INTEGER maximum value of ISIZE for calculating mu and sigma lengths [$opts{S}] - -f REAL minimal number of sigma fold for filtering pairs [$opts{f}] - -d dump normal pairs into a file [<prefix.norm.bam\/sam>] (optional) - -o STRING output directory [$working_dir] - -\n/) if (@ARGV == 0 && -t STDIN); - -unless (-d $opts{o}){ - mkdir $opts{o} or die; -} -$opts{o}.="/" if($opts{o}!~/\/$/); - -my $mates_file=shift(@ARGV); - -$mates_file=readlink($mates_file); - -my $bad_mates_file=(split(/\//,$mates_file))[$#_]; - -if($bad_mates_file=~/.(s|b)am$/){ - $bad_mates_file=~s/.(b|s)am$/.ab.sam/; - $bad_mates_file=$opts{o}.$bad_mates_file; -} - -else{ - die "Error: mate_file with the extension <.bam> or <.sam> needed !\n"; -} - -my $good_mates_file; -if($opts{d}){ - $good_mates_file=(split(/\//,$mates_file))[$#_]; - $good_mates_file=~s/.(b|s)am$/.norm.sam/; - $good_mates_file=$opts{o}.$good_mates_file; -} - -my $log_file=$opts{o}.$opts{N}.".svdetect_preprocessing.log"; #GALAXY - -#------------------------------------------------------------------------------# -#Calculate mu and sigma - -open LOG,">$log_file" or die "$0: can't open ".$log_file.":$!\n"; - -print LOG "\# Calculating mu and sigma lengths...\n"; -print LOG "-- file=$mates_file\n"; -print LOG "-- n=$opts{n}\n"; -print LOG "-- ISIZE min=$opts{s}, max=$opts{S}\n"; - -my ($record, $sumX,$sumX2) = (0,0,0); -my $warn=$opts{n}/10; -my $prev_pair="FIRST"; - -my $bam=($mates_file =~ /.bam$/)? 1:0; - -if($bam){ - open(MATES, "${SAMTOOLS_BIN_DIR}/samtools view $mates_file |") or die "$0: can't open ".$mates_file.":$!\n"; -}else{ - open MATES, "<".$mates_file or die "$0: can't open ".$mates_file.":$!\n"; -} - -while(<MATES>){ - - my @t=split; - - next if ($t[0]=~/^@/); - - my $current_pair=$t[0]; - next if($current_pair eq $prev_pair); - $prev_pair=$current_pair; - - my ($chr1,$chr2,$length)=($t[2],$t[6],abs($t[8])); - - next if (($t[1]&0x0004) || ($t[1]&0x0008)); - next if ($length<$opts{s} || $length>$opts{S}) ; - - if($chr2 eq "="){ - - $sumX += $length; #add to sum and sum^2 for mean and variance calculation - $sumX2 += $length*$length; - $record++; - } - - if($record>$warn){ - print LOG "-- $warn pairs analysed\n"; - $warn+=$warn; - } - - last if ($record>$opts{n}); - -} -close (MATES); - -$record--; -my $mu = $sumX/$record; -my $sigma = sqrt($sumX2/$record - $mu*$mu); - -print LOG "-- Total : $record pairs analysed\n"; -print LOG "-- mu length = ".decimal($mu,1).", sigma length = ".decimal($sigma,1)."\n"; - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Preprocessing pairs - -$warn=100000; - -$record=0; -my %count=( ab=>0, norm=>0, chr=>0, sense=>0, dist=>0, unmap=>0); - -my $read_type=($opts{t})? "Illumina":"SOLiD"; -my $pair_type=($opts{p})? "paired-end":"mate-paired"; - -print LOG "\# Preprocessing pairs...\n"; -print LOG "-- file= $mates_file\n"; -print LOG "-- type= $read_type $pair_type reads\n"; -print LOG "-- sigma threshold= $opts{f}\n"; -print LOG "-- using ".decimal($mu-$opts{f}*$sigma,4)."-".decimal($mu+$opts{f}*$sigma,4)." as normal range of insert size\n"; - -my @header; - -if($bam){ - open(HEADER, "${SAMTOOLS_BIN_DIR}/samtools view -H $mates_file |") or die "$0: can't open ".$mates_file.":$!\n"; - @header=<HEADER>; - close HEADER; - open(MATES, "${SAMTOOLS_BIN_DIR}/samtools view $mates_file |") or die "$0: can't open ".$mates_file.":$!\n"; -}else{ - open MATES, "<".$mates_file or die "$0: can't open ".$mates_file.":$!\n"; -} - -open AB, ">$bad_mates_file" or die "$0: can't write in the output: $bad_mates_file :$!\n"; -print AB @header if($bam); - -if($opts{d}){ - open NORM, ">$good_mates_file" or die "$0: can't write in the output: $good_mates_file :$!\n"; - print NORM @header if($bam); -} - -$prev_pair="FIRST"; -my $prev_bad; - -while(<MATES>){ - - my @t=split; - my $bad=0; - - if ($t[0]=~/^@/){ - print AB; - print NORM if ($opts{d}); - next; - } - - my $current_pair=$t[0]; - if($current_pair eq $prev_pair){ - next if($prev_bad==-1); - if($prev_bad){ - print AB; - }elsif(!$prev_bad){ - print NORM if($opts{d}); - } - next; - } - - $prev_pair=$current_pair; - - my ($chr1,$chr2,$pos1,$pos2,$length)=($t[2],$t[6],$t[3],$t[7], abs($t[8])); - - if (($t[1]&0x0004) || ($t[1]&0x0008)){ - $prev_bad=-1; - $count{unmap}++; - $record++; - next; - - } - - my $strand1 = (($t[1]&0x0010))? 'R':'F'; - my $strand2 = (($t[1]&0x0020))? 'R':'F'; - my $order1 = (($t[1]&0x0040))? '1':'2'; - my $order2 = (($t[1]&0x0080))? '1':'2'; - - if($order1 == 2){ - ($strand1,$strand2)=($strand2,$strand1); - ($chr1,$chr2)=($chr2,$chr1); - ($pos1,$pos2)=($pos2,$pos1); - ($order1,$order2)=($order2,$order1); - } - - my $sense=$strand1.$strand2; - - if($chr1 ne "=" && $chr2 ne "="){ - $bad=1; - $count{chr}++; - } - - if($opts{p}){ #paired-end - if(!(($sense eq "FR" && $pos1<$pos2) || ($sense eq "RF" && $pos2<$pos1))){ - $bad=1; - $count{sense}++; - } - }else{ #mate-pair - if($opts{t}){ #Illumina - if(!(($sense eq "FR" && $pos2<$pos1) || ($sense eq "RF" && $pos1<$pos2))){ - $bad=1; - $count{sense}++; - } - }else{ #SOLiD - if(!(($sense eq "FF" && $pos2<$pos1) || ($sense eq "RR" && $pos1<$pos2))){ - $bad=1; - $count{sense}++; - } - } - } - - if(($chr1 eq "=" || $chr2 eq "=") && ($length <$mu - $opts{f}*$sigma || $length>$mu + $opts{f}*$sigma)){ - $bad=1; - $count{dist}++; - } - - if($bad){ - print AB; - $count{ab}++; - $prev_bad=$bad; - }else{ - print NORM if ($opts{d}); - $count{norm}++; - $prev_bad=$bad; - } - - $record++; - - if($record>$warn){ - print LOG "-- $warn pairs analysed\n"; - $warn+=100000; - } -} - -close AB; -close NORM if($opts{d}); - -print LOG "-- Total : $record pairs analysed\n"; -print LOG "-- $count{unmap} pairs whose one or both reads are unmapped\n"; -print LOG "-- ".($count{ab}+$count{norm})." mapped pairs\n"; -print LOG "---- $count{ab} abnormal mapped pairs\n"; -print LOG "------ $count{chr} pairs mapped on two different chromosomes\n"; -print LOG "------ $count{sense} pairs with incorrect strand orientation and\/or pair order\n"; -print LOG "------ $count{dist} pairs with incorrect insert size distance\n"; -print LOG "--- $count{norm} correct mapped pairs\n"; - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#OUTPUT - -if($bam){ - - my $bam_file=$bad_mates_file; - $bam_file=~s/.sam$/.bam/; - print LOG "\# Converting sam to bam for abnormal mapped pairs\n"; - system("${SAMTOOLS_BIN_DIR}/samtools view -bS $bad_mates_file > $bam_file 2>".$opts{o}."samtools.log"); - unlink($bad_mates_file); - print LOG "-- output created: $bam_file\n"; - - system "rm $pt_bad_mates_file ; ln -s $bam_file $pt_bad_mates_file"; #GALAXY - - if($opts{d}){ - $bam_file=$good_mates_file; - $bam_file=~s/.sam$/.bam/; - print LOG "\# Converting sam to bam for correct mapped pairs\n"; - system("${SAMTOOLS_BIN_DIR}/samtools view -bS $good_mates_file > $bam_file 2>".$opts{o}."samtools.log"); - unlink($good_mates_file); - print LOG "-- output created: $bam_file\n"; - - system "rm $pt_good_mates_file ; ln -s $bam_file $pt_good_mates_file"; #GALAXY - - } - -} - -else{ - print LOG "-- output created: $bad_mates_file\n"; - print LOG "-- output created: $good_mates_file\n" if($opts{d}); -} - -close LOG; - -system "rm $pt_log_file ; ln -s $log_file $pt_log_file"; #GALAXY - - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub decimal{ - - my $num=shift; - my $digs_to_cut=shift; - - $num=sprintf("%.".($digs_to_cut-1)."f", $num) if ($num=~/\d+\.(\d){$digs_to_cut,}/); - - return $num; -} -#------------------------------------------------------------------------------#
--- a/svdetect/BAM_preprocessingPairs.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -<tool id="svdetect_preprocessing" name="BAM preprocessing"> - - <description>to get abnormal pairs</description> - - <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name - #if $newBam.pairNormal=="yes" - -d -x '$normBAM' - #end if - '$inputBam' - </command> - - <inputs> - <param name="sample_name" type="text" value="sample" label="Sample Name"/> - <param name="inputBam" type="data" format="bam" label="BAM input file"/> - <param name="readType" type="select" label="Read type"> - <option value="1">Illumina</option> - <option value="0">SOLiD</option> - </param> - <param name="pairType" type="select" label="Library type"> - <option value="1">Paired-end</option> - <option value="0">Mate-Pair</option> - </param> - <conditional name="newBam"> - <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="yes"> - <!-- do nothing here --> - </when> - <when value="no"> - <!-- do nothing here --> - </when> - </conditional> - <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/> - <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/> - <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/> - <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/> - </inputs> - - <outputs> - <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/> - <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/> - <data format="bam" name="normBAM" label="${$sample_name}.norm.bam"> - <filter>newBam['pairNormal'] == 'yes'</filter> - </data> - </outputs> - - <help> - -**What it does** - -Bam_preprocessingPairs - Version 0.5 - -Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect. - -From all pairs mapped onto the reference genome, this script outputs abnormal pairs: - - * mapped on two different chromosomes - * with an incorrect strand orientation and/or pair order - * with an insert size distance +- sigma threshold - -into a file prefix.ab.bam/sam sorted by read names - --BAM/SAM File input format only. - -SAMtools required for BAM files - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. - - </help> - -</tool>
--- a/svdetect/SVDetect_compare.pl Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,716 +0,0 @@ -#!/usr/bin/perl -w - -=pod - -=head1 NAME - -SVDetect Compare for Galaxy - -Version: 0.8b for Galaxy - -=head1 SYNOPSIS - -SVDetect_compare.pl links2compare -conf <configuration_file> [-help] [-man] - -=cut - -# ------------------------------------------------------------------- - -use strict; -use warnings; - -use Pod::Usage; -use Getopt::Long; - -use Config::General; -use Tie::IxHash; - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#PARSE THE COMMAND LINE -my %OPT; -GetOptions(\%OPT, - 'conf=s', - 'out1=s', #GALAXY - 'out2=s', #GALAXY - 'out3=s', #GALAXY - 'out4=s', #GALAXY - 'out5=s', #GALAXY - 'out6=s', #GALAXY - 'out7=s', #GALAXY - 'out8=s', #GALAXY - 'out9=s', #GALAXY - 'l=s', #GALAXY - 'N=s', #GALAXY - 'help', - 'man' - ); - -pod2usage() if $OPT{help}; -pod2usage(-verbose=>2) if $OPT{man}; -pod2usage(-message=> "$!", -exitval => 2) if (!defined $OPT{conf}); - - -pod2usage() if(@ARGV<1); - -tie (my %func, 'Tie::IxHash',links2compare=>\&links2compare); - -foreach my $command (@ARGV){ - pod2usage(-message=> "Unknown command \"$command\"", -exitval => 2) if (!defined($func{$command})); -} -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#READ THE CONFIGURATION FILE -my $conf=Config::General->new( -ConfigFile => $OPT{conf}, - -Tie => "Tie::IxHash", - -AllowMultiOptions => 1, - -LowerCaseNames => 1, - -AutoTrue => 1); -my %CONF= $conf->getall; -validateconfiguration(\%CONF); #validation of the configuration parameters - - -my $SAMTOOLS_BIN_DIR="/bioinfo/local/samtools"; #GALAXY -my $BEDTOOLS_BIN_DIR="/bioinfo/local/BEDTools/bin"; #GALAXY - -my $pt_log_file=$OPT{l}; #GALAXY -my $log_file=$CONF{general}{output_dir}.$OPT{N}.".svdetect_compare.log"; #GALAXY -open LOG,">$log_file" or die "$0: can't open ".$log_file.":$!\n";#GALAXY - -my @pt_sv_file=($OPT{out1},$OPT{out2},$OPT{out3}) if($OPT{out1}); #GALAXY common,sample,reference -my @pt_circos_file=($OPT{out4},$OPT{out5},$OPT{out6}) if($OPT{out4}); #GALAXY common,sample,reference -my @pt_bed_file=($OPT{out7},$OPT{out8},$OPT{out9}) if($OPT{out7}); #GALAXY common,sample,reference - -$CONF{compare}{sample_link_file}=readlink($CONF{compare}{sample_link_file});#GALAXY -$CONF{compare}{sample_link_file}=~s/.sv.txt//; #GALAXY - -$CONF{compare}{reference_link_file}=readlink($CONF{compare}{reference_link_file});#GALAXY -$CONF{compare}{reference_link_file}=~s/.sv.txt//; #GALAXY - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#COMMAND EXECUTION -foreach my $command (@ARGV){ - &{$func{$command}}(); -} -print LOG "-- end\n"; - -close LOG;#GALAXY -system "rm $pt_log_file ; ln -s $log_file $pt_log_file"; #GALAXY - -exit(0); -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#FUNCTIONS - -# -----------------------------------------------------------------------------# -#MAIN FUNCTION number 5:Comparison between samples, common or specific links -sub links2compare{ - - my @compare_files; - - compareSamples($CONF{general}{output_dir}, - $CONF{compare}{list_samples}, - $CONF{compare}{sample_link_file}, - $CONF{compare}{reference_link_file}, - $CONF{compare}{min_overlap}, - $CONF{compare}{same_sv_type}, - \@compare_files); - - my $pt_ind=0; - - for my $input_file (@compare_files){ - - $input_file=$CONF{general}{output_dir}.$input_file; - - my $output_file=$input_file; - $output_file=~s/unique$/compared/; - - sortLinks($input_file, $output_file,1); - - if($CONF{compare}{circos_output}){ - links2segdup($CONF{circos}{organism_id}, - $CONF{circos}{colorcode}, - $output_file, - $output_file.".segdup.txt"); - system "rm $pt_circos_file[$pt_ind]; ln -s $output_file.segdup.txt $pt_circos_file[$pt_ind]" if (defined $pt_circos_file[$pt_ind]); #GALAXY - } - - if($CONF{compare}{bed_output}){ - links2bedfile($CONF{compare}{read_lengths}, - $CONF{bed}{colorcode}, - $output_file, - $output_file.".bed"); - system "rm $pt_bed_file[$pt_ind]; ln -s $output_file.bed $pt_bed_file[$pt_ind]" if (defined $pt_bed_file[$pt_ind]); #GALAXY - } - - if($CONF{compare}{sv_output}){ - - links2SVfile ($output_file, $output_file.".sv.txt"); - system "rm $pt_sv_file[$pt_ind]; ln -s $output_file.sv.txt $pt_sv_file[$pt_ind]" if (defined $pt_sv_file[$pt_ind]); #GALAXY - } - $pt_ind++; - - } - unlink(@compare_files); - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub compareSamples{ - - my ($dir,$list_samples,$sample_file,$reference_file,$min_overlap,$same_sv_type,$file_names)=@_; - - my @bedpefiles; - my @list=split(",",$list_samples); - my @list_files=($sample_file,$reference_file); - - print LOG "\# Comparison procedure...\n"; - print LOG "-- samples=$list_samples\n". - "-- minimum overlap=$min_overlap\n". - "-- same SV type=$same_sv_type\n"; - - #conversion of links to bedPE format file - print LOG "-- Conversion of links.filtered files to bedPE format\n"; - for my $s (0..$#list) { - - links2bedPElinksfile($list[$s],$list_files[$s],$list_files[$s].".bedpe.txt"); - push(@bedpefiles,$list_files[$s].".bedpe.txt"); - - } - - #get common links between all samples compared - print LOG "-- Getting common links between all samples with BEDTools\n"; - my $common_name=join(".",@list); - - my $nb=scalar @list; - my $command=""; - my $prompt=">"; - - while ($nb>0){ - - for my $i (0..$#list_files){ - - $command.="$BEDTOOLS_BIN_DIR/pairToPair -type both -f $min_overlap -a ".$list_files[$i].".bedpe.txt"; - my $pipe=0; - - for my $j ($i+1..$#list_files){ - - $command.="| $BEDTOOLS_BIN_DIR/pairToPair -type both -f $min_overlap -a stdin" if($pipe); - $command.=" -b ".$list_files[$j].".bedpe.txt"; - $pipe=1; - - } - - $command.=$prompt.$dir.$common_name.".bedpe.tmp;"; - $prompt=">>"; - - my $first=shift(@list_files); push(@list_files,$first); - last; - } - $nb--; - } - - system ($command); - - push(@bedpefiles,$dir.$common_name.".bedpe.tmp"); - - #Post comparison to get common links if same type only (as an option) - open( FILE, "<".$dir.$common_name.".bedpe.tmp") or die "Can't open".$dir.$common_name.".bedpe.tmp : $!"; - open( OUT, ">".$dir.$common_name.".bedpe.unique") or die "Can't write in ".$dir.$common_name.".bedpe.unique : $!"; - - while(<FILE>){ - my @t=split("\t",$_); - my $s=(split("_",$t[6]))[0]; - my ($sv1,$sv2)=($t[7],$t[18]); - splice(@t,11,$#t); - - if($same_sv_type){ - print OUT join("\t",@t)."\n" if($sv1 eq $sv2); - }else{ - print OUT join("\t",@t)."\n"; - } - } - close FILE; - close OUT; - - bedPElinks2linksfile($dir.$common_name.".bedpe.unique", $dir.$common_name.".unique"); - push(@bedpefiles,$dir.$common_name.".bedpe.unique"); - push(@$file_names,$common_name.".unique"); - print LOG "-- output created: ".$dir.$common_name.".compared\n"; - - #get specific links for each sample - print LOG "-- Getting specific links for each sample\n"; - for my $s (0..$#list) { - system("grep -Fxv -f ".$dir.$common_name.".bedpe.unique ".$list_files[$s].".bedpe.txt >".$dir.$list[$s].".bedpe.unique"); - bedPElinks2linksfile($dir.$list[$s].".bedpe.unique",$dir.$list[$s].".unique"); - push(@bedpefiles,$dir.$list[$s].".bedpe.unique"); - push(@$file_names,$list[$s].".unique"); - print LOG "-- output created: ".$dir.$list[$s].".compared\n"; - } - - unlink(@bedpefiles); - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#convert the links file to the circos format -sub links2segdup{ - - my($id,$color_code,$links_file,$segdup_file)=@_; - - print LOG "\# Converting to the circos format...\n"; - - tie (my %hcolor,'Tie::IxHash'); #color-code hash table - foreach my $col (keys %{$color_code}){ - my ($min_links,$max_links)=split(",",$color_code->{$col}); - $hcolor{$col}=[$min_links,$max_links]; - } - - open LINKS, "<$links_file" or die "$0: can't open $links_file :$!\n"; - open SEGDUP, ">$segdup_file" or die "$0: can't write in the output: $segdup_file :$!\n"; - - my $index=1; - while(<LINKS>){ - - my ($chr1,$start1,$end1,$chr2,$start2,$end2,$count)=(split)[0,1,2,3,4,5,6]; - - my $color=getColor($count,\%hcolor,"circos"); #get the color-code according the number of links - - print SEGDUP "$index\t$id$chr1\t$start1\t$end1\tcolor=$color\n". #circos output - "$index\t$id$chr2\t$start2\t$end2\tcolor=$color\n"; - $index++; - } - - close LINKS; - close SEGDUP; - print LOG "-- output created: $segdup_file\n"; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#convert the links file to the bedPE format for BEDTools usage -sub links2bedPElinksfile{ - - my ($sample,$links_file,$bedpe_file)=@_; - - open LINKS, "<$links_file" or die "$0: can't open $links_file :$!\n"; - open BEDPE, ">$bedpe_file" or die "$0: can't write in the output: $bedpe_file :$!\n"; - - my $nb_links=1; - - while(<LINKS>){ - - chomp; - my @t=split("\t",$_); - my ($chr1,$start1,$end1,$chr2,$start2,$end2)=splice(@t,0,6); - my $type=($chr1 eq $chr2)? "INTRA":"INTER"; - $type.="_".$t[10]; - - $start1--; $start2--; - - print BEDPE "$chr1\t$start1\t$end1\t$chr2\t$start2\t$end2". - "\t$sample"."_link$nb_links\t$type\t.\t.". - "\t".join("|",@t)."\n"; - - $nb_links++; - } - - close LINKS; - close BEDPE; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub bedPElinks2linksfile{ - - my ($bedpe_file,$links_file)=@_; - - open BEDPE, "<$bedpe_file" or die "$0: can't open: $bedpe_file :$!\n"; - open LINKS, ">$links_file" or die "$0: can't write in the output $links_file :$!\n"; - - while(<BEDPE>){ - - chomp; - my $sample=(split("_",(split("\t",$_))[6]))[0]; - my @t1=(split("\t",$_))[0,1,2,3,4,5]; - my @t2=split(/\|/,(split("\t",$_))[10]); - push(@t2,$sample); - - print LINKS join("\t",@t1)."\t".join("\t",@t2)."\n"; - - } - close BEDPE; - close LINKS; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#convert the links file to the bed format -sub links2bedfile{ - - my ($tag_length,$color_code,$links_file,$bed_file)=@_; - - print LOG "\# Converting to the bed format...\n"; - - my $compare=1; - if($links_file!~/compared$/){ - $compare=0; - $tag_length->{none}->{1}=$tag_length->{1}; - $tag_length->{none}->{2}=$tag_length->{2}; - } - - #color-code hash table - tie (my %hcolor,'Tie::IxHash'); - my %color_order; - $color_order{"255,255,255"}=0; - my $n=1; - foreach my $col (keys %{$color_code}){ - my ($min_links,$max_links)=split(",",$color_code->{$col}); - $hcolor{$col}=[$min_links,$max_links]; - $color_order{$col}=$n; - $n++; - } - - my %pair; - my %pt; - $n=1; - open LINKS, "<$links_file" or die "$0: can't open $links_file:$!\n"; - - my %str=( "F"=>"+", "R"=>"-" ); - - while(<LINKS>){ - - my @t=split; - my $sample=($compare)? pop(@t):"none"; - - my $chr1=$t[0]; - my $chr2=$t[3]; - $chr1 = "chr".$chr1 unless ($chr1 =~ m/chr/i); - $chr2 = "chr".$chr2 unless ($chr2 =~ m/chr/i); - my $same_chr=($chr1 eq $chr2)? 1:0; - - my $count=$t[6]; - my $color=getColor($count,\%hcolor,"bed"); - - my @pairs=deleteBadOrderSensePairs(split(",",$t[7])); - my @strand1=deleteBadOrderSensePairs(split(",",$t[8])); - my @strand2=deleteBadOrderSensePairs(split(",",$t[9])); - my @ends_order1=deleteBadOrderSensePairs(split(",",$t[10])); - my @ends_order2=deleteBadOrderSensePairs(split(",",$t[11])); - my @position1=deleteBadOrderSensePairs(split(",",$t[14])); - my @position2=deleteBadOrderSensePairs(split(",",$t[15])); - my @start1; my @end1; getCoordswithLeftMost(\@start1,\@end1,\@position1,\@strand1,\@ends_order1,$tag_length->{$sample}); - my @start2; my @end2; getCoordswithLeftMost(\@start2,\@end2,\@position2,\@strand2,\@ends_order2,$tag_length->{$sample}); - - - for my $p (0..$#pairs){ - - if (!exists $pair{$pairs[$p]}){ - - if($same_chr){ - - $pair{$pairs[$p]}->{0}=[ $chr1, $start1[$p]-1, $end2[$p], $pairs[$p], 0, $str{$strand1[$p]}, - $start1[$p]-1, $end2[$p], $color, - 2, $tag_length->{$sample}->{$ends_order1[$p]}.",".$tag_length->{$sample}->{$ends_order2[$p]}, "0,".($start2[$p]-$start1[$p]) ]; - $pt{$n}=$pair{$pairs[$p]}->{0}; - $n++; - - }else{ - - $pair{$pairs[$p]}->{1}=[ $chr1, $start1[$p]-1, $end1[$p] , $pairs[$p]."/1", 0, $str{$strand1[$p]}, - $start1[$p]-1, $end1[$p], $color, - 1, $tag_length->{$sample}->{$ends_order1[$p]}, 0]; - $pt{$n}=$pair{$pairs[$p]}->{1}; - $n++; - - - $pair{$pairs[$p]}->{2}=[ $chr2, $start2[$p]-1, $end2[$p], $pairs[$p]."/2", 0, $str{$strand2[$p]}, - $start2[$p]-1, $end2[$p], $color, - 1, $tag_length->{$sample}->{$ends_order2[$p]}, 0]; - $pt{$n}=$pair{$pairs[$p]}->{2}; - $n++; - } - }else{ - - if($same_chr){ - ${$pair{$pairs[$p]}->{0}}[8]=$color if($color_order{$color}>$color_order{${$pair{$pairs[$p]}->{0}}[8]}); - }else{ - ${$pair{$pairs[$p]}->{1}}[8]=$color if($color_order{$color}>$color_order{${$pair{$pairs[$p]}->{1}}[8]}); - ${$pair{$pairs[$p]}->{2}}[8]=$color if($color_order{$color}>$color_order{${$pair{$pairs[$p]}->{2}}[8]}); - } - } - } - } - close LINKS; - - my $nb_pairs=$n-1; - - open BED, ">$bed_file" or die "$0: can't write in the output: $bed_file :$!\n"; - print BED "track name=\"$bed_file\" description=\"mate pairs involved in links\" ". - "visibility=2 itemRgb=\"On\"\n"; - - for my $i (1..$nb_pairs){ - print BED join("\t",@{$pt{$i}})."\n"; - } - - close BED; - - print LOG "-- output created: $bed_file\n"; - - undef %pair; - undef %pt; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub links2SVfile{ - - my($links_file,$sv_file)=@_; - - print LOG "\# Converting to the sv output table...\n"; - open LINKS, "<$links_file" or die "$0: can't open $links_file:$!\n"; - open SV, ">$sv_file" or die "$0: can't write in the output: $sv_file :$!\n"; - - my @header=qw(chr_type SV_type BAL_type chromosome1 start1-end1 average_dist - chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering - final_score breakpoint1_start1-end1 breakpoint2_start2-end2); - - my $nb_links=0; - - while (<LINKS>){ - - my @t=split; - my @sv=(); - my $sv_type="-"; - my $strand_ratio="-"; - my $eq_ratio="-"; - my $eq_type="-"; - my $insert_ratio="-"; - my $link="-"; - my ($bk1, $bk2)=("-","-"); - my $score="-"; - - my ($chr1,$start1,$end1)=($t[0],$t[1],$t[2]); - my ($chr2,$start2,$end2)=($t[3],$t[4],$t[5]); - my $nb_pairs=$t[6]; - $chr1 = "chr".$chr1 unless ($chr1 =~ m/chr/i); - $chr2 = "chr".$chr2 unless ($chr2 =~ m/chr/i); - my $chr_type=($chr1 eq $chr2)? "INTRA":"INTER"; - - #if strand filtering - if (defined $t[16]){ - #if inter-chr link - $sv_type=$t[16]; - if(defined $t[17] && $t[17]=~/^(\d+)\/(\d+)$/){ - $strand_ratio=floor($1/$2*100)."%"; - $score=$t[18]; - } - if(defined $t[18] && $t[18]=~/^(\d+)\/(\d+)$/){ - #if intra-chr link with insert size filtering - $strand_ratio=floor($1/$2*100)."%"; - $link=floor($t[17]); - if($sv_type!~/^INV/){ - $insert_ratio=floor($1/$2*100)."%" if($t[19]=~/^(\d+)\/(\d+)$/); - $score=$t[20]; - }else{ - $score=$t[19]; - } - } - } - - if(defined $t[18] && ($t[18] eq "UNBAL" || $t[18] eq "BAL")){ - - #if strand and order filtering only and/or interchr link - $eq_type=$t[18]; - $eq_ratio=floor($1/$2*100)."%" if($t[19]=~/^(\d+)\/(\d+)$/); - ($bk1, $bk2)=($t[20],$t[21]); - foreach my $bk ($bk1, $bk2){$bk=~s/\),\(/ /g; $bk=~s/(\(|\))//g; $bk=~s/,/-/g;} - $score=$t[22]; - - }elsif(defined $t[19] && ($t[19] eq "UNBAL" || $t[19] eq "BAL")){ - - #if all three filtering - $link=floor($t[17]); - $eq_type=$t[19]; - $eq_ratio=floor($1/$2*100)."%" if($t[20]=~/^(\d+)\/(\d+)$/); - - if(defined $t[21] && $t[21]=~/^(\d+)\/(\d+)$/){ - $insert_ratio=floor($1/$2*100)."%"; - ($bk1, $bk2)=($t[22],$t[23]); - $score=$t[24]; - - }else{ - ($bk1, $bk2)=($t[21],$t[22]); - $score=$t[23]; - } - foreach my $bk ($bk1, $bk2){$bk=~s/\),\(/ /g; $bk=~s/(\(|\))//g; $bk=~s/,/-/g;} - - } - - - push(@sv, $chr_type, $sv_type,$eq_type); - push(@sv,"$chr1\t$start1-$end1"); - push(@sv, $link); - push(@sv,"$chr2\t$start2-$end2", - $nb_pairs,$strand_ratio,$eq_ratio,$insert_ratio, decimal($score,4), $bk1, $bk2); - - - print SV join("\t",@sv)."\n"; - } - - close LINKS; - close SV; - - system "sort -k 9,9nr -k 13,13nr $sv_file > $sv_file.sorted"; - - open SV, "<".$sv_file.".sorted" or die "$0: can't open in the output: $sv_file".".sorted :$!\n"; - my @links=<SV>; - close SV; - - open SV, ">$sv_file" or die "$0: can't write in the output: $sv_file :$!\n"; - - print SV join("\t",@header)."\n"; - print SV @links; - close SV; - - unlink($sv_file.".sorted"); - - print LOG "-- output created: $sv_file\n"; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub deleteBadOrderSensePairs{ - - my (@tab)=@_; - my @tab2; - - foreach my $v (@tab){ - - $v=~s/[\(\)]//g; - push(@tab2,$v) if($v!~/[\$\*\@]$/); - } - return @tab2; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#gets starts and ends Coords when start=leftmost given positions, directions and orders -sub getCoordswithLeftMost { - - my ($starts,$ends,$positions,$strand,$end_order,$tag_length) = @_; - - for my $i (0..scalar(@{$positions})-1) { - - if($strand->[$i] eq 'F'){ - $starts->[$i]=$positions->[$i]; - $ends->[$i]=$positions->[$i]+$tag_length->{$end_order->[$i]}-1; - }else{ - $starts->[$i]=$positions->[$i]-$tag_length->{$end_order->[$i]}+1; - $ends->[$i]=$positions->[$i]; - } - } -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub floor { - my $nb = $_[0]; - $nb=~ s/\..*//; - return $nb; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub decimal{ - - my $num=shift; - my $digs_to_cut=shift; - - $num=sprintf("%.".($digs_to_cut-1)."f", $num) if ($num=~/\d+\.(\d){$digs_to_cut,}/); - - return $num; -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Sort links according the concerned chromosomes and their coordinates -sub sortLinks{ - - my ($links_file,$sortedlinks_file,$unique)=@_; - - print LOG "# Sorting links...\n"; - - my $pipe=($unique)? "| sort -u":""; - system "sort -k 1,1 -k 4,4 -k 2,2n -k 5,5n -k 8,8n $links_file $pipe > $sortedlinks_file"; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getColor{ - - my($count,$hcolor,$format)=@_; - for my $col ( keys % { $hcolor} ) { - return $col if($count>=$hcolor->{$col}->[0] && $count<=$hcolor->{$col}->[1]); - } - return "white" if($format eq "circos"); - return "255,255,255" if($format eq "bed"); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#check if the configuration file is correct -sub validateconfiguration{ - - my %conf=%{$_[0]}; - my $list_prgs="@ARGV"; - - my @circos_params=qw(organism_id colorcode); - my @bed_params=qw(colorcode); - my @compare_params=qw(list_samples list_read_lengths sample_link_file reference_link_file); - - unless (defined($conf{general}{output_dir})) { - $conf{general}{output_dir} = "."; - } - unless (-d $conf{general}{output_dir}){ - mkdir $conf{general}{output_dir} or die; - } - $conf{general}{output_dir}.="/" if($conf{general}{output_dir}!~/\/$/); - - - if($list_prgs=~/links2compare/){ - foreach my $p (@compare_params) { - die("Error Config : The compare parameter \"$p\" is not defined\n") if (!defined $conf{compare}{$p}); - } - - unless (defined($conf{compare}{same_sv_type})) { - $conf{compare}{same_sv_type} = 0; - } - - unless (defined($conf{compare}{min_overlap})) { - $conf{compare}{min_overlap} = 1E-9; - } - - if($conf{compare}{circos_output}){ - foreach my $p (@circos_params) { - next if($list_prgs=~/^ratio/ && $p eq "colorcode"); - die("Error Config : The circos parameter \"$p\" is not defined\n") if (!defined $conf{circos}{$p}); - } - } - if($conf{compare}{bed_output}){ - foreach my $p (@bed_params) { - die("Error Config : The bed parameter \"$p\" is not defined\n") if (!defined $conf{bed}{$p}); - } - die("Error Config : The compare parameter \"list_read_lengths\" is not defined\n") if (!defined $conf{compare}{list_read_lengths}); - - my @samples=split(",",$conf{compare}{list_samples}); - my @read_lengths=split(",",$conf{compare}{list_read_lengths}); - for my $i (0..$#samples){ - my @l=split("-",$read_lengths[$i]); - $conf{compare}{read_lengths}{$samples[$i]}={ 1=> $l[0], 2=> $l[1]}; - } - } - } - - -} -#------------------------------------------------------------------------------# -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#
--- a/svdetect/SVDetect_compare.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,218 +0,0 @@ -<tool id="svdetect_compare" name="Compare"> - -<description>structural variants between two samples</description> - -<command interpreter="perl">SVDetect_compare.pl links2compare -conf '$config_file' -l '$log_file' -N '$sample_name.$reference_name' - -#if $links2SV --out1 '$common_sv_file' --out2 '$sample_sv_file' --out3 '$reference_sv_file' -#end if - -#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2circos --out4 '$common_circos_file' --out5 '$sample_circos_file' --out6 '$reference_circos_file' -#end if - -#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2bed --out7 '$common_bed_file' --out8 '$sample_bed_file' --out9 '$reference_bed_file' -#end if - -</command> - -<inputs> - <param name="sample_name" type="text" size="20" value="sample" label="Sample Name"/> - <param name="sample_read1_length" type="integer" size="10" value="50" label="Sample read 1 length (bp)"/> - <param name="sample_read2_length" type="integer" size="10" value="50" label="Sample read 2 length (bp)"/> - <param name="sample_mates_file" type="data" format="sv" label="Sample input file" help=".sv file"/> - - <param name="reference_name" type="text" size="20" value="reference" label="Reference Name"/> - <param name="reference_read1_length" type="integer" size="10" value="50" label="Reference read 1 length (bp)"/> - <param name="reference_read2_length" type="integer" size="10" value="50" label="Reference read 2 length (bp)"/> - <param name="reference_mates_file" type="data" format="sv" label="Reference input file" help=".sv file"/> - - <param name="min_overlap" type="float" size="10" value="0.05" label="Minimum overlap of links required as a fraction"/> - <param name="same_sv_type" label="Comparison of SVs with the same type only ?" type="boolean" truevalue="1" falsevalue="0" checked="True"/> - - <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="1" falsevalue="0" checked="True"/> - - <conditional name="file_conversion"> - <param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs"> - <option value="do_not_convert">No</option> - <option value="convert">Yes</option> - </param> - <when value="do_not_convert"> - <!-- do nothing here --> - </when> - <when value="convert"> - <param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="1" falsevalue="0" checked="True"/> - <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="1" falsevalue="0" checked="False"/> - <param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/> - <repeat name="color_code" title="Color-code" min="1" max="7"> - <param name="color" type="select" label="Color"> - <option value="grey">grey</option> - <option value="black">black</option> - <option value="blue">blue</option> - <option value="green">green</option> - <option value="purple">purple</option> - <option value="orange">orange</option> - <option value="red">red</option> - </param> - <param name="interval" type="text" value="1,3" label="Interval"/> - </repeat> - </when> - </conditional> -</inputs> - - - -<outputs> - <data format="sv" name="common_sv_file" label="common.compared.sv"> - <filter>links2SV is True</filter> - </data> - <data format="sv" name="sample_sv_file" label="${sample_name}.compared.sv"> - <filter>links2SV is True</filter> - </data> - <data format="sv" name="reference_sv_file" label="${reference_name}.compared.sv"> - <filter>links2SV is True</filter> - </data> - - <data format="segdup" name="common_circos_file" label="common.compared.segdup"> - <filter>( - file_conversion['file_conversion_select']=="convert" and - file_conversion['links2circos'] is True - ) - </filter> - </data> - <data format="segdup" name="sample_circos_file" label="${sample_name}.compared.segdup"> - <filter>( - file_conversion['file_conversion_select']=="convert" and - file_conversion['links2circos'] is True - ) - </filter> - </data> - <data format="segdup" name="reference_circos_file" label="${reference_name}.compared.segdup"> - <filter>( - file_conversion['file_conversion_select']=="convert" and - file_conversion['links2circos'] is True - ) - </filter> - </data> - - <data format="bed" name="common_bed_file" label="common.compared.bed"> - <filter>( - file_conversion['file_conversion_select']=="convert" and - file_conversion['links2bed'] is True - ) - </filter> - </data> - <data format="bed" name="sample_bed_file" label="${sample_name}.compared.bed"> - <filter>( - file_conversion['file_conversion_select']=="convert" and - file_conversion['links2bed'] is True - ) - </filter> - </data> - <data format="bed" name="reference_bed_file" label="${reference_name}.compared.bed"> - <filter>( - file_conversion['file_conversion_select']=="convert" and - file_conversion['links2bed'] is True - ) - </filter> - </data> - - <data format="txt" name="log_file" label="${sample_name}.${reference_name}.svdetect_compare.log"/> -</outputs> - - - -<configfiles> - <configfile name="config_file"> -<general> -output_dir=$__new_file_path__/svdetect -</general> - -#if $file_conversion.file_conversion_select == "convert" -#if $file_conversion.links2circos -<circos> -organism_id=${file_conversion.organism_id} -<colorcode> -#for $color_repeat in $file_conversion.color_code -${color_repeat.color}=${color_repeat.interval} -#end for -</colorcode> -</circos> -#end if -#if $file_conversion.links2bed -<bed> -<colorcode> -#for $color_repeat in $file_conversion.color_code -#if str($color_repeat.color)== "grey" -190,190,190=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "black" -0,0,0=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "blue" -0,0,255=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "green" -0,255,0=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "purple" -153,50,205=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "orange" -255,140,0=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "red" -255,0,0=${color_repeat.interval} -#end if -#end for -</colorcode> -</bed> -#end if -#end if - -<compare> -list_samples=${sample_name},${reference_name} -list_read_lengths=${sample_read1_length}-${sample_read2_length},${reference_read1_length}-${reference_read2_length} -sample_link_file=${sample_mates_file} -reference_link_file=${reference_mates_file} -min_overlap=${min_overlap} -same_sv_type=${same_sv_type} -sv_output=${links2SV} -#if $file_conversion.file_conversion_select == "convert" -circos_output=${$file_conversion.links2circos} -bed_output=${$file_conversion.links2bed} -#end if -</compare> - - </configfile> -</configfiles> - - <help> -**What it does** - -SVDetect - Version : 0.8b - -Comparison of clusters between two samples to get common or sample-specific SVs - -This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets -and to identify common and sample-specific SVs (like the usual sample/reference design). -Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison. - -Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. - </help> - -</tool>
--- a/svdetect/SVDetect_import.sh Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#!/bin/bash - - -while getopts "i:o:" optionName; do -case "$optionName" in - -i) INPUT="$OPTARG";; -o) OUTPUT="$OPTARG";; - -esac -done - -rm $OUTPUT - -ln -s $INPUT $OUTPUT
--- a/svdetect/SVDetect_import.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -<tool id="svdetect_import" name="Import data"> - <description>BAM, chromosome info or sv files</description> - <command interpreter="bash">SVDetect_import.sh -i $file_path - #if str($type.file_type)=="bam" - -o $outbamfile - #elif str($type.file_type)=="len" - -o $outlenfile - #elif str($type.file_type)=="sv" - -o $outsvfile - #end if - </command> - <inputs> - <param name="file_name" type="text" value="file1" label="File Name"/> - <conditional name="type"> - <param name="file_type" type="select" label="Select the file type to import" help="BAM file (BAM) or text file (SAM, chromosome list or a SV tabulated text file)"> - <option value="bam">BAM file (.bam)</option> - <option value="len">Chromosome info file (.len)</option> - <option value="sv">SVDetect output file (.sv)</option> - </param> - <when value="bam"> - <!-- do nothing here --> - </when> - <when value="len"> - <!-- do nothing here --> - </when> - <when value="sv"> - <!-- do nothing here --> - </when> - </conditional> - <param name="file_path" type="text" size="150" label="Path to file"/> - </inputs> - <outputs> - <data format="bam" name="outbamfile" label="${file_name}.bam"> - <filter>type['file_type']=="bam"</filter> - </data> - <data format="len" name="outlenfile" label="${file_name}.len"> - <filter>type['file_type']=="len"</filter> - </data> - <data format="sv" name="outsvfile" label="${file_name}.sv"> - <filter>type['file_type']=="sv"</filter> - </data> - </outputs> - <help> -**What it does** - -This tool allows you to import quickly a BAM file, a chromosome info file or a SVDetect output file from you computer as inputs for SVDetect. - - -**Example of chromosome file** - -Input len file:: - - 1 chr1 247249719 - 2 chr2 242951149 - 3 chr3 199501827 - 4 chr4 191273063 - 5 chr5 180857866 - 6 chr6 170899992 - 7 chr7 158821424 - 8 chr8 146274826 - 9 chr9 140273252 - 10 chr10 135374737 - 11 chr11 134452384 - 12 chr12 132349534 - 13 chr13 114142980 - 14 chr14 106368585 - 15 chr15 100338915 - 16 chr16 88827254 - 17 chr17 78774742 - 18 chr18 76117153 - 19 chr19 63811651 - 20 chr20 62435964 - 21 chr21 46944323 - 22 chr22 49691432 - 23 chrX 154913754 - 24 chrY 57772954 - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. - </help> - -</tool>
--- a/svdetect/SVDetect_run_parallel.pl Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3537 +0,0 @@ -#!/usr/bin/perl -w - -=pod - -=head1 NAME - -SVDetect - Program designed to the detection of structural variations -from paired-end/mate-pair sequencing data, compatible with SOLiD and Illumina (>=1.3) reads - -Version: 0.8b for Galaxy - -=head1 SYNOPSIS - -SVDetect <command> -conf <configuration_file> [-help] [-man] - - Command: - - linking detection and isolation of links - filtering filtering of links according different parameters - links2circos links conversion to circos format - links2bed paired-ends of links converted to bed format (UCSC) - links2SV formatted output to show most significant SVs - cnv calculate copy-number profiles - ratio2circos ratio conversion to circos density format - ratio2bedgraph ratio conversion to bedGraph density format (UCSC) - -=head1 DESCRIPTION - -This is a command-line interface to SVDetect. - - -=head1 AUTHORS - -Bruno Zeitouni E<lt>bruno.zeitouni@curie.frE<gt>, -Valentina Boeva E<lt>valentina.boeva@curie.frE<gt> - -=cut - -# ------------------------------------------------------------------- - -use strict; -use warnings; - -use Pod::Usage; -use Getopt::Long; - -use Config::General; -use Tie::IxHash; -use FileHandle; -use Parallel::ForkManager; - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#PARSE THE COMMAND LINE -my %OPT; -GetOptions(\%OPT, - 'conf=s', - 'out1=s', #GALAXY - 'out2=s', #GALAXY - 'out3=s', #GALAXY - 'out4=s', #GALAXY - 'out5=s', #GALAXY - 'l=s', #GALAXY - 'N=s',#GALAXY - 'help',#GALAXY - 'man' - ); - -pod2usage() if $OPT{help}; -pod2usage(-verbose=>2) if $OPT{man}; -pod2usage(-message=> "$!", -exitval => 2) if (!defined $OPT{conf}); - -pod2usage() if(@ARGV<1); - -tie (my %func, 'Tie::IxHash',linking=>\&createlinks, - filtering=>\&filterlinks, - links2circos=>\&links2circos, - links2bed=>\&links2bed, - links2compare=>\&links2compare, - links2SV=>\&links2SV, - cnv=>\&cnv, - ratio2circos=>\&ratio2circos, - ratio2bedgraph=>\&ratio2bedgraph); - -foreach my $command (@ARGV){ - pod2usage(-message=> "Unknown command \"$command\"", -exitval => 2) if (!defined($func{$command})); -} -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# - - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#READ THE CONFIGURATION FILE -my $conf=Config::General->new( -ConfigFile => $OPT{conf}, - -Tie => "Tie::IxHash", - -AllowMultiOptions => 1, - -LowerCaseNames => 1, - -AutoTrue => 1); -my %CONF= $conf->getall; -validateconfiguration(\%CONF); #validation of the configuration parameters - -my $SAMTOOLS_BIN_DIR="/bioinfo/local/samtools"; #GALAXY - -my $pt_log_file=$OPT{l}; #GALAXY -my $pt_links_file=$OPT{out1} if($OPT{out1}); #GALAXY -my $pt_flinks_file=$OPT{out2} if($OPT{out2}); #GALAXY -my $pt_sv_file=$OPT{out3} if($OPT{out3}); #GALAXY -my $pt_circos_file=$OPT{out4} if($OPT{out4}); #GALAXY -my $pt_bed_file=$OPT{out5} if($OPT{out5}); #GALAXY - -$CONF{general}{mates_file}=readlink($CONF{general}{mates_file});#GALAXY -$CONF{general}{cmap_file}=readlink($CONF{general}{cmap_file});#GALAXY - -my $log_file=$CONF{general}{output_dir}.$OPT{N}.".svdetect_run.log"; #GALAXY -open LOG,">$log_file" or die "$0: can't open ".$log_file.":$!\n";#GALAXY -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#COMMAND EXECUTION -foreach my $command (@ARGV){ - &{$func{$command}}(); -} -print LOG "-- end\n";#GALAXY - -close LOG;#GALAXY -system "rm $pt_log_file ; ln -s $log_file $pt_log_file"; #GALAXY -exit(0); -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# - - -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::# -#FUNCTIONS -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 1: Detection of links from mate-pairs data -sub createlinks{ - - my %CHR; #main hash table 1: fragments, links - my %CHRID; - my @MATEFILES; - - my $output_prefix=$CONF{general}{mates_file}.".".$CONF{general}{sv_type}; - my @path=split(/\//,$output_prefix); - $output_prefix=$CONF{general}{output_dir}.$path[$#path]; - my $tmp_mates_prefix=$CONF{general}{tmp_dir}."mates/".$path[$#path]; - my $tmp_links_prefix=$CONF{general}{tmp_dir}."links/".$path[$#path]; - - shearingChromosome(\%CHR, \%CHRID, #making the genomic fragment library with the detection parameters - $CONF{detection}{window_size}, - $CONF{detection}{step_length}, - $CONF{general}{cmap_file}); - - if($CONF{detection}{split_mate_file}){ - - splitMateFile(\%CHR, \%CHRID, \@MATEFILES, $tmp_mates_prefix, - $CONF{general}{sv_type}, - $CONF{general}{mates_file}, - $CONF{general}{input_format}, - $CONF{general}{read_lengths} - ); - }else{ - - @MATEFILES=qx{ls $tmp_mates_prefix*} or die "# Error: No splitted mate files already created at $CONF{general}{tmp_dir} :$!"; - chomp(@MATEFILES); - print LOG "# Splitted mate files already created.\n"; - } - - - #Parallelization of the linking per chromosome for intra + interchrs - my $pm = new Parallel::ForkManager($CONF{general}{num_threads}); - - foreach my $matefile (@MATEFILES){ - - my $pid = $pm->start and next; - getlinks(\%CHR, \%CHRID, $matefile); - $pm->finish; - - } - $pm->wait_all_children; - - #Merge the chromosome links file into only one - my @LINKFILES= qx{ls $tmp_links_prefix*links} or die "# Error: No links files created at $CONF{general}{tmp_dir} :$!"; - chomp(@LINKFILES); - catFiles( \@LINKFILES => "$output_prefix.links" ); - - system "rm $pt_links_file; ln -s $output_prefix.links $pt_links_file" if (defined $pt_links_file); #GALAXY - print LOG "# Linking end procedure : output created: $output_prefix.links\n"; - #unlink(@LINKFILES); - #unlink(@MATEFILES); - - undef %CHR; - undef %CHRID; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getlinks { - - my ($chr,$chrID,$tmp_mates_prefix)=@_; - - my $tmp_links_prefix=$tmp_mates_prefix; - $tmp_links_prefix=~s/\/mates\//\/links\//; - - my %PAIR; #main hash table 2: pairs - - linking($chr,$chrID, \%PAIR, #creation of all links from chromosome coordinates of pairs - $CONF{general}{read_lengths}, - $CONF{detection}{window_size}, - $CONF{detection}{step_length}, - $tmp_mates_prefix, - $CONF{general}{input_format}, - $CONF{general}{sv_type}, - "$tmp_links_prefix.links.mapped" - ); - - getUniqueLinks("$tmp_links_prefix.links.mapped", #remove the doublons - "$tmp_links_prefix.links.unique"); - - defineCoordsLinks($chr,$chrID, \%PAIR, #definition of the precise coordinates of links - $CONF{general}{input_format}, - $CONF{general}{sv_type}, - $CONF{general}{read_lengths}, - "$tmp_links_prefix.links.unique", - "$tmp_links_prefix.links.unique_defined"); - - sortLinks("$tmp_links_prefix.links.unique_defined", #sorting links from coordinates - "$tmp_links_prefix.links.sorted"); - - removeFullyOverlappedLinks("$tmp_links_prefix.links.sorted", #remove redundant links - "$tmp_links_prefix.links",1); #file output - - - undef %PAIR; - - unlink("$tmp_links_prefix.links.mapped", - "$tmp_links_prefix.links.unique", - "$tmp_links_prefix.links.unique_defined", - "$tmp_links_prefix.links.sorted"); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub splitMateFile{ - - my ($chr,$chrID,$files_list,$output_prefix,$sv_type,$mates_file,$input_format,$tag_length)=@_; - - print LOG "# Splitting the mate file \"$mates_file\" for parallel processing...\n"; - - my %filesHandle; - - #fichier matefile inter - if($sv_type=~/^(all|inter)$/){ - my $newFileName="$output_prefix.interchrs"; - push(@{$files_list},$newFileName); - my $fh = new FileHandle; - $fh->open(">$newFileName"); - $filesHandle{inter}=$fh; - } - - #fichiers matefiles intra - if($sv_type=~/^(all|intra)$/){ - foreach my $k (1..$chr->{nb_chrs}){ - my $newFileName=$output_prefix.".".$chr->{$k}->{name}; - push(@{$files_list},$newFileName); - my $fh = new FileHandle; - $fh->open(">$newFileName"); - $filesHandle{$k}=$fh; - } - } - - if ($mates_file =~ /.gz$/) { - open(MATES, "gunzip -c $mates_file |") or die "$0: can't open ".$mates_file.":$!\n"; #gzcat - }elsif($mates_file =~ /.bam$/){ - open(MATES, "$SAMTOOLS_BIN_DIR/samtools view $mates_file |") or die "$0: can't open ".$mates_file.":$!\n";#GALAXY - }else{ - open MATES, "<".$mates_file or die "$0: can't open ".$mates_file.":$!\n"; - } - - - while(<MATES>){ - - my @t=split; - my ($chr_read1, $chr_read2, $firstbase_read1, $firstbase_read2, $end_order_read1,$end_order_read2); - - next if (!readMateFile(\$chr_read1, \$chr_read2, \$firstbase_read1, \$firstbase_read2, \$end_order_read1, \$end_order_read2, \@t, $input_format,$tag_length)); - - next unless (exists $chrID->{$chr_read1} && exists $chrID->{$chr_read2}); - - ($chr_read1, $chr_read2)= ($chrID->{$chr_read1},$chrID->{$chr_read2}); - - if( ($sv_type=~/^(all|inter)$/) && ($chr_read1 ne $chr_read2) ){ - my $fh2print=$filesHandle{inter}; - print $fh2print join("\t",@t)."\n"; - } - - if( ($sv_type=~/^(all|intra)$/) && ($chr_read1 eq $chr_read2) ){ - my $fh2print=$filesHandle{$chr_read1}; - print $fh2print join("\t",@t)."\n"; - - } - } - - foreach my $name (keys %filesHandle){ - my $fh=$filesHandle{$name}; - $fh->close; - } - - print LOG "# Splitted mate files of \"$mates_file\" created.\n"; -} - - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub filterlinks{ - - my %CHR; - my %CHRID; - my @LINKFILES; - my @FLINKFILES; - - my $output_prefix=$CONF{general}{mates_file}.".".$CONF{general}{sv_type}; - my @path=split(/\//,$output_prefix); - $output_prefix=$CONF{general}{output_dir}.$path[$#path]; - my $tmp_links_prefix=$CONF{general}{tmp_dir}."links/".$path[$#path]; - - createChrHashTables(\%CHR,\%CHRID, - $CONF{general}{cmap_file}); - - if($CONF{filtering}{split_link_file}){ - - splitLinkFile(\%CHR, \%CHRID, \@LINKFILES, - $tmp_links_prefix, - $CONF{general}{sv_type}, - "$output_prefix.links", - ); - }else{ - - @LINKFILES=qx{ls $tmp_links_prefix*links} or die "# Error: No splitted link files already created\n"; - chomp(@LINKFILES); - print LOG "# Splitted link files already created.\n"; - } - - #Parallelization of the filtering per chromosome for intra + interchrs - my $pm = new Parallel::ForkManager($CONF{general}{num_threads}); - - foreach my $linkfile (@LINKFILES){ - - my $pid = $pm->start and next; - getFilteredlinks(\%CHR, \%CHRID, $linkfile); - $pm->finish; - - } - $pm->wait_all_children; - - #Merge the chromosome links file into only one - @FLINKFILES= qx{ls $tmp_links_prefix*filtered} or die "# Error: No links files created\n"; - chomp(@FLINKFILES); - catFiles( \@FLINKFILES => "$output_prefix.links.filtered" ); - - system "rm $pt_flinks_file; ln -s $output_prefix.links.filtered $pt_flinks_file" if (defined $pt_flinks_file); #GALAXY - print LOG"# Filtering end procedure : output created: $output_prefix.links.filtered\n"; - - undef %CHR; - undef %CHRID; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub splitLinkFile{ - - my ($chr,$chrID,$files_list,$input_prefix,$sv_type,$link_file)=@_; - - print LOG "# Splitting the link file for parallel processing...\n"; - - my %filesHandle; - - #fichier matefile inter - if($sv_type=~/^(all|inter)$/){ - my $newFileName="$input_prefix.interchrs.links"; - push(@{$files_list},$newFileName); - my $fh = new FileHandle; - $fh->open(">$newFileName"); - $filesHandle{inter}=$fh; - } - - #fichiers matefiles intra - if($sv_type=~/^(all|intra)$/){ - foreach my $k (1..$chr->{nb_chrs}){ - my $newFileName=$input_prefix.".".$chr->{$k}->{name}.".links"; - push(@{$files_list},$newFileName); - my $fh = new FileHandle; - $fh->open(">$newFileName"); - $filesHandle{$k}=$fh; - } - } - - open LINKS, "<".$link_file or die "$0: can't open ".$link_file.":$!\n"; - while(<LINKS>){ - - my @t=split; - my ($chr_read1,$chr_read2)=($t[0],$t[3]); - - next unless (exists $chrID->{$chr_read1} && exists $chrID->{$chr_read2}); - - ($chr_read1, $chr_read2)= ($chrID->{$chr_read1},$chrID->{$chr_read2}); - - if( ($sv_type=~/^(all|inter)$/) && ($chr_read1 ne $chr_read2) ){ - my $fh2print=$filesHandle{inter}; - print $fh2print join("\t",@t)."\n"; - } - - if( ($sv_type=~/^(all|intra)$/) && ($chr_read1 eq $chr_read2) ){ - my $fh2print=$filesHandle{$chr_read1}; - print $fh2print join("\t",@t)."\n"; - - } - } - - foreach my $name (keys %filesHandle){ - my $fh=$filesHandle{$name}; - $fh->close; - } - - print LOG "# Splitted link files created.\n"; -} - - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 2: Filtering processing -sub getFilteredlinks { - - my ($chr,$chrID,$tmp_links_prefix)=@_; - my %PAIR; - - strandFiltering($chr,$chrID, - $CONF{filtering}{nb_pairs_threshold}, #filtering of links - $CONF{filtering}{strand_filtering}, - $CONF{filtering}{chromosomes}, - $CONF{general}{input_format}, - $CONF{general}{cmap_file}, - $CONF{general}{mates_orientation}, - $CONF{general}{read_lengths}, - $tmp_links_prefix, - "$tmp_links_prefix.filtered", - ); - - if($CONF{filtering}{strand_filtering}){ #re-definition of links coordinates with strand filtering - - my @tmpfiles; - - rename("$tmp_links_prefix.filtered","$tmp_links_prefix.filtered_unique"); - - getUniqueLinks("$tmp_links_prefix.filtered_unique", - "$tmp_links_prefix.filtered"); - - push(@tmpfiles,"$tmp_links_prefix.filtered_unique"); - - if($CONF{filtering}{order_filtering}){ #filtering using the order - - rename("$tmp_links_prefix.filtered","$tmp_links_prefix.filtered_ordered"); - - orderFiltering($chr,$chrID, - $CONF{filtering}{nb_pairs_threshold}, - $CONF{filtering}{nb_pairs_order_threshold}, - $CONF{filtering}{mu_length}, - $CONF{filtering}{sigma_length}, - $CONF{general}{mates_orientation}, - $CONF{general}{read_lengths}, - "$tmp_links_prefix.filtered_ordered", - "$tmp_links_prefix.filtered", - ); - - push(@tmpfiles,"$tmp_links_prefix.filtered_ordered"); - } - - if (($CONF{filtering}{insert_size_filtering})&& - ($CONF{general}{sv_type} ne 'inter')){ - - rename("$tmp_links_prefix.filtered","$tmp_links_prefix.filtered_withoutIndelSize"); - - addInsertionInfo($chr,$chrID, - $CONF{filtering}{nb_pairs_threshold}, - $CONF{filtering}{order_filtering}, - $CONF{filtering}{indel_sigma_threshold}, - $CONF{filtering}{dup_sigma_threshold}, - $CONF{filtering}{singleton_sigma_threshold}, - $CONF{filtering}{mu_length}, - $CONF{filtering}{sigma_length}, - $CONF{general}{mates_orientation}, - $CONF{general}{read_lengths}, - "$tmp_links_prefix.filtered_withoutIndelSize", - "$tmp_links_prefix.filtered" - ); - - push(@tmpfiles,"$tmp_links_prefix.filtered_withoutIndelSize"); - } - - sortLinks("$tmp_links_prefix.filtered", - "$tmp_links_prefix.filtered_sorted"); - - removeFullyOverlappedLinks("$tmp_links_prefix.filtered_sorted", - "$tmp_links_prefix.filtered_nodup", - ); - - postFiltering("$tmp_links_prefix.filtered_nodup", - "$tmp_links_prefix.filtered", - $CONF{filtering}{final_score_threshold}); - - push(@tmpfiles,"$tmp_links_prefix.filtered_sorted","$tmp_links_prefix.filtered_nodup"); - - unlink(@tmpfiles); - - - } - undef %PAIR; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 3: Circos format conversion for links -sub links2circos{ - - my $input_file=$CONF{general}{mates_file}.".".$CONF{general}{sv_type}.".links.filtered"; - my @path=split(/\//,$input_file); - $input_file=$CONF{general}{output_dir}.$path[$#path]; - - my $output_file.=$input_file.".segdup.txt"; - - links2segdup($CONF{circos}{organism_id}, - $CONF{circos}{colorcode}, - $input_file, - $output_file); #circos file output - - system "rm $pt_circos_file; ln -s $output_file $pt_circos_file" if (defined $pt_circos_file); #GALAXY -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 4: Bed format conversion for links -sub links2bed{ - - my $input_file=$CONF{general}{mates_file}.".".$CONF{general}{sv_type}.".links.filtered"; - my @path=split(/\//,$input_file); - $input_file=$CONF{general}{output_dir}.$path[$#path]; - - my $output_file.=$input_file.".bed.txt"; - - links2bedfile($CONF{general}{read_lengths}, - $CONF{bed}{colorcode}, - $input_file, - $output_file); #bed file output - - system "rm $pt_bed_file; ln -s $output_file $pt_bed_file" if (defined $pt_bed_file); #GALAXY - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 6: Bed format conversion for links -sub links2SV{ - - my $input_file=$CONF{general}{mates_file}.".".$CONF{general}{sv_type}.".links.filtered"; - - my @path=split(/\//,$input_file); - $input_file=$CONF{general}{output_dir}.$path[$#path]; - - my $output_file.=$input_file.".sv.txt"; - - - links2SVfile( $input_file, - $output_file); - - system "rm $pt_sv_file; ln -s $output_file $pt_sv_file" if (defined $pt_sv_file); #GALAXY -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 7: copy number variations, coverage ratio calculation -sub cnv{ - - my %CHR; - my %CHRID; - my @MATEFILES; - my @MATEFILES_REF; - - my $output_prefix=$CONF{general}{mates_file}; - my $output_prefix_ref=$CONF{detection}{mates_file_ref}; - my @path=split(/\//,$output_prefix); - my @path_ref=split(/\//,$output_prefix_ref); - $output_prefix=$CONF{general}{output_dir}.$path[$#path]; - $output_prefix_ref=$CONF{general}{output_dir}.$path_ref[$#path_ref]; - my $tmp_mates_prefix=$CONF{general}{tmp_dir}."mates/".$path[$#path]; - my $tmp_mates_prefix_ref=$CONF{general}{tmp_dir}."mates/".$path_ref[$#path_ref]; - my $tmp_density_prefix=$CONF{general}{tmp_dir}."density/".$path[$#path]; - - shearingChromosome(\%CHR, \%CHRID, #making the genomic fragment library with the detection parameters - $CONF{detection}{window_size}, - $CONF{detection}{step_length}, - $CONF{general}{cmap_file}); - - if($CONF{detection}{split_mate_file}){ - - splitMateFile(\%CHR, \%CHRID, \@MATEFILES, $tmp_mates_prefix, - "intra", - $CONF{general}{mates_file}, - $CONF{general}{input_format}, - $CONF{general}{read_lengths} - ); - - splitMateFile(\%CHR, \%CHRID, \@MATEFILES_REF, $tmp_mates_prefix_ref, - "intra", - $CONF{detection}{mates_file_ref}, - $CONF{general}{input_format}, - $CONF{general}{read_lengths} - ); - - - }else{ - - @MATEFILES=qx{ls $tmp_mates_prefix*} or die "# Error: No splitted sample mate files of \"$CONF{general}{mates_file}\" already created at $CONF{general}{tmp_dir} :$!"; - chomp(@MATEFILES); - @MATEFILES_REF=qx{ls $tmp_mates_prefix_ref*} or die "# Error: No splitted reference mate files of \"$CONF{detection}{mates_file_ref}\" already created at $CONF{general}{tmp_dir} :$!"; - chomp(@MATEFILES_REF); - print LOG "# Splitted sample and reference mate files already created.\n"; - } - - #Parallelization of the cnv per chromosome - my $pm = new Parallel::ForkManager($CONF{general}{num_threads}); - - foreach my $file (0..$#MATEFILES){ - - my $pid = $pm->start and next; - - densityCalculation(\%CHR, \%CHRID, $file, - $CONF{general}{read_lengths}, - $CONF{detection}{window_size}, - $CONF{detection}{step_length}, - \@MATEFILES, - \@MATEFILES_REF, - $MATEFILES[$file].".density", - $CONF{general}{input_format}); - - $pm->finish; - - } - $pm->wait_all_children; - - #Merge the chromosome links file into only one - my @DENSITYFILES= qx{ls $tmp_density_prefix*density} or die "# Error: No density files created at $CONF{general}{tmp_dir} :$!"; - chomp(@DENSITYFILES); - catFiles( \@DENSITYFILES => "$output_prefix.density" ); - - print LOG "# cnv end procedure : output created: $output_prefix.density\n"; - - - undef %CHR; - undef %CHRID; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 8: Circos format conversion for cnv ratios -sub ratio2circos{ - - my $input_file=$CONF{general}{mates_file}.".density"; - - my @path=split(/\//,$input_file); - $input_file=$CONF{general}{output_dir}.$path[$#path]; - - my $output_file.=$input_file.".segdup.txt"; - - ratio2segdup($CONF{circos}{organism_id}, - $input_file, - $output_file); -} -#------------------------------------------------------------------------------# -#MAIN FUNCTION number 9: BedGraph format conversion for cnv ratios -sub ratio2bedgraph{ - - my $input_file=$CONF{general}{mates_file}.".density"; - - my @path=split(/\//,$input_file); - $input_file=$CONF{general}{output_dir}.$path[$#path]; - - my $output_file.=$input_file.".bedgraph.txt"; - - ratio2bedfile($input_file, - $output_file); #bed file output -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Creation of the fragment library -sub shearingChromosome{ - - print LOG "# Making the fragments library...\n"; - - my ($chr,$chrID,$window,$step,$cmap_file)=@_; #window and step sizes parameters - - createChrHashTables($chr,$chrID,$cmap_file); #hash tables: chromosome ID <=> chromsomes Name - - foreach my $k (1..$chr->{nb_chrs}){ - - print LOG"-- $chr->{$k}->{name}\n"; - - my $frag=1; - for (my $start=0; $start<$chr->{$k}->{length}; $start+=$step){ - - my $end=($start<($chr->{$k}->{length})-$window)? $start+$window-1:($chr->{$k}->{length})-1; - $chr->{$k}->{$frag}=[$start,$end]; #creation of fragments, coordinates storage - - if($end==($chr->{$k}->{length})-1){ - $chr->{$k}->{nb_frag}=$frag; #nb of fragments per chromosome - last; - } - $frag++; - } - } -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Creation of chromosome hash tables from the cmap file -sub createChrHashTables{ - - my ($chr,$chrID,$cmap_file)=@_; - $chr->{nb_chrs}=0; - - open CMAP, "<".$cmap_file or die "$0: can't open ".$cmap_file.":$!\n"; - while(<CMAP>){ - - if(/^\s+$/){ next;} - my ($k,$name,$length) = split; - $chr->{$k}->{name}=$name; - $chr->{$k}->{length}=$length; - $chrID->{$name}=$k; - $chr->{nb_chrs}++; - - } - close CMAP; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Read the mate file according the input format file (solid, eland or sam) -sub readMateFile{ - - my ($chr1,$chr2,$pos1,$pos2,$order1,$order2,$t,$file_type,$tag_length)=@_; - my ($strand1,$strand2); - - if($file_type eq "solid"){ - - ($$chr1,$$chr2,$$pos1,$$pos2,$$order1,$$order2)=($$t[6],$$t[7],$$t[8]+1,$$t[9]+1,1,2); #0-based - - }else{ - my ($tag_length1,$tag_length2); - ($$chr1,$$chr2,$$pos1,$strand1,$$pos2,$strand2,$$order1,$$order2,$tag_length1,$tag_length2)=($$t[11],$$t[12],$$t[7],$$t[8],$$t[9],$$t[10],1,2,length($$t[1]),length($$t[2])) #1-based - if($file_type eq "eland"); - - if($file_type eq "sam"){ - - return 0 if ($$t[0]=~/^@/); #header sam filtered out - - ($$chr1,$$chr2,$$pos1,$$pos2)=($$t[2],$$t[6],$$t[3],$$t[7]); - - return 0 if (($$t[1]&0x0004) || ($$t[1]&0x0008)); - - $$chr2=$$chr1 if($$chr2 eq "="); - - $strand1 = (($$t[1]&0x0010))? 'R':'F'; - $strand2 = (($$t[1]&0x0020))? 'R':'F'; - - $$order1= (($$t[1]&0x0040))? '1':'2'; - $$order2= (($$t[1]&0x0080))? '1':'2'; - $tag_length1 = $tag_length->{$$order1}; - $tag_length2 = $tag_length->{$$order2}; - } - - $$pos1 = -($$pos1+$tag_length1) if ($strand1 eq "R"); #get sequencing starts - $$pos2 = -($$pos2+$tag_length2) if ($strand2 eq "R"); - } - return 1; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Parsing of the mates files and creation of links between 2 chromosomal fragments -sub linking{ - - my ($chr,$chrID,$pair,$tag_length,$window_dist,$step,$mates_file,$input_format,$sv_type,$links_file)=@_; - my %link; - - my $record=0; - my $nb_links=0; - my $warn=10000; - - my @sfile=split(/\./,$mates_file); - my $fchr=$sfile[$#sfile]; - - my $fh = new FileHandle; - - print LOG "# $fchr : Linking procedure...\n"; - print LOG "-- file=$mates_file\n". - "-- chromosome=$fchr\n". - "-- input format=$input_format\n". - "-- type=$sv_type\n". - "-- read1 length=$tag_length->{1}, read2 length=$tag_length->{2}\n". - "-- window size=$window_dist, step length=$step\n"; - - if ($mates_file =~ /.gz$/) { - $fh->open("gunzip -c $mates_file |") or die "$0: can't open ".$mates_file.":$!\n"; #gzcat - }elsif($mates_file =~ /.bam$/){ - $fh->open("$SAMTOOLS_BIN_DIR/samtools view $mates_file |") or die "$0: can't open ".$mates_file.":$!\n";#GALAXY - }else{ - $fh->open("<".$mates_file) or die "$0: can't open ".$mates_file.":$!\n"; - } - - - while(<$fh>){ - - my @t=split; #for each mate-pair - my $mate=$t[0]; - my ($chr_read1, $chr_read2, $firstbase_read1, $firstbase_read2, $end_order_read1,$end_order_read2); - - next if(exists $$pair{$mate}); - - next if (!readMateFile(\$chr_read1, \$chr_read2, \$firstbase_read1, \$firstbase_read2, \$end_order_read1, \$end_order_read2, \@t, $input_format,$tag_length)); - - next unless (exists $chrID->{$chr_read1} && exists $chrID->{$chr_read2}); - - ($chr_read1, $chr_read2)= ($chrID->{$chr_read1},$chrID->{$chr_read2}); - - if($sv_type ne "all"){ - if( ($sv_type eq "inter") && ($chr_read1 ne $chr_read2) || - ($sv_type eq "intra") && ($chr_read1 eq $chr_read2) ){ - }else{ - next; - } - } - - $$pair{$mate}=[$chr_read1, $chr_read2, $firstbase_read1, $firstbase_read2, $end_order_read1, $end_order_read2 ]; #fill out the hash pair table (ready for the defineCoordsLinks function) - - $record++; - - my ($coord_start_read1,$coord_end_read1,$coord_start_read2,$coord_end_read2); #get the coordinates of each read - - recupCoords($firstbase_read1,\$coord_start_read1,\$coord_end_read1,$tag_length->{$end_order_read1},$input_format); - recupCoords($firstbase_read2,\$coord_start_read2,\$coord_end_read2,$tag_length->{$end_order_read2},$input_format); - - for(my $i=1;$i<=$chr->{$chr_read1}->{'nb_frag'};$i++){ #fast genome parsing for link creation - - if (abs ($coord_start_read1-${$chr->{$chr_read1}->{$i}}[0]) <= $window_dist){ - - if(overlap($coord_start_read1,$coord_end_read1,${$chr->{$chr_read1}->{$i}}[0],${$chr->{$chr_read1}->{$i}}[1])){ - - for(my $j=1;$j<=$chr->{$chr_read2}->{'nb_frag'};$j++){ - - if (abs ($coord_start_read2-${$chr->{$chr_read2}->{$j}}[0]) <= $window_dist) { - - if(overlap($coord_start_read2,$coord_end_read2,${$chr->{$chr_read2}->{$j}}[0],${$chr->{$chr_read2}->{$j}}[1])){ - - makeLink(\%link,$chr_read1,$i,$chr_read2,$j,$mate,\$nb_links); #make the link - } - - }else{ - - $j=getNextFrag($coord_start_read2,$j,${$chr->{$chr_read2}->{$j}}[0],$chr->{$chr_read2}->{nb_frag},$window_dist,$step); - } - } - } - - }else{ - - $i=getNextFrag($coord_start_read1,$i,${$chr->{$chr_read1}->{$i}}[0],$chr->{$chr_read1}->{nb_frag},$window_dist,$step); - } - } - - if($record>=$warn){ - print LOG "-- $fchr : $warn mate-pairs analysed - $nb_links links done\n"; - $warn+=10000; - } - } - $fh->close; - - if(!$nb_links){ - print LOG "-- $fchr : No mate-pairs !\n". - "-- $fchr : No links have been found with the selected type of structural variations \($sv_type\)\n"; - } - - print LOG "-- $fchr : Total : $record mate-pairs analysed - $nb_links links done\n"; - - print LOG "-- $fchr : writing...\n"; - - $fh = new FileHandle; - - $fh->open(">".$links_file) or die "$0: can't write in the output ".$links_file." :$!\n"; - - foreach my $chr1 ( sort { $a <=> $b} keys %link){ #Sorted links output - - foreach my $chr2 ( sort { $a <=> $b} keys %{$link{$chr1}}){ - - foreach my $frag1 ( sort { $a <=> $b} keys %{$link{$chr1}{$chr2}}){ - - foreach my $frag2 ( sort { $a <=> $b} keys %{$link{$chr1}{$chr2}{$frag1}}){ - - my @count=split(",",$link{$chr1}{$chr2}{$frag1}{$frag2}); - print $fh "$chr->{$chr1}->{name}\t".(${$chr->{$chr1}->{$frag1}}[0]+1)."\t".(${$chr->{$chr1}->{$frag1}}[1]+1)."\t". - "$chr->{$chr2}->{name}\t".(${$chr->{$chr2}->{$frag2}}[0]+1)."\t".(${$chr->{$chr2}->{$frag2}}[1]+1)."\t". - scalar @count."\t". #nb of read - $link{$chr1}{$chr2}{$frag1}{$frag2}."\n"; #mate list - } - } - } - } - - $fh->close; - - undef %link; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#remove exact links doublons according to the mate list -sub getUniqueLinks{ - - my ($links_file,$nrlinks_file)=@_; - my %links; - my %pt; - my $nb_links; - my $n=1; - - my $record=0; - my $warn=300000; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - my $fh = new FileHandle; - - print LOG "# $fchr : Getting unique links...\n"; - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - - while(<$fh>){ - - my @t=split; - my $mates=$t[7]; - $record++; - - if(!exists $links{$mates}){ #Unique links selection - - $links{$mates}=[@t]; - $pt{$n}=$links{$mates}; - $n++; - - - }else{ #get the link coordinates from the mate-pairs list - - for my $i (1,2,4,5){ #get the shortest regions - - $links{$mates}->[$i]=($t[$i]>$links{$mates}->[$i])? $t[$i]:$links{$mates}->[$i] #maximum start - if($i==1 || $i==4); - $links{$mates}->[$i]=($t[$i]<$links{$mates}->[$i])? $t[$i]:$links{$mates}->[$i] #minimum end - if($i==2 || $i==5); - } - } - if($record>=$warn){ - print LOG "-- $fchr : $warn links analysed - ".($n-1)." unique links done\n"; - $warn+=300000; - } - } - $fh->close; - - $nb_links=$n-1; - print LOG "-- $fchr : Total : $record links analysed - $nb_links unique links done\n"; - - $fh = new FileHandle; - $fh->open(">$nrlinks_file") or die "$0: can't write in the output: $nrlinks_file :$!\n"; - print LOG "-- $fchr : writing...\n"; - for my $i (1..$nb_links){ - - print $fh join("\t",@{$pt{$i}})."\n"; #all links output - } - - $fh->close; - - undef %links; - undef %pt; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#get the new coordinates of each link from the mate list -sub defineCoordsLinks{ - - my ($chr,$chrID,$pair,$input_format,$sv_type,$tag_length,$links_file,$clinks_file)=@_; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - my $fh = new FileHandle; - my $fh2 = new FileHandle; - - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - $fh2->open(">$clinks_file") or die "$0: can't write in the output: $clinks_file :$!\n"; - - print LOG "# $fchr : Defining precise link coordinates...\n"; - - my $record=0; - my $warn=100000; - - my %coords; - my %strands; - my %order; - my %ends_order; - - while(<$fh>){ - - - my ($col1,$col2)=(1,2); #for an intrachromosomal link - my $diffchr=0; #difference between chr1 and chr2 - my ($chr1,$chr2,$mates_list,$npairs)=(split)[0,3,7,8]; - ($chr1,$chr2) = ($chrID->{$chr1},$chrID->{$chr2}); - if ($chr1 != $chr2){ #for an interchromosomal link - $col1=$col2=0; #no distinction - $diffchr=1; - } - - my @pairs=split(",",$mates_list); - - $coords{$col1}{$chr1}->{start}=undef; - $coords{$col1}{$chr1}->{end}=undef; - $coords{$col2}{$chr2}->{start}=undef; - $coords{$col2}{$chr2}->{end}=undef; - $strands{$col1}{$chr1}=undef; - $strands{$col2}{$chr2}=undef; - $ends_order{$col1}{$chr1}=undef; - $ends_order{$col2}{$chr2}=undef; - - - $order{$col1}{$chr1}->{index}->{1}=undef; - $order{$col1}{$chr1}->{index}->{2}=undef; - $order{$col2}{$chr2}->{index}->{1}=undef; - $order{$col2}{$chr2}->{index}->{2}=undef; - $order{$col1}{$chr1}->{order}=undef; - $order{$col2}{$chr2}->{order}=undef; - - $record++; - - for my $p (0..$#pairs){ #for each pair - - my ($coord_start_read1,$coord_end_read1); - my ($coord_start_read2,$coord_end_read2); - my $strand_read1=recupCoords(${$$pair{$pairs[$p]}}[2],\$coord_start_read1,\$coord_end_read1,$tag_length->{${$$pair{$pairs[$p]}}[4]},$input_format); - my $strand_read2=recupCoords(${$$pair{$pairs[$p]}}[3],\$coord_start_read2,\$coord_end_read2,$tag_length->{${$$pair{$pairs[$p]}}[5]},$input_format); - - if(!$diffchr){ #for a intrachromosomal link - if($coord_start_read2<$coord_start_read1){ #get the closer start coordinate for each column - ($col1,$col2)=(2,1); - }else{ - ($col1,$col2)=(1,2); - } - } - - push(@{$coords{$col1}{${$$pair{$pairs[$p]}}[0]}->{start}},$coord_start_read1); #get coords and strands of f3 and r3 reads - push(@{$coords{$col1}{${$$pair{$pairs[$p]}}[0]}->{end}},$coord_end_read1); - push(@{$coords{$col2}{${$$pair{$pairs[$p]}}[1]}->{start}},$coord_start_read2); - push(@{$coords{$col2}{${$$pair{$pairs[$p]}}[1]}->{end}},$coord_end_read2); - push(@{$strands{$col1}{${$$pair{$pairs[$p]}}[0]}},$strand_read1); - push(@{$strands{$col2}{${$$pair{$pairs[$p]}}[1]}},$strand_read2); - push(@{$ends_order{$col1}{${$$pair{$pairs[$p]}}[0]}},${$$pair{$pairs[$p]}}[4]); - push(@{$ends_order{$col2}{${$$pair{$pairs[$p]}}[1]}},${$$pair{$pairs[$p]}}[5]); - } - - ($col1,$col2)=(1,2) if(!$diffchr); - - my $coord_start_chr1=min(min(@{$coords{$col1}{$chr1}->{start}}),min(@{$coords{$col1}{$chr1}->{end}})); #get the biggest region - my $coord_end_chr1=max(max(@{$coords{$col1}{$chr1}->{start}}),max(@{$coords{$col1}{$chr1}->{end}})); - my $coord_start_chr2=min(min(@{$coords{$col2}{$chr2}->{start}}),min(@{$coords{$col2}{$chr2}->{end}})); - my $coord_end_chr2=max(max(@{$coords{$col2}{$chr2}->{start}}),max(@{$coords{$col2}{$chr2}->{end}})); - - @{$order{$col1}{$chr1}->{index}->{1}}= sort {${$coords{$col1}{$chr1}->{start}}[$a] <=> ${$coords{$col1}{$chr1}->{start}}[$b]} 0 .. $#{$coords{$col1}{$chr1}->{start}}; - @{$order{$col2}{$chr2}->{index}->{1}}= sort {${$coords{$col2}{$chr2}->{start}}[$a] <=> ${$coords{$col2}{$chr2}->{start}}[$b]} 0 .. $#{$coords{$col2}{$chr2}->{start}}; - - foreach my $i (@{$order{$col1}{$chr1}->{index}->{1}}){ #get the rank of the chr2 reads according to the sorted chr1 reads (start coordinate sorting) - foreach my $j (@{$order{$col2}{$chr2}->{index}->{1}}){ - - if(${$order{$col1}{$chr1}->{index}->{1}}[$i] == ${$order{$col2}{$chr2}->{index}->{1}}[$j]){ - ${$order{$col1}{$chr1}->{index}->{2}}[$i]=$i; - ${$order{$col2}{$chr2}->{index}->{2}}[$i]=$j; - last; - } - } - } - - foreach my $i (@{$order{$col1}{$chr1}->{index}->{2}}){ #use rank chr1 as an ID - foreach my $j (@{$order{$col2}{$chr2}->{index}->{2}}){ - - if(${$order{$col1}{$chr1}->{index}->{2}}[$i] == ${$order{$col2}{$chr2}->{index}->{2}}[$j]){ - ${$order{$col1}{$chr1}->{order}}[$i]=$i+1; - ${$order{$col2}{$chr2}->{order}}[$i]=$j+1; - last; - } - } - } - - @pairs=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},\@pairs);#sorting of the pairs, strands, and start coords from the sorted chr2 reads - @{$strands{$col1}{$chr1}}=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},$strands{$col1}{$chr1}); - @{$strands{$col2}{$chr2}}=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},$strands{$col2}{$chr2}); - @{$ends_order{$col1}{$chr1}}=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},$ends_order{$col1}{$chr1}); - @{$ends_order{$col2}{$chr2}}=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},$ends_order{$col2}{$chr2}); - @{$coords{$col1}{$chr1}->{start}}=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},$coords{$col1}{$chr1}->{start}); - @{$coords{$col2}{$chr2}->{start}}=sortTablebyIndex(\@{$order{$col1}{$chr1}->{index}->{1}},$coords{$col2}{$chr2}->{start}); - - - my @link=($chr->{$chr1}->{name}, $coord_start_chr1 , $coord_end_chr1, #all information output - $chr->{$chr2}->{name}, $coord_start_chr2 , $coord_end_chr2, - scalar @pairs, - join(",",@pairs), - join(",",@{$strands{$col1}{$chr1}}), - join(",",@{$strands{$col2}{$chr2}}), - join(",",@{$ends_order{$col1}{$chr1}}), - join(",",@{$ends_order{$col2}{$chr2}}), - join(",",@{$order{$col1}{$chr1}->{order}}), - join(",",@{$order{$col2}{$chr2}->{order}}), - join(",",@{$coords{$col1}{$chr1}->{start}}), - join(",",@{$coords{$col2}{$chr2}->{start}})); - - print $fh2 join("\t",@link)."\n"; - - if($record>=$warn){ - print LOG "-- $fchr : $warn links processed\n"; - $warn+=100000; - } - } - $fh->close; - $fh2->close; - - print LOG "-- $fchr : Total : $record links processed\n"; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Sort links according the concerned chromosomes and their coordinates -sub sortLinks{ - - my ($links_file,$sortedlinks_file,$unique)=@_; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - - print LOG "# $fchr : Sorting links...\n"; - - my $pipe=($unique)? "| sort -u":""; - system "sort -k 1,1 -k 4,4 -k 2,2n -k 5,5n -k 8,8n $links_file $pipe > $sortedlinks_file"; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#removal of fully overlapped links -sub removeFullyOverlappedLinks{ - - my ($links_file,$nrlinks_file,$warn_out)=@_; - - my %pt; - my $n=1; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - my $fh = new FileHandle; - - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - while(<$fh>){ - - my @t=split("\t",$_); - $pt{$n}=[@t]; - $n++; - } - $fh->close; - - my $nb_links=$n-1; - my $nb=$nb_links; - - my %pt2; - my $nb2=1; - my $record=0; - my $warn=10000; - - print LOG "# $fchr : Removing fully overlapped links...\n"; - - LINK: - - for my $i (1..$nb){ - - my @link=(); - my @next_link=(); - my $ind1=$i; - - $record++; - if($record>=$warn){ - print LOG "-- $fchr : $warn unique links analysed - ".($nb2-1)." non-overlapped links done\n"; - $warn+=10000; - } - - if(exists $pt{$ind1}){ - @link=@{$pt{$ind1}}; #link1 - }else{ - next LINK; - } - - my ($chr1,$start1,$end1,$chr2,$start2,$end2)=($link[0],$link[1],$link[2],$link[3],$link[4],$link[5]); #get info of link1 - my @mates=deleteBadOrderSensePairs(split(",",$link[7])); - - my $ind2=$ind1+1; - $ind2++ while (!exists $pt{$ind2}&& $ind2<=$nb); #get the next found link - - if($ind2<=$nb){ - - @next_link=@{$pt{$ind2}}; #link2 - my ($chr3,$start3,$end3,$chr4,$start4,$end4)=($next_link[0],$next_link[1],$next_link[2],$next_link[3],$next_link[4],$next_link[5]); #get info of link2 - my @next_mates=deleteBadOrderSensePairs(split(",",$next_link[7])); - - while(($chr1 eq $chr3 && $chr2 eq $chr4) && overlap($start1,$end1,$start3,$end3)){ #loop here according to the chr1 coordinates, need an overlap between links to enter - - if(!overlap($start2,$end2,$start4,$end4)){ #if no overlap with chr2 coordinates ->next link2 - - $ind2++; - $ind2++ while (!exists $pt{$ind2}&& $ind2<=$nb); - - if($ind2>$nb){ #if no more link in the file -> save link1 - - $pt2{$nb2}=\@link; - $nb2++; - next LINK; - } - - @next_link=@{$pt{$ind2}}; - ($chr3,$start3,$end3,$chr4,$start4,$end4)=($next_link[0],$next_link[1],$next_link[2],$next_link[3],$next_link[4],$next_link[5]); - @next_mates=deleteBadOrderSensePairs(split(",",$next_link[7])); - next; - } - - my %mates=map{$_ =>1} @mates; #get the equal number of mates - my @same_mates = grep( $mates{$_}, @next_mates ); - my $nb_mates= scalar @same_mates; - - if($nb_mates == scalar @mates){ - - delete $pt{$ind1}; #if pairs of link 1 are all included in link 2 -> delete link1 - next LINK; #go to link2, link2 becomes link1 - - }else{ - delete $pt{$ind2} if($nb_mates == scalar @next_mates); #if pairs of link2 are all included in link 1 -> delete link2 - $ind2++; #we continue by checking the next link2 - $ind2++ while (!exists $pt{$ind2}&& $ind2<=$nb); - - if($ind2>$nb){ #if no more link in the file -> save link1 - - $pt2{$nb2}=\@link; - $nb2++; - next LINK; - } - - @next_link=@{$pt{$ind2}}; #get info of link2 - ($chr3,$start3,$end3,$chr4,$start4,$end4)=($next_link[0],$next_link[1],$next_link[2],$next_link[3],$next_link[4],$next_link[5]); - @next_mates=deleteBadOrderSensePairs(split(",",$next_link[7])); - - } - } - } - $pt2{$nb2}=\@link; #if no (more) link with chr1 coordinates overlap -> save link1 - $nb2++; - } - - print LOG "-- $fchr : Total : $nb_links unique links analysed - ".($nb2-1)." non-overlapped links done\n"; - - #OUTPUT - - $fh = new FileHandle; - $fh->open(">$nrlinks_file") or die "$0: can't write in the output: $nrlinks_file :$!\n"; - print LOG "-- $fchr : writing...\n"; - for my $i (1..$nb2-1){ - - print $fh join("\t",@{$pt2{$i}}); #all links output - } - - close $fh; - - print LOG "-- $fchr : output created: $nrlinks_file\n" if($warn_out); - - undef %pt; - undef %pt2; -} -#------------------------------------------------------------------------------# -sub postFiltering { - - my ($links_file,$pflinks_file, $finalScore_thres)=@_; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - - my ($nb,$nb2)=(0,0); - - print LOG "# $fchr : Post-filtering links...\n"; - print LOG "-- $fchr : final score threshold = $finalScore_thres\n"; - - my $fh = new FileHandle; - my $fh2 = new FileHandle; - - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - $fh2->open(">$pflinks_file") or die "$0: can't write in the output: $pflinks_file :$!\n"; - - - while(<$fh>){ - - my @t=split("\t",$_); - my $score=$t[$#t-1]; - - if($score >= $finalScore_thres){ - print $fh2 join("\t", @t); - $nb2++; - } - $nb++; - } - $fh->close; - $fh2->close; - - print LOG "-- $fchr : Total : $nb unique links analysed - $nb2 links kept\n"; - print LOG "-- $fchr : output created: $pflinks_file\n"; -} - - - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Filtering of the links -sub strandFiltering{ - - my($chr,$chrID,$pairs_threshold,$strand_filtering,$chromosomes, - $input_format,$cmap_file,$mate_sense, $tag_length,$links_file,$flinks_file)=@_; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-1]; - - - my %chrs; - my %chrs1; - my %chrs2; - my $nb_chrs; - my $exclude; - - if($chromosomes){ - my @chrs=split(",",$chromosomes); - $nb_chrs=scalar @chrs; - $exclude=($chrs[0]=~/^\-/)? 1:0; - for my $chrName (@chrs){ - $chrName=~s/^(\-)//; - my $col=($chrName=~s/_(1|2)$//); - - if(!$col){ - $chrs{$chrID->{$chrName}}=undef - }else{ - $chrs1{$chrID->{$chrName}}=undef if($1==1); - $chrs2{$chrID->{$chrName}}=undef if($1==2); - } - } - } - - my $record=0; - my $nb_links=0; - my $warn=10000; - - my $sens_ratio_threshold=0.6; - - print LOG "\# Filtering procedure...\n"; - print LOG "\# Number of pairs and strand filtering...\n"; - print LOG "-- file=$links_file\n"; - print LOG "-- nb_pairs_threshold=$pairs_threshold, strand_filtering=".(($strand_filtering)? "yes":"no"). - ", chromosomes=".(($chromosomes)? "$chromosomes":"all")."\n"; - - - - my $fh = new FileHandle; - my $fh2 = new FileHandle; - - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - $fh2->open(">$flinks_file") or die "$0: can't write in the output: $flinks_file :$!\n"; - - while(<$fh>){ - - my @t=split; #for each link - my $is_good=1; - $record++; - - - if($chromosomes){ - - my ($chr1,$chr2)=($chrID->{$t[0]},$chrID->{$t[3]}); - - if(!$exclude){ - $is_good=(exists $chrs{$chr1} && exists $chrs{$chr2})? 1:0; - $is_good=(exists $chrs1{$chr1} && exists $chrs2{$chr2})? 1:0 if(!$is_good); - $is_good=($nb_chrs==1 && (exists $chrs1{$chr1} || exists $chrs2{$chr2}))? 1:0 if(!$is_good); - }else{ - $is_good=(exists $chrs{$chr1} || exists $chrs{$chr2})? 0:1; - $is_good=(exists $chrs1{$chr1} || exists $chrs2{$chr2})? 0:1 if($is_good); - } - } - - $is_good = ($is_good && $t[6] >= $pairs_threshold)? 1 :0; #filtering according the number of pairs - if($is_good && $strand_filtering){ #if filtering according the strand sense - - my @mates=split(/,/,$t[7]); #get the concordant pairs in the strand sense - my @strands1=split(/,/,$t[8]); - my @strands2=split(/,/,$t[9]); - - my %mate_class=( 'FF' => 0, 'RR' => 0, 'FR' => 0, 'RF' => 0); - - my %mate_reverse=( 'FF' => 'RR', 'RR' => 'FF', #group1: FF,RR - 'FR' => 'RF', 'RF' => 'FR'); #group2: FR,RF - - my %mate_class2=( $mate_sense=>"NORMAL_SENSE", inverseSense($mate_sense)=>"NORMAL_SENSE", - substr($mate_sense,0,1).inverseSense(substr($mate_sense,1,1))=>"REVERSE_SENSE", - inverseSense(substr($mate_sense,0,1)).substr($mate_sense,1,1)=>"REVERSE_SENSE"); - - if($t[6] == 1){ - - push(@t,$mate_class2{$strands1[0].$strands2[0]},"1/1",1,1); - - }else{ - - tie (my %class,'Tie::IxHash'); - my $split; - - foreach my $i (0..$#mates){ - $mate_class{$strands1[$i].$strands2[$i]}++; #get the over-represented group - } - - my $nb_same_sens_class=$mate_class{FF}+$mate_class{RR}; - my $nb_diff_sens_class=$mate_class{FR}+$mate_class{RF}; - my $sens_ratio=max($nb_same_sens_class,$nb_diff_sens_class)/($nb_same_sens_class+$nb_diff_sens_class); - - if($sens_ratio < $sens_ratio_threshold){ - %class=(1=>'FF', 2=>'FR'); - $split=1; - }else{ - $class{1}=($nb_same_sens_class > $nb_diff_sens_class)? 'FF':'FR'; #if yes get the concerned class - $split=0; - } - - $is_good=getConsistentSenseLinks(\@t,\@mates,\@strands1,\@strands2,$tag_length,$mate_sense,\%mate_reverse,\%mate_class2,\%class,$split,$pairs_threshold); - } - } - - if($is_good){ #PRINT - - my $nb=scalar @t; - if($nb > 20){ - my @t2=splice(@t,0,20); - print $fh2 join("\t",@t2)."\n"; - $nb_links++; - } - $nb_links++; - print $fh2 join("\t",@t)."\n"; - } - - if($record>=$warn){ - print LOG "-- $fchr : $warn links analysed - $nb_links links kept\n"; - $warn+=10000; - } - } - $fh->close; - $fh2->close; - - print LOG "-- $fchr : No links have been found with the selected filtering parameters\n" if(!$nb_links); - - print LOG "-- $fchr : Total : $record links analysed - $nb_links links kept\n"; - - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getConsistentSenseLinks{ - - my ($t,$mates,$strands1,$strands2,$tag_length,$mate_sense, $mate_reverse,$mate_class2, $class, $split,$thres)=@_; - - my $npairs=scalar @$mates; - - my @ends_order1 = split (/,/,$$t[10]); - my @ends_order2 = split (/,/,$$t[11]); - my @order1 = split (/,/,$$t[12]); - my @order2 = split (/,/,$$t[13]); - my @positions1 = split (/,/,$$t[14]); - my @positions2 = split (/,/,$$t[15]); - - my @newlink; - - foreach my $ind (keys %{$class} ){ - - tie (my %flink,'Tie::IxHash'); - my @orders2remove=(); - - foreach my $i (0..$#{$mates}){ #get the pairs belonging the over-represented group - - if((($$strands1[$i].$$strands2[$i]) eq $$class{$ind}) || (($$strands1[$i].$$strands2[$i]) eq $$mate_reverse{$$class{$ind}})){ - push(@{$flink{mates}},$$mates[$i]); - push(@{$flink{strands1}},$$strands1[$i]); - push(@{$flink{strands2}},$$strands2[$i]); - push(@{$flink{ends_order1}},$ends_order1[$i]); - push(@{$flink{ends_order2}},$ends_order2[$i]); - push(@{$flink{positions1}},$positions1[$i]); - push(@{$flink{positions2}},$positions2[$i]); - - }else{ - push(@orders2remove,$order1[$i]); - } - } - - @{$flink{order1}}=(); - @{$flink{order2}}=(); - if(scalar @orders2remove > 0){ - getNewOrders(\@order1,\@order2,\@orders2remove,$flink{order1},$flink{order2}) - }else{ - @{$flink{order1}}=@order1; - @{$flink{order2}}=@order2; - } - - my @ends1; getEnds(\@ends1,$flink{positions1},$flink{strands1},$flink{ends_order1},$tag_length); - my @ends2; getEnds(\@ends2,$flink{positions2},$flink{strands2},$flink{ends_order2},$tag_length); - - my $fnpairs=scalar @{$flink{mates}}; - my $strand_filtering_ratio=$fnpairs."/".$npairs; - my $real_ratio=$fnpairs/$npairs; - - if($fnpairs>=$thres){ #filtering according the number of pairs - - push(@newlink, - $$t[0], - min(min(@{$flink{positions1}}),min(@ends1)), - max(max(@{$flink{positions1}}),max(@ends1)), - $$t[3], - min(min(@{$flink{positions2}}),min(@ends2)), - max(max(@{$flink{positions2}}),max(@ends2)), - $fnpairs, - join(",",@{$flink{mates}}), - join(",",@{$flink{strands1}}), - join(",",@{$flink{strands2}}), - join(",",@{$flink{ends_order1}}), - join(",",@{$flink{ends_order2}}), - join(",",@{$flink{order1}}), - join(",",@{$flink{order2}}), - join(",",@{$flink{positions1}}), - join(",",@{$flink{positions2}}), - $$mate_class2{${$flink{strands1}}[0].${$flink{strands2}}[0]}, - $strand_filtering_ratio, - $real_ratio, - $npairs - ); - } - } - - if (grep {defined($_)} @newlink) { - @$t=@newlink; - return 1 - } - return 0; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getNewOrders{ - - my($tab1,$tab2,$list,$newtab1,$newtab2)=@_; - my $j=1; - my $k=1; - for my $i (0..$#{$tab2}){ - my $c=0; - for my $j (0..$#{$list}){ - $c++ if(${$list}[$j] < ${$tab2}[$i]); - if(${$list}[$j] == ${$tab2}[$i]){ - $c=-1; last; - } - } - if($c!=-1){ - push(@{$newtab2}, ${$tab2}[$i]-$c); - push(@{$newtab1}, $k); - $k++; - } - } -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#Filtering of the links using their order -sub orderFiltering { - - my ($chr,$chrID,$nb_pairs_threshold,$nb_pairs_order_threshold,$mu,$sigma,$mate_sense,$tag_length,$links_file,$flinks_file)=@_; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - - my $diff_sense_ends=(($mate_sense eq "FR") || ($mate_sense eq "RF"))? 1:0; - - my $record=0; - my $warn=10000; - my $nb_links=0; - - my $quant05 = 1.644854; - my $quant001 = 3.090232; - my $alphaDist = $quant05 * 2 * $sigma; - my $maxFragmentLength = &floor($quant001 * $sigma + $mu); - - print LOG "\# Filtering by order...\n"; - print LOG "-- mu length=$mu, sigma length=$sigma, nb pairs order threshold=$nb_pairs_order_threshold\n"; - print LOG "-- distance between comparable pairs was set to $alphaDist\n"; - print LOG "-- maximal fragment length was set to $maxFragmentLength\n"; - - - my $fh = new FileHandle; - my $fh2 = new FileHandle; - - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - $fh2->open(">$flinks_file") or die "$0: can't write in the output: $flinks_file :$!\n"; - - while(<$fh>){ - - $record++; - my @t = split; - my ($chr1,$chr2,$mates_list)=@t[0,3,7]; - my @pairs=split(",",$mates_list); - ($chr1,$chr2) = ($chrID->{$chr1},$chrID->{$chr2}); - my ($coord_start_chr1,$coord_end_chr1,$coord_start_chr2,$coord_end_chr2) = @t[1,2,4,5]; - my $numberOfPairs = $t[6]; - my @strand1 = split (/,/,$t[8]); - my @strand2 = split (/,/,$t[9]); - my @ends_order1 = split (/,/,$t[10]); - my @ends_order2 = split (/,/,$t[11]); - my @order1 = split (/,/,$t[12]); - my @order2 = split (/,/,$t[13]); - my @positions1 = split (/,/,$t[14]); - my @positions2 = split (/,/,$t[15]); - my @ends1; getEnds(\@ends1,\@positions1,\@strand1,\@ends_order1,$tag_length); - my @ends2; getEnds(\@ends2,\@positions2,\@strand2,\@ends_order2,$tag_length); - my $clusterCoordinates_chr1; - my $clusterCoordinates_chr2; - my $reads_left = 0; - - my $ifRenv = $t[16]; - my $strand_ratio_filtering=$t[17]; - - #kind of strand filtering. For example, will keep only FFF-RRR from a link FFRF-RRRF if <F-R> orientation is correct - my ($singleBreakpoint, %badInFRSense) = findBadInFRSenseSOLiDSolexa(\@strand1,\@strand2,\@ends_order1,\@ends_order2,\@order1,\@order2,$mate_sense); - #find pairs type F-RRRR or FFFF-R in the case if <R-F> orientation is correct - #These pairs are annotated as BED pairs forever! They won't be recycled! - my $table; - for my $i (0..$numberOfPairs-1) { #fill the table with non adequate pairs: pairID numberOfNonAdPairs nonAdPairIDs - my $nonAdeq = 0; - for my $j (0..$i-1) { - if (exists($table->{$j}->{$i})) { - $nonAdeq++; - $table->{$i}->{$j} = 1; - } - } - for my $j ($i+1..$numberOfPairs-1) { - if ($positions1[$j]-$positions1[$i]>$alphaDist) { - if (&reversed ($i,$j,$ifRenv,\@positions2)) { - $nonAdeq++; - $table->{$i}->{$j} = 1; - } - } - } - $table->{$i}->{nonAdeq} = $nonAdeq; - } - - for my $bad (keys %badInFRSense) { #remove pairs type F-RRRR or FFFF-R in the case of <R-F> orientation - &remove($bad,$table); - } - - my @falseReads; - #RRRR-F -> RRRR or R-FFFF -> FFFF - @falseReads = findBadInRFSenseSOLiDSolexa(\@strand1,\@ends_order1,$mate_sense, keys %{$table}); - #these pairs will be recycled later as $secondTable - for my $bad (@falseReads) { - &remove($bad,$table); - } - - my $bad = &check($table); - while ($bad ne "OK") { #clear the table to reject non adequate pairs in the sense of ORDER - # push (@falseReads, $bad); remove completely!!! - &remove($bad,$table); - $bad = &check($table); - } - - $reads_left = scalar keys %{$table}; - my $coord_start_chr1_cluster1 = min(min(@positions1[sort {$a<=>$b} keys %{$table}]),min(@ends1[sort {$a<=>$b} keys %{$table}])); - my $coord_end_chr1_cluster1 = max(max(@positions1[sort {$a<=>$b} keys %{$table}]),max(@ends1[sort {$a<=>$b} keys %{$table}])); - my $coord_start_chr2_cluster1 = min(min(@positions2[sort {$a<=>$b} keys %{$table}]),min(@ends2[sort {$a<=>$b} keys %{$table}])); - my $coord_end_chr2_cluster1 = max(max(@positions2[sort {$a<=>$b} keys %{$table}]),max(@ends2[sort {$a<=>$b} keys %{$table}])); - - $clusterCoordinates_chr1 = '('.$coord_start_chr1_cluster1.','.$coord_end_chr1_cluster1.')'; - $clusterCoordinates_chr2 = '('.$coord_start_chr2_cluster1.','.$coord_end_chr2_cluster1.')'; - - my $ifBalanced = 'UNBAL'; - my $secondTable; - my $clusterCoordinates; - my ($break_pont_chr1,$break_pont_chr2); - - my $signatureType=""; - - my $maxCoord1 =$chr->{$chr1}->{length}; - my $maxCoord2 =$chr->{$chr2}->{length}; - - if (scalar @falseReads) { - @falseReads = sort @falseReads; - #now delete FRFR choosing the majority - my @newfalseReads; #find and remove pairs type RRRR-F or R-FFFF - @newfalseReads = findBadInRFSenseSOLiDSolexa(\@strand1,\@ends_order1,$mate_sense,@falseReads); #these @newfalseReads won't be recycled - my %hashTmp; - for my $count1 (0..scalar(@falseReads)-1) { - my $i = $falseReads[$count1]; - $hashTmp{$i} = 1; - for my $bad (@newfalseReads) { - if ($bad == $i) { - delete $hashTmp{$i}; - next; - } - } - } - @falseReads = sort keys %hashTmp; #what is left - for my $count1 (0..scalar(@falseReads)-1) { #fill the table for reads which were previously rejected - my $nonAdeq = 0; - my $i = $falseReads[$count1]; - - for my $count2 (0..$count1-1) { - my $j = $falseReads[$count2]; - if (exists($secondTable->{$j}->{$i})) { - $nonAdeq++; - $secondTable->{$i}->{$j} = 1; - } - } - for my $count2 ($count1+1..scalar(@falseReads)-1) { - my $j = $falseReads[$count2]; - if ($positions1[$j]-$positions1[$i]>$alphaDist) { - if (&reversed ($i,$j,$ifRenv,\@positions2)) { - $nonAdeq++; - $secondTable->{$i}->{$j} = 1; - } - } - } - $secondTable->{$i}->{nonAdeq} = $nonAdeq; - } - - my @falseReads2; - my $bad = &check($secondTable); - while ($bad ne "OK") { #clear the table to reject non adequate pairs - push (@falseReads2, $bad); - &remove($bad,$secondTable); - $bad = &check($secondTable); - } - if (scalar keys %{$secondTable} >= $nb_pairs_order_threshold) { - my $coord_start_chr1_cluster2 = min(min(@positions1[sort {$a<=>$b} keys %{$secondTable}]),min(@ends1[sort {$a<=>$b} keys %{$secondTable}])); - my $coord_end_chr1_cluster2 = max(max(@positions1[sort {$a<=>$b} keys %{$secondTable}]),max(@ends1[sort {$a<=>$b} keys %{$secondTable}])); - my $coord_start_chr2_cluster2 = min(min(@positions2[sort {$a<=>$b} keys %{$secondTable}]),min(@ends2[sort {$a<=>$b} keys %{$secondTable}])); - my $coord_end_chr2_cluster2 = max(max(@positions2[sort {$a<=>$b} keys %{$secondTable}]),max(@ends2[sort {$a<=>$b} keys %{$secondTable}])); - - $ifBalanced = 'BAL'; - - if ($ifBalanced eq 'BAL') { - - if (scalar keys %{$table} < $nb_pairs_order_threshold) { - $ifBalanced = 'UNBAL'; #kill cluster 1! - ($table,$secondTable)=($secondTable,$table); #this means that one needs to exchange cluster1 with cluster2 - $reads_left = scalar keys %{$table}; - $coord_start_chr1_cluster1 = $coord_start_chr1_cluster2; - $coord_end_chr1_cluster1 = $coord_end_chr1_cluster2; - $coord_start_chr2_cluster1 = $coord_start_chr2_cluster2; - $coord_end_chr2_cluster1 = $coord_end_chr2_cluster2; - $clusterCoordinates_chr1 = '('.$coord_start_chr1_cluster1.','.$coord_end_chr1_cluster1.')'; - $clusterCoordinates_chr2 = '('.$coord_start_chr2_cluster1.','.$coord_end_chr2_cluster1.')'; - - } else { - - $reads_left += scalar keys %{$secondTable}; - next if ($reads_left < $nb_pairs_threshold); - - if ($coord_end_chr1_cluster2 < $coord_start_chr1_cluster1) { - ($table,$secondTable)=($secondTable,$table); #this means that one needs to exchange cluster1 with cluster2 - - ($coord_start_chr1_cluster1,$coord_start_chr1_cluster2) = ($coord_start_chr1_cluster2,$coord_start_chr1_cluster1); - ($coord_end_chr1_cluster1,$coord_end_chr1_cluster2)=($coord_end_chr1_cluster2,$coord_end_chr1_cluster1); - ($coord_start_chr2_cluster1,$coord_start_chr2_cluster2)=($coord_start_chr2_cluster2,$coord_start_chr2_cluster1); - ($coord_end_chr2_cluster1 , $coord_end_chr2_cluster2)=($coord_end_chr2_cluster2 , $coord_end_chr2_cluster1); - - $clusterCoordinates_chr1 = '('.$coord_start_chr1_cluster1.','.$coord_end_chr1_cluster1.'),'.$clusterCoordinates_chr1; - $clusterCoordinates_chr2 = '('.$coord_start_chr2_cluster1.','.$coord_end_chr2_cluster1.'),'.$clusterCoordinates_chr2; - }else { - $clusterCoordinates_chr1 .= ',('.$coord_start_chr1_cluster2.','.$coord_end_chr1_cluster2.')'; - $clusterCoordinates_chr2 .= ',('.$coord_start_chr2_cluster2.','.$coord_end_chr2_cluster2.')'; - } - $coord_start_chr1 = min($coord_start_chr1_cluster1,$coord_start_chr1_cluster2); - $coord_end_chr1 = max($coord_end_chr1_cluster1,$coord_end_chr1_cluster2); - $coord_start_chr2 = min($coord_start_chr2_cluster1,$coord_start_chr2_cluster2); - $coord_end_chr2 = max($coord_end_chr2_cluster1,$coord_end_chr2_cluster2); - #to calculate breakpoints one need to take into account read orientation in claster.. - my $leftLetterOk = substr($mate_sense, 0, 1); #R - my $rightLetterOk = substr($mate_sense, 1, 1); #F - - - my @index1 = keys %{$table}; - my @index2 = keys %{$secondTable}; - - my (@generalStrand1,@generalStrand2) = 0; - - if ($leftLetterOk eq $rightLetterOk) { #SOLID mate-pairs - $leftLetterOk = 'R'; - $rightLetterOk = 'F'; - @generalStrand1 = translateSolidToRF(\@strand1,\@ends_order1); - @generalStrand2 = translateSolidToRF(\@strand2,\@ends_order2); - } else { - @generalStrand1 = @strand1; - @generalStrand2 = @strand2; # TODO check if it is correct - } - if ($generalStrand1[$index1[0]] eq $leftLetterOk && $generalStrand1[$index2[0]] eq $rightLetterOk) { #(R,F) - $break_pont_chr1 = '('.$coord_end_chr1_cluster1.','.$coord_start_chr1_cluster2.')'; - - if ($generalStrand2[$index1[0]] eq $rightLetterOk && $generalStrand2[$index2[0]] eq $leftLetterOk) { - if ($coord_end_chr2_cluster1 >= $coord_end_chr2_cluster2) { - $break_pont_chr2 = '('.$coord_end_chr2_cluster2.','.$coord_start_chr2_cluster1.')'; - $signatureType = "TRANSLOC"; - } else { - $break_pont_chr2 = '('.max(($coord_end_chr2_cluster1-$maxFragmentLength),1).','.$coord_start_chr2_cluster1.')'; - $break_pont_chr2 .= ',('.$coord_end_chr2_cluster2.','.min(($coord_start_chr2_cluster2+$maxFragmentLength),$maxCoord2).')'; - $signatureType = "INS_FRAGMT"; - } - - } elsif ($generalStrand2[$index1[0]] eq $leftLetterOk && $generalStrand2[$index2[0]] eq $rightLetterOk) { - if ($coord_end_chr2_cluster1 >= $coord_end_chr2_cluster2) { - $break_pont_chr2 = '('.max(($coord_end_chr2_cluster2-$maxFragmentLength),1).','.$coord_start_chr2_cluster2.')'; - $break_pont_chr2 .= ',('.$coord_end_chr2_cluster1.','.min(($coord_start_chr2_cluster1+$maxFragmentLength),$maxCoord2).')'; - $signatureType = "INV_INS_FRAGMT"; - } else { - $break_pont_chr2 = '('.$coord_end_chr2_cluster1.','.$coord_start_chr2_cluster2.')'; - $signatureType = "INV_TRANSLOC"; - } - } else { - #should not occur - print STDERR "\nError in orderFiltering\n\n"; - } - } - - elsif ($generalStrand1[$index1[0]] eq $rightLetterOk && $generalStrand1[$index2[0]] eq $leftLetterOk) { #(F,R) - $break_pont_chr1 = '('.max(($coord_end_chr1_cluster1-$maxFragmentLength),1).','.$coord_start_chr1_cluster1.')'; - $break_pont_chr1 .= ',('.$coord_end_chr1_cluster2.','.min(($coord_start_chr1_cluster2+$maxFragmentLength),$maxCoord1).')'; - if ($generalStrand2[$index1[0]] eq $rightLetterOk && $generalStrand2[$index2[0]] eq $leftLetterOk) { - if ($coord_end_chr2_cluster1 >= $coord_end_chr2_cluster2) { - $break_pont_chr2 = '('.$coord_end_chr2_cluster2.','.$coord_start_chr2_cluster1.')'; - $signatureType = "INV_INS_FRAGMT"; - } else { - $break_pont_chr2 = '('.max(($coord_end_chr2_cluster1-$maxFragmentLength),1).','.$coord_start_chr2_cluster1.')'; - $break_pont_chr2 .= ',('.$coord_end_chr2_cluster2.','.min(($coord_start_chr2_cluster2+$maxFragmentLength),$maxCoord2).')'; - $signatureType = "INV_COAMPLICON"; - } - - } elsif ($generalStrand2[$index1[0]] eq $leftLetterOk && $generalStrand2[$index2[0]] eq $rightLetterOk) { - if ($coord_end_chr2_cluster1 >= $coord_end_chr2_cluster2) { - $break_pont_chr2 = '('.max(($coord_end_chr2_cluster2-$maxFragmentLength),1).','.$coord_start_chr2_cluster2.')'; - $break_pont_chr2 .= ',('.$coord_end_chr2_cluster1.','.min(($coord_start_chr2_cluster1+$maxFragmentLength),$maxCoord2).')'; - $signatureType = "COAMPLICON"; - } else { - $break_pont_chr2 = '('.$coord_end_chr2_cluster1.','.$coord_start_chr2_cluster2.')'; - $signatureType = "INS_FRAGMT"; - } - } else { - #should not occur - $signatureType = "UNDEFINED"; - } - } - else { # (F,F) or (R,R) something strange. We will discard the smallest cluster - $ifBalanced = 'UNBAL'; - if (scalar keys %{$secondTable} > scalar keys %{$table}) { - ($table,$secondTable)=($secondTable,$table); #this means that one needs to exchange cluster1 with cluster2 - - $coord_start_chr1_cluster1 = $coord_start_chr1_cluster2; - $coord_end_chr1_cluster1 = $coord_end_chr1_cluster2; - $coord_start_chr2_cluster1 = $coord_start_chr2_cluster2; - $coord_end_chr2_cluster1 = $coord_end_chr2_cluster2; - $clusterCoordinates_chr1 = '('.$coord_start_chr1_cluster1.','.$coord_end_chr1_cluster1.')'; - $clusterCoordinates_chr2 = '('.$coord_start_chr2_cluster1.','.$coord_end_chr2_cluster1.')'; - } - $reads_left = scalar keys %{$table}; - } - if ($ifBalanced eq 'BAL') { - $ifRenv = $signatureType; - } - } - } - } - } - if ($ifBalanced ne 'BAL') { - #define possible break point - $coord_start_chr1 = $coord_start_chr1_cluster1; - $coord_end_chr1 = $coord_end_chr1_cluster1; - $coord_start_chr2 = $coord_start_chr2_cluster1; - $coord_end_chr2 = $coord_end_chr2_cluster1; - - my $region_length_chr1 = $coord_end_chr1-$coord_start_chr1; - my $region_length_chr2 = $coord_end_chr2-$coord_start_chr2; - - my $leftLetterOk = substr($mate_sense, 0, 1); #R - my $rightLetterOk = substr($mate_sense, 1, 1); #F - - my @index = keys %{$table}; - unless ($diff_sense_ends) { - my $firstEndOrder1 = $ends_order1[$index[0]]; - my $firstEndOrder2 = $ends_order2[$index[0]]; - $break_pont_chr1 = (($strand1[$index[0]] eq 'R' && $firstEndOrder1 == 2) || ($strand1[$index[0]] eq 'F' && $firstEndOrder1 == 1))?'('.$coord_end_chr1.','.min(($coord_start_chr1+$maxFragmentLength),$maxCoord1).')':'('.max(($coord_end_chr1-$maxFragmentLength),1).','.$coord_start_chr1.')'; - $break_pont_chr2 = (($strand2[$index[0]] eq 'R' && $firstEndOrder2 == 2) || ($strand2[$index[0]] eq 'F' && $firstEndOrder2 == 1))?'('.$coord_end_chr2.','.min(($coord_start_chr2+$maxFragmentLength),$maxCoord2).')':'('.max(($coord_end_chr2-$maxFragmentLength),1).','.$coord_start_chr2.')'; - } else { - $break_pont_chr1 = ($strand1[$index[0]] eq $leftLetterOk )?'('.$coord_end_chr1.','.min(($coord_start_chr1+$maxFragmentLength),$maxCoord1).')':'('.max(($coord_end_chr1-$maxFragmentLength),1).','.$coord_start_chr1.')'; - $break_pont_chr2 = ($strand2[$index[0]] eq $leftLetterOk )?'('.$coord_end_chr2.','.min(($coord_start_chr2+$maxFragmentLength),$maxCoord2).')':'('.max(($coord_end_chr2-$maxFragmentLength),1).','.$coord_start_chr2.')'; - } - - if ($chr1 ne $chr2){ - $ifRenv="INV_TRANSLOC" if($ifRenv eq "REVERSE_SENSE"); - $ifRenv="TRANSLOC" if($ifRenv eq "NORMAL_SENSE"); - } - } - - if (($ifBalanced eq 'BAL')&&( (scalar keys %{$table}) + (scalar keys %{$secondTable}) < $nb_pairs_threshold)) { - next; #discard the link - } - if (($ifBalanced eq 'UNBAL')&&(scalar keys %{$table} < $nb_pairs_threshold)) { - next; #discard the link - } - my $ratioTxt = "$reads_left/".(scalar @pairs); - my ($n1,$nTot) = split ("/",$strand_ratio_filtering); - my $ratioReal = $reads_left/$nTot; - - if ($coord_start_chr1<=0) { - $coord_start_chr1=1; - } - if ($coord_start_chr2<=0) { - $coord_start_chr2=1; - } - #create output - my @link=($chr->{$chr1}->{name}, $coord_start_chr1 , $coord_end_chr1, #all information output - $chr->{$chr2}->{name}, $coord_start_chr2 , $coord_end_chr2, - $reads_left, - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@pairs), - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@strand1), - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@strand2), - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@ends_order1), - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@ends_order2), - &redraw(2,$table,$secondTable,\%badInFRSense,$ifBalanced,\@order1), - &redraw(2,$table,$secondTable,\%badInFRSense,$ifBalanced,\@order2), - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@positions1), - &redraw(1,$table,$secondTable,\%badInFRSense,$ifBalanced,\@positions2), - $ifRenv, - $strand_ratio_filtering, - $ifBalanced, $ratioTxt, $break_pont_chr1, $break_pont_chr2, - $ratioReal, $nTot); - - $nb_links++; - print $fh2 join("\t",@link)."\n"; - - if($record>=$warn){ - print LOG "-- $fchr : $warn links analysed - $nb_links links kept\n"; - $warn+=10000; - } - - } - $fh->close; - $fh2->close; - - print LOG "-- $fchr : Total : $record links analysed - $nb_links links kept\n"; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#gets information about ends positions given start, direction and order -sub getEnds { - my ($ends,$starts,$strand,$end_order,$tag_length) = @_; - for my $i (0..scalar(@{$starts})-1) { - $ends->[$i] = getEnd($starts->[$i],$strand->[$i],$end_order->[$i],$tag_length); - } -} -sub getEnd { - my ($start,$strand, $end_order,$tag_length) = @_; - return ($strand eq 'F')? $start+$tag_length->{$end_order}-1:$start-$tag_length->{$end_order}+1; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#gets starts and ends Coords when start=leftmost given positions, directions and orders -sub getCoordswithLeftMost { - - my ($starts,$ends,$positions,$strand,$end_order,$tag_length) = @_; - - for my $i (0..scalar(@{$positions})-1) { - - if($strand->[$i] eq 'F'){ - $starts->[$i]=$positions->[$i]; - $ends->[$i]=$positions->[$i]+$tag_length->{$end_order->[$i]}-1; - }else{ - $starts->[$i]=$positions->[$i]-$tag_length->{$end_order->[$i]}+1; - $ends->[$i]=$positions->[$i]; - } - } -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub addInsertionInfo { #add field with INS,DEL,NA and distance between clusters and performs filtering - - my ($chr,$chrID,$nb_pairs_threshold,$order_filtering,$indel_sigma_threshold,$dup_sigma_threshold,$singleton_sigma_threshold,$mu,$sigma,$mate_sense,$tag_length,$links_file,$flinks_file)=@_; - - my @sfile=split(/\./,$links_file); - my $fchr=$sfile[$#sfile-2]; - - - my $diff_sense_ends=(($mate_sense eq "FR") || ($mate_sense eq "RF"))? 1:0; - - my $record=0; - my $nb_links=0; - my $warn=10000; - - print LOG "\# Filtering out normal pairs using insert size...\n"; - print LOG "-- mu length=$mu, sigma length=$sigma, indel sigma threshold=$indel_sigma_threshold, dup sigma threshold=$dup_sigma_threshold\n"; - print LOG "-- using ".($mu-$indel_sigma_threshold*$sigma)."-". - ($mu+$indel_sigma_threshold*$sigma)." as normal range of insert size for indels\n"; - print LOG "-- using ".($mu-$dup_sigma_threshold*$sigma)."-". - ($mu+$dup_sigma_threshold*$sigma)." as normal range of insert size for duplications\n"; - print LOG "-- using ".($mu-$singleton_sigma_threshold*$sigma)." as the upper limit of insert size for singletons\n" if($mate_sense eq "RF"); - - my $fh = new FileHandle; - my $fh2 = new FileHandle; - - $fh->open("<$links_file") or die "$0: can't open $links_file :$!\n"; - $fh2->open(">$flinks_file") or die "$0: can't write in the output: $flinks_file :$!\n"; - - while(<$fh>){ - - $record++; - my @t = split; - my ($chr1,$chr2,$mates_list)=@t[0,3,7]; - - if($chrID->{$chr1} ne $chrID->{$chr2}) { #if inter-chromosomal link here (because sv_type=all), - $nb_links++; - - $t[16]="INV_TRANSLOC" if($t[16] eq "REVERSE_SENSE"); - $t[16]="TRANSLOC" if($t[16] eq "NORMAL_SENSE"); - - $t[16].= "\t"; - $t[19].= "\t"; - - print $fh2 join("\t",@t)."\n"; - - if($record>=$warn){ - print LOG "-- $fchr : $warn links processed - $nb_links links kept\n"; - $warn+=10000; - } - next; - } - - my $ifRenv = $t[16]; - my $ifBalanced = "UNBAL"; - $ifBalanced = $t[18] if ($order_filtering); - - my $numberOfPairs = $t[6]; - my @positions1 = deleteBadOrderSensePairs(split (/,/,$t[14])); - my @positions2 = deleteBadOrderSensePairs(split (/,/,$t[15])); - - if ($ifBalanced eq "BAL") { - - if ($ifRenv eq "INV_TRANSLOC") { - $ifRenv = "INV_FRAGMT"; #for intrachromosomal inverted translocation is the same as inverted fragment - } - if ($ifRenv eq "NORMAL_SENSE") { - $ifRenv = "TRANSLOC"; - } - if ($ifRenv eq "REVERSE_SENSE") { - $ifRenv = "INV_FRAGMT"; #for intrachromosomal inverted translocation is the same as inverted fragment - } - $t[19].= "\t"; - - my $meanDistance = 0; - - for my $i (0..$numberOfPairs-1) { - $meanDistance += $positions2[$i]-$positions1[$i]; - } - $meanDistance /= $numberOfPairs; - - $t[16] = $ifRenv."\t".$meanDistance; - #dont touch the annotation. It should be already OK. - - } else { - #only for unbalanced - - my $ifoverlap=overlap($t[1],$t[2],$t[4],$t[5]); - - my $ends_sense_class = (deleteBadOrderSensePairs(split (/,/,$t[8])))[0]. - (deleteBadOrderSensePairs(split (/,/,$t[9])))[0]; - my $ends_order_class = (deleteBadOrderSensePairs(split (/,/,$t[10])))[0]. - (deleteBadOrderSensePairs(split (/,/,$t[11])))[0]; - - my $indel_type = $ifRenv; - - my $meanDistance = "N/A"; - - ($meanDistance, $indel_type) = checkIndel ($numberOfPairs, #identify insertion type for rearrangments without inversion, calculates distance between cluster - \@positions1, #assign N/A to $indel_type if unknown - \@positions2, - $ifRenv, - $ifoverlap, - $indel_sigma_threshold, - $dup_sigma_threshold, - $singleton_sigma_threshold, - $mu, - $sigma, - $ifBalanced, - $ends_sense_class, - $ends_order_class, - $mate_sense, - $diff_sense_ends, - ); - - #filtering of pairs with distance inconsistant with the SV - if ($ifRenv ne "REVERSE_SENSE") { - my $maxCoord1 =$chr->{$chrID->{$chr1}}->{length}; - my $maxCoord2 =$chr->{$chrID->{$chr2}}->{length}; - $meanDistance = recalc_t_usingInsertSizeInfo(\@t,$mu,$sigma,$meanDistance,$tag_length,$diff_sense_ends,$mate_sense, - $maxCoord1,$maxCoord2,$ends_sense_class,$ends_order_class,$nb_pairs_threshold,$order_filtering); - next if ($t[6] < $nb_pairs_threshold); - }else{ - $t[19].= "\t"; - } - $t[16] = $indel_type."\t".$meanDistance; - } - - $nb_links++; - - print $fh2 join("\t",@t)."\n"; - if($record>=$warn){ - print LOG "-- $fchr : $warn links processed - $nb_links links kept\n"; - $warn+=10000; - } - } - $fh->close; - $fh2->close; - - print LOG "-- $fchr : Total : $record links analysed - $nb_links links kept\n"; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub checkIndel { - - my ($numberOfPairs, $positions1, $positions2, $ifRenv, $ifoverlap, $indel_sigma_threshold, $dup_sigma_threshold, $singleton_sigma_threshold, - $mu, $sigma, $ifBalanced,$ends_sense_class,$ends_order_class,$mate_sense,$diff_sense_ends) = @_; - - my $meanDistance = 0; - - for my $i (0..$numberOfPairs-1) { - $meanDistance += $positions2->[$i]-$positions1->[$i]; - } - $meanDistance /= $numberOfPairs; - - return ($meanDistance,"INV_DUPLI") if (($ifRenv eq "REVERSE_SENSE") && ($meanDistance<$mu+$dup_sigma_threshold*$sigma) ); - - return ($meanDistance,"INVERSION") if ($ifRenv eq "REVERSE_SENSE"); - - if($diff_sense_ends){ - return ($meanDistance, "LARGE_DUPLI") if ($ends_sense_class ne $mate_sense) && ($meanDistance>$mu+$dup_sigma_threshold*$sigma) ; - return ($meanDistance, "SINGLETON") if (($meanDistance<$mu-$singleton_sigma_threshold*$sigma) && $mate_sense eq "RF" && ($ends_sense_class eq inverseSense($mate_sense))); - }else{ - return ($meanDistance, "LARGE_DUPLI") if (($ends_sense_class eq $mate_sense) && ($ends_order_class eq "12") || ($ends_sense_class eq inverseSense($mate_sense)) && ($ends_order_class eq "21")) && - ($meanDistance>$mu+$dup_sigma_threshold*$sigma) ; - } - - return ($meanDistance, "SMALL_DUPLI") if (($meanDistance<$mu-$dup_sigma_threshold*$sigma) && $ifoverlap); - - return ($meanDistance, "DUPLICATION") if ($diff_sense_ends && ($ends_sense_class ne $mate_sense) && ($meanDistance<$mu-$dup_sigma_threshold*$sigma) ) ; - - return ($meanDistance, "INSERTION") if ($meanDistance<$mu -$indel_sigma_threshold*$sigma); - return ($meanDistance, "DELETION") if ($meanDistance>$mu+$indel_sigma_threshold*$sigma); - - return ($meanDistance, "UNDEFINED"); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#sub reacalulate @t so that get rid of unconsistent pairs (unconsistent insert size ) -sub recalc_t_usingInsertSizeInfo { - my($t,$mu,$sigma,$meanDistance,$tag_length,$diff_sense_ends,$mate_sense,$maxCoord1,$maxCoord2,$ends_sense_class,$ends_order_class,$nb_pairs_threshold,$order_filtering) = @_; - - my @badPairs; - - my @positions1 = getAllEntries($t->[14]); - my @positions2 = getAllEntries($t->[15]); - - if ($meanDistance < $mu) { - for my $i (0..scalar(@positions1)-1) { - if (substr($positions2[$i],-1,1) ne '$' && substr($positions2[$i],-1,1) ne '*' && $positions2[$i]-$positions1[$i]>=$mu) { - push(@badPairs,$i); - } - } - } else { - for my $i (0..scalar(@positions1)-1) { - if (substr($positions2[$i],-1,1) ne '$' && substr($positions2[$i],-1,1) ne '*' && $positions2[$i]-$positions1[$i]<=$mu) { - push(@badPairs,$i); - } - } - } - - if (scalar (@badPairs)>0) { - #print join("\t",@badPairs).": ".join("\t",@t)."\n"; - #remove these inconsistant links - $t->[6] -= scalar(@badPairs); #numberOfPairs - return if ($t->[6] < $nb_pairs_threshold); - - $t->[7] = mark_values(\@badPairs, $t->[7]); - $t->[8] = mark_values(\@badPairs, $t->[8]); - $t->[9] = mark_values(\@badPairs, $t->[9]); - $t->[10] = mark_values(\@badPairs, $t->[10]); - $t->[11] = mark_values(\@badPairs, $t->[11]); - - $t->[12] = mark_indexes(\@badPairs, $t->[12]); - $t->[13] = mark_indexes(\@badPairs, $t->[13]); - - $t->[14] = mark_values(\@badPairs, $t->[14]); - $t->[15] = mark_values(\@badPairs, $t->[15]); - $t->[19] = recalculate_ratio($t->[6],$t->[19]) if ($order_filtering); #add the second ratio - $t->[17] = recalculate_ratio($t->[6],$t->[17]) unless ($order_filtering); - ($t->[1],$t->[2]) = recalculate_boundaries($t->[14],$t->[8],$t->[10],$tag_length); - ($t->[4],$t->[5]) = recalculate_boundaries($t->[15],$t->[9],$t->[11],$tag_length); - - #recalc breakpoints: - my $quant001 = 3.090232; - my $maxFragmentLength = &floor($quant001 * $sigma + $mu); - $t->[20] = recalc_breakpoints($mate_sense,$maxCoord1,$t->[14],substr($ends_sense_class,0,1),substr($ends_order_class,0,1),$t->[1],$t->[2],$maxFragmentLength,$diff_sense_ends ) if ($order_filtering); - $t->[21] = recalc_breakpoints($mate_sense,$maxCoord2,$t->[15],substr($ends_sense_class,1,1),substr($ends_order_class,1,1),$t->[4],$t->[5],$maxFragmentLength,$diff_sense_ends ) if ($order_filtering); - #recalc total ratio - $t->[22] = $t->[6] / $t->[23] if ($order_filtering); - $t->[18] = $t->[6] / $t->[19] unless ($order_filtering); - - @positions1 = deleteBadOrderSensePairs(split (/,/,$t->[14])); - @positions2 = deleteBadOrderSensePairs(split (/,/,$t->[15])); - - $meanDistance = 0; - - for my $i (0..scalar(@positions1)-1) { - $meanDistance += $positions2[$i]-$positions1[$i]; - } - $meanDistance /= scalar(@positions1); - - } else { - $t->[17] = recalculate_ratio((split(/\//,$t->[17]))[0],$t->[17]) unless ($order_filtering); - $t->[19] = recalculate_ratio((split(/\//,$t->[19]))[0],$t->[19]) if ($order_filtering); - - } #nothing has been filtered - return $meanDistance; -} - -sub recalculate_ratio { - my ($left, $ratio) = @_; - my @elements = split (/\//,$ratio); - $elements[1]= $elements[0]; - $elements[0]=$left; - return $ratio."\t".join("/",@elements); -} - -sub recalc_breakpoints { - my ($mate_sense,$maxCoord,$startString,$strand,$firstEndOrder,$coord_start_chr,$coord_end_chr,$maxFragmentLength,$diff_sense_ends ) = @_; - my $break_pont_chr; - - my $leftLetterOk = substr($mate_sense, 0, 1); #R - my $rightLetterOk = substr($mate_sense, 1, 1); #F - - - my @positions = deleteBadOrderSensePairs(split (/,/,$startString)); - - unless ($diff_sense_ends) { - $break_pont_chr = (($strand eq 'R' && $firstEndOrder == 2) || ($strand eq 'F' && $firstEndOrder == 1))?'('.$coord_end_chr.','.min(($coord_start_chr+$maxFragmentLength),$maxCoord).')':'('.max(($coord_end_chr-$maxFragmentLength),1).','.$coord_start_chr.')'; - } else { - $break_pont_chr = ($strand eq $leftLetterOk)?'('.$coord_end_chr.','.min(($coord_start_chr+$maxFragmentLength),$maxCoord).')':'('.max(($coord_end_chr-$maxFragmentLength),1).','.$coord_start_chr.')'; - } - return $break_pont_chr; -} -sub recalculate_boundaries { - my ($startString,$senseString,$endsOrderString,$tag_length) = @_; - my @positions = deleteBadOrderSensePairs(split (/,/,$startString)); - my @strands = deleteBadOrderSensePairs(split (/,/,$senseString)); - my @ends_orders = deleteBadOrderSensePairs(split (/,/,$endsOrderString)); - my @ends; getEnds(\@ends,\@positions,\@strands,\@ends_orders,$tag_length); - my $coord_start_cluster = min(min(@positions),min(@ends)); - my $coord_end_cluster = max(max(@positions),max(@ends)); - return ($coord_start_cluster,$coord_end_cluster); -} - -sub remove_indexes { - my ($bads, $string) = @_; - my @elements = deleteBadOrderSensePairs(split (/,/,$string)); - for my $i (reverse sort %{$bads}) { - delete $elements[$i]; - } - return "(".join(",",@elements).")"; -} -##add @ to to elements -sub mark_values { - my ($bads, $string) = @_; - my @elements = getAllEntries($string); - for my $i (@{$bads}) { - $elements[$i] .= "@"; - } - return "(".join(",",@elements).")"; -} -##add @ to to indexes -sub mark_indexes { - my ($bads, $string) = @_; - my @elements = getAllEntries($string); - for my $i ((0..scalar(@elements)-1)) { - for my $j (@{$bads}) { - $elements[$i] .= "@" if ($elements[$i] eq ($j+1)); - } - } - - return "(".join(",",@elements).")"; -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub redraw { - - my ($type,$table,$secondTable,$badInFRSense,$ifBalanced,$arr) = @_; - - my $out; - my @first_arr; - if ($ifBalanced eq 'BAL') { - my @second_arr; - my $lastPushed = 1; - if ($type == 1) { - for my $i (0 .. scalar(@{$arr})-1) { - if (exists ($table->{$i})) { - push(@first_arr,$arr->[$i]); - $lastPushed = 1; - }elsif (exists ($secondTable->{$i})) { - push(@second_arr,$arr->[$i]); - $lastPushed = 2; - } elsif ($lastPushed == 1) { - if (exists ($badInFRSense->{$i})) { - push(@first_arr,$arr->[$i]."\$"); - }else { - push(@first_arr,$arr->[$i]."*"); - } - } elsif ($lastPushed == 2) { - if (exists ($badInFRSense->{$i})) { - push(@second_arr,$arr->[$i]."\$"); - }else { - push(@second_arr,$arr->[$i]."*"); - } - } else {print "Error!";exit;} - } - } else { - for my $i (@{$arr}) { - if (exists ($table->{$i-1})) { - push(@first_arr,$i); - $lastPushed = 1; - }elsif (exists ($secondTable->{$i-1})) { - push(@second_arr,$i); - $lastPushed = 2; - } elsif ($lastPushed == 1) { - if (exists ($badInFRSense->{$i-1})) { - push(@first_arr,$i."\$"); - }else { - push(@first_arr,$i."*"); - } - } elsif ($lastPushed == 2) { - if (exists ($badInFRSense->{$i-1})) { - push(@second_arr,$i."\$"); - }else { - push(@second_arr,$i."*"); - } - } else {print "Error!";exit;} - } - } - $out = '('.join(",",@first_arr).'),('.join(",",@second_arr).')'; - } - else { - if ($type == 1) { - for my $i (0 .. scalar(@{$arr})-1) { - if (exists ($table->{$i})) { - push(@first_arr,$arr->[$i]); - } else { - if (exists ($badInFRSense->{$i})) { - push(@first_arr,$arr->[$i]."\$"); - }else { - push(@first_arr,$arr->[$i]."*"); - } - } - } - } else { - for my $i (@{$arr}) { - if (exists ($table->{$i-1})) { - push(@first_arr,$i); - } else { - if (exists ($badInFRSense->{$i-1})) { - push(@first_arr,$i."\$"); - }else { - push(@first_arr,$i."*"); - } - } - } - } - $out = '('.join(",",@first_arr).')'; - } - return $out; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub check { - - my $table = $_[0]; - my $bad = 'OK'; - my $max = 0; - for my $i (sort {$a<=>$b} keys %{$table}) { - unless ($table->{$i}->{nonAdeq} == 0) { - if ($max<$table->{$i}->{nonAdeq}) { - $max=$table->{$i}->{nonAdeq}; - $bad = $i; - } - } - } - return $bad; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub reversed { - - my ($i,$j,$ifRenv,$positions) = @_; - if (($ifRenv eq 'REVERSE_SENSE' && $positions->[$i]<$positions->[$j]) || ($ifRenv ne 'REVERSE_SENSE' && $positions->[$i]>$positions->[$j])){ - return 1; - } - return 0; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub remove { - - my ($bad,$table) = @_; - for my $i (sort {$a<=>$b} keys %{$table}) { - if ($bad == $i) { - delete($table->{$i});; - } else { - if (exists($table->{$i}->{$bad})) { - delete($table->{$i}->{$bad}); - $table->{$i}->{nonAdeq}--; - } - } - } -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub findBadInRFSenseSOLiDSolexa { #choose maximum: FFFFs or RRRRs - - my ($strand,$ends_order,$mate_sense,@keysLeft) = @_; - - my $leftLetterOk = substr($mate_sense, 0, 1); #R - my $rightLetterOk = substr($mate_sense, 1, 1); #F - - my (@standardArray); - if ($leftLetterOk eq $rightLetterOk) { #SOLID mate-pairs - $leftLetterOk = 'R'; - $rightLetterOk = 'F'; - @standardArray = translateSolidToRF($strand,$ends_order); - } else { - @standardArray = @{$strand}; - } - - my $ifR = 0; - my @Rs; - - for my $i (@keysLeft) { - if ($standardArray[$i] eq $leftLetterOk) { - $ifR++; - push(@Rs,$i); - } - } - - - my $ifF = 0; - my @Fs; - - for my $i (@keysLeft) { - if ($standardArray[$i] eq $rightLetterOk) { - $ifF++; - push(@Fs,$i); - } - } - - if($ifR>=$ifF) { - return @Fs; - } - return @Rs; -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub findBadInFRSenseSOLiDSolexa { #should work both for SOLiD and Solexa - - my ($strand1,$strand2,$ends_order1,$ends_order2,$order1,$order2) = ($_[0],$_[1],$_[2],$_[3],$_[4],$_[5]); - my $mate_sense = $_[6]; - - my $leftLetterOk = substr($mate_sense, 0, 1); #R - my $rightLetterOk = substr($mate_sense, 1, 1); #F - - my (@standardArray1,@standardArray2); - - if ($leftLetterOk eq $rightLetterOk) { #SOLID mate-pairs - $leftLetterOk = 'R'; - $rightLetterOk = 'F'; - @standardArray1 = translateSolidToRF($strand1,$ends_order1); - my @arr = getOrderedStrands($strand2,$order2); - my @ends2 = getOrderedStrands($ends_order2,$order2); - @standardArray2 = translateSolidToRF(\@arr,\@ends2); - - } else { - @standardArray1 = @{$strand1}; - @standardArray2 = getOrderedStrands($strand2,$order2); - } - - #we will try 4 possibilities, 2 for each end of the link: RFRR-FFF->RFFFF , RFRR-FFF->RRRFFF - - #for the first end: - - my @array = @standardArray1; - my %badInFRSense1; - for my $i (1..scalar (@array)-1){ # FRFRFFFF -> FFFFFF and RRFRFRFFFF -> RRFFFFFF - if ($array[$i-1] eq $rightLetterOk && $array[$i] eq $leftLetterOk) { - $badInFRSense1{$i}=1; - $array[$i] = $rightLetterOk; - } - } - my $numberRRRFFF_or_FFF_1 = scalar(@array)-scalar(keys %badInFRSense1); - @array = @standardArray1; - my %badInFRSense0; - for my $i (reverse(1..scalar (@array)-1)){ # FRFRFFFFRR -> FFFFFFRR - if ($array[$i-1] eq $rightLetterOk && $array[$i] eq $leftLetterOk) { - $badInFRSense0{$i-1}=1; - $array[$i-1] = $leftLetterOk; - - } - } - my $numberRRF1 = scalar(@array)-scalar(keys %badInFRSense0); - - #for the second end: - @array = @standardArray2; - - my %badInFRSense3; - for my $i (1..scalar(@array)-1){ - if ($array[$i-1] eq $rightLetterOk && $array[$i] eq $leftLetterOk) { - $badInFRSense3{$order2->[$i]}=1; - $array[$i] = $rightLetterOk; - } - } - my $numberRRRFFF_or_FFF_2 = scalar(@array)-scalar(keys %badInFRSense3); - - @array = @standardArray2; - my %badInFRSense5; - for my $i (reverse(1..scalar (@array)-1)){ # FRFRFFFF -> FFFFFF - if ($array[$i-1] eq $rightLetterOk && $array[$i] eq $leftLetterOk) { - $badInFRSense5{$i-1}=1; - $array[$i-1] = $leftLetterOk; - } - } - my $numberRRF2 = scalar(@array)-scalar(keys %badInFRSense5); - - if ($numberRRF1>=$numberRRRFFF_or_FFF_1 && $numberRRF1 >= $numberRRRFFF_or_FFF_2 && $numberRRF1 >=$numberRRF2) { - return (1,%badInFRSense0); - } - - if ($numberRRRFFF_or_FFF_1 >=$numberRRF1 && $numberRRRFFF_or_FFF_1 >= $numberRRRFFF_or_FFF_2 && $numberRRRFFF_or_FFF_1 >= $numberRRF2) { - return (1,%badInFRSense1); - } - - if ($numberRRRFFF_or_FFF_2 >= $numberRRF1 && $numberRRRFFF_or_FFF_2 >= $numberRRRFFF_or_FFF_1 && $numberRRRFFF_or_FFF_2 >=$numberRRF2) { - return (2,%badInFRSense3); - } - - if ($numberRRF2 >= $numberRRF1 && $numberRRF2 >= $numberRRRFFF_or_FFF_1 && $numberRRF2 >= $numberRRRFFF_or_FFF_2 ) { - return (2,%badInFRSense5); - } - - #should not get here: - print STDERR "Error in findBadInFRSenseSOLiDSolexa()!\n"; - return (1,%badInFRSense1); -} - -sub getOrderedStrands { - my ($strand,$order) = ($_[0],$_[1]); - my @arr; - for my $i (0..scalar(@{$strand})-1) { - push(@arr,$strand->[$order->[$i]-1]); - } - return @arr; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub checkClusters { - - my ($ifRenv,$coord_start_chr1_cluster1,$coord_start_chr1_cluster2,$coord_start_chr2_cluster1,$coord_start_chr2_cluster2) = @_; - if ($ifRenv eq 'REVERSE_SENSE') { - if ($coord_start_chr1_cluster1 <= $coord_start_chr1_cluster2) { - return ($coord_start_chr2_cluster1 <= $coord_start_chr2_cluster2)?1:0; - } - return ($coord_start_chr2_cluster1 >= $coord_start_chr2_cluster2)?1:0; - } - #if NORM - if ($coord_start_chr1_cluster1 <= $coord_start_chr1_cluster2) { - return ($coord_start_chr2_cluster1 >= $coord_start_chr2_cluster2)?1:0; - } - return ($coord_start_chr2_cluster1 <= $coord_start_chr2_cluster2)?1:0; -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub translateSolidToRF { - my ($strandArr,$ends_orderArr)=@_; - my @array; - for my $i (0..scalar(@{$strandArr})-1) { - if ($ends_orderArr->[$i]==1 && $strandArr->[$i] eq 'F') { - push(@array,'F'); - } - if ($ends_orderArr->[$i]==2 && $strandArr->[$i] eq 'F') { - push(@array,'R'); - } - if ($ends_orderArr->[$i]==1 && $strandArr->[$i] eq 'R') { - push(@array,'R'); - } - if ($ends_orderArr->[$i]==2 && $strandArr->[$i] eq 'R') { - push(@array,'F'); - } - } - return @array; -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#convert the links file to the circos format -sub links2segdup{ - - my($id,$color_code,$links_file,$segdup_file)=@_; - - print LOG "# Converting to the circos format...\n"; - - tie (my %hcolor,'Tie::IxHash'); #color-code hash table - foreach my $col (keys %{$color_code}){ - my ($min_links,$max_links)=split(",",$color_code->{$col}); - $hcolor{$col}=[$min_links,$max_links]; - } - - open LINKS, "<$links_file" or die "$0: can't open $links_file :$!\n"; - open SEGDUP, ">$segdup_file" or die "$0: can't write in the output: $segdup_file :$!\n"; - - my $index=1; - while(<LINKS>){ - - my ($chr1,$start1,$end1,$chr2,$start2,$end2,$count)=(split)[0,1,2,3,4,5,6]; - - my $color=getColor($count,\%hcolor,"circos"); #get the color-code according the number of links - - print SEGDUP "$index\t$id$chr1\t$start1\t$end1\tcolor=$color\n". #circos output - "$index\t$id$chr2\t$start2\t$end2\tcolor=$color\n"; - $index++; - } - - close LINKS; - close SEGDUP; - print LOG "-- output created: $segdup_file\n"; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#convert the links file to the bedPE format for BEDTools usage -sub links2bedPElinksfile{ - - my ($sample,$links_file,$bedpe_file)=@_; - - open LINKS, "<$links_file" or die "$0: can't open $links_file :$!\n"; - open BEDPE, ">$bedpe_file" or die "$0: can't write in the output: $bedpe_file :$!\n"; - - my $nb_links=1; - - while(<LINKS>){ - - chomp; - my @t=split("\t",$_); - my ($chr1,$start1,$end1,$chr2,$start2,$end2)=splice(@t,0,6); - my $type=($chr1 eq $chr2)? "INTRA":"INTER"; - $type.="_".$t[10]; - - $start1--; $start2--; - - print BEDPE "$chr1\t$start1\t$end1\t$chr2\t$start2\t$end2". - "\t$sample"."_link$nb_links\t$type\t.\t.". - "\t".join("|",@t)."\n"; - - $nb_links++; - } - - close LINKS; - close BEDPE; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub bedPElinks2linksfile{ - - my ($bedpe_file,$links_file)=@_; - - open BEDPE, "<$bedpe_file" or die "$0: can't open: $bedpe_file :$!\n"; - open LINKS, ">$links_file" or die "$0: can't write in the output $links_file :$!\n"; - - while(<BEDPE>){ - - chomp; - my $sample=(split("_",(split("\t",$_))[6]))[0]; - my @t1=(split("\t",$_))[0,1,2,3,4,5]; - my @t2=split(/\|/,(split("\t",$_))[10]); - push(@t2,$sample); - - print LINKS join("\t",@t1)."\t".join("\t",@t2)."\n"; - - } - close BEDPE; - close LINKS; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#convert the links file to the bed format -sub links2bedfile{ - - my ($tag_length,$color_code,$links_file,$bed_file)=@_; - - print LOG "# Converting to the bed format...\n"; - - my $compare=1; - if($links_file!~/compared$/){ - $compare=0; - $tag_length->{none}->{1}=$tag_length->{1}; - $tag_length->{none}->{2}=$tag_length->{2}; - } - - #color-code hash table - tie (my %hcolor,'Tie::IxHash'); - my %color_order; - my $n=1; - foreach my $col (keys %{$color_code}){ - my ($min_links,$max_links)=split(",",$color_code->{$col}); - $hcolor{$col}=[$min_links,$max_links]; - $color_order{$col}=$n; - $n++; - } - - my %pair; - my %pt; - $n=1; - open LINKS, "<$links_file" or die "$0: can't open $links_file:$!\n"; - - my %str=( "F"=>"+", "R"=>"-" ); - - while(<LINKS>){ - - my @t=split; - my $sample=($compare)? pop(@t):"none"; - - my $chr1=$t[0]; - my $chr2=$t[3]; - $chr1 = "chr".$chr1 unless ($chr1 =~ m/chr/i); - $chr2 = "chr".$chr2 unless ($chr2 =~ m/chr/i); - my $same_chr=($chr1 eq $chr2)? 1:0; - - my $count=$t[6]; - my $color=getColor($count,\%hcolor,"bed"); - - my @pairs=deleteBadOrderSensePairs(split(",",$t[7])); - my @strand1=deleteBadOrderSensePairs(split(",",$t[8])); - my @strand2=deleteBadOrderSensePairs(split(",",$t[9])); - my @ends_order1=deleteBadOrderSensePairs(split(",",$t[10])); - my @ends_order2=deleteBadOrderSensePairs(split(",",$t[11])); - my @position1=deleteBadOrderSensePairs(split(",",$t[14])); - my @position2=deleteBadOrderSensePairs(split(",",$t[15])); - my @start1; my @end1; getCoordswithLeftMost(\@start1,\@end1,\@position1,\@strand1,\@ends_order1,$tag_length->{$sample}); - my @start2; my @end2; getCoordswithLeftMost(\@start2,\@end2,\@position2,\@strand2,\@ends_order2,$tag_length->{$sample}); - - - for my $p (0..$#pairs){ - - if (!exists $pair{$pairs[$p]}){ - - if($same_chr){ - - $pair{$pairs[$p]}->{0}=[ $chr1, $start1[$p]-1, $end2[$p], $pairs[$p], 0, $str{$strand1[$p]}, - $start1[$p]-1, $end2[$p], $color, - 2, $tag_length->{$sample}->{$ends_order1[$p]}.",".$tag_length->{$sample}->{$ends_order2[$p]}, "0,".($start2[$p]-$start1[$p]) ]; - $pt{$n}=$pair{$pairs[$p]}->{0}; - $n++; - - }else{ - - $pair{$pairs[$p]}->{1}=[ $chr1, $start1[$p]-1, $end1[$p] , $pairs[$p]."/1", 0, $str{$strand1[$p]}, - $start1[$p]-1, $end1[$p], $color, - 1, $tag_length->{$sample}->{$ends_order1[$p]}, 0]; - $pt{$n}=$pair{$pairs[$p]}->{1}; - $n++; - - - $pair{$pairs[$p]}->{2}=[ $chr2, $start2[$p]-1, $end2[$p], $pairs[$p]."/2", 0, $str{$strand2[$p]}, - $start2[$p]-1, $end2[$p], $color, - 1, $tag_length->{$sample}->{$ends_order2[$p]}, 0]; - $pt{$n}=$pair{$pairs[$p]}->{2}; - $n++; - } - }else{ - - if($same_chr){ - ${$pair{$pairs[$p]}->{0}}[8]=$color if($color_order{$color}>$color_order{${$pair{$pairs[$p]}->{0}}[8]}); - }else{ - ${$pair{$pairs[$p]}->{1}}[8]=$color if($color_order{$color}>$color_order{${$pair{$pairs[$p]}->{1}}[8]}); - ${$pair{$pairs[$p]}->{2}}[8]=$color if($color_order{$color}>$color_order{${$pair{$pairs[$p]}->{2}}[8]}); - } - } - } - } - close LINKS; - - my $nb_pairs=$n-1; - - open BED, ">$bed_file" or die "$0: can't write in the output: $bed_file :$!\n"; - print BED "track name=\"$bed_file\" description=\"mate pairs involved in links\" ". - "visibility=2 itemRgb=\"On\"\n"; - - for my $i (1..$nb_pairs){ - print BED join("\t",@{$pt{$i}})."\n"; - } - - close BED; - - print LOG "-- output created: $bed_file\n"; - - undef %pair; - undef %pt; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub deleteBadOrderSensePairs{ - - my (@tab)=@_; - my @tab2; - - foreach my $v (@tab){ - - $v=~s/[\(\)]//g; - push(@tab2,$v) if($v!~/[\$\*\@]$/); - } - return @tab2; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getAllEntries{ - my (@tab)=split (/,/,$_[0]); - my @tab2; - - foreach my $v (@tab){ - - $v=~s/[\(\)]//g; - push(@tab2,$v); - } - return @tab2; -}#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getAllEntriesWOspecialChar{ - my (@tab)=split (/,/,$_[0]); - my @tab2; - - foreach my $v (@tab){ - - $v=~s/[\(\)\$\*\@]//g; - push(@tab2,$v); - } - return @tab2; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub links2SVfile{ - - my($links_file,$sv_file)=@_; - - print LOG "# Converting to the sv output table...\n"; - open LINKS, "<$links_file" or die "$0: can't open $links_file:$!\n"; - open SV, ">$sv_file" or die "$0: can't write in the output: $sv_file :$!\n"; - - my @header=qw(chr_type SV_type BAL_type chromosome1 start1-end1 average_dist - chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering - final_score breakpoint1_start1-end1 breakpoint2_start2-end2); - - my $nb_links=0; - - while (<LINKS>){ - - my @t=split; - my @sv=(); - my $sv_type="-"; - my $strand_ratio="-"; - my $eq_ratio="-"; - my $eq_type="-"; - my $insert_ratio="-"; - my $link="-"; - my ($bk1, $bk2)=("-","-"); - my $score="-"; - - my ($chr1,$start1,$end1)=($t[0],$t[1],$t[2]); - my ($chr2,$start2,$end2)=($t[3],$t[4],$t[5]); - my $nb_pairs=$t[6]; - $chr1 = "chr".$chr1 unless ($chr1 =~ m/chr/i); - $chr2 = "chr".$chr2 unless ($chr2 =~ m/chr/i); - my $chr_type=($chr1 eq $chr2)? "INTRA":"INTER"; - - #if strand filtering - if (defined $t[16]){ - #if inter-chr link - $sv_type=$t[16]; - if(defined $t[17] && $t[17]=~/^(\d+)\/(\d+)$/){ - $strand_ratio=floor($1/$2*100)."%"; - $score=$t[18]; - } - if(defined $t[18] && $t[18]=~/^(\d+)\/(\d+)$/){ - #if intra-chr link with insert size filtering - $strand_ratio=floor($1/$2*100)."%"; - $link=floor($t[17]); - if($sv_type!~/^INV/){ - $insert_ratio=floor($1/$2*100)."%" if($t[19]=~/^(\d+)\/(\d+)$/); - $score=$t[20]; - }else{ - $score=$t[19]; - } - } - } - - if(defined $t[18] && ($t[18] eq "UNBAL" || $t[18] eq "BAL")){ - - #if strand and order filtering only and/or interchr link - $eq_type=$t[18]; - $eq_ratio=floor($1/$2*100)."%" if($t[19]=~/^(\d+)\/(\d+)$/); - ($bk1, $bk2)=($t[20],$t[21]); - foreach my $bk ($bk1, $bk2){$bk=~s/\),\(/ /g; $bk=~s/(\(|\))//g; $bk=~s/,/-/g;} - $score=$t[22]; - - }elsif(defined $t[19] && ($t[19] eq "UNBAL" || $t[19] eq "BAL")){ - - #if all three filtering - $link=floor($t[17]); - $eq_type=$t[19]; - $eq_ratio=floor($1/$2*100)."%" if($t[20]=~/^(\d+)\/(\d+)$/); - - if(defined $t[21] && $t[21]=~/^(\d+)\/(\d+)$/){ - $insert_ratio=floor($1/$2*100)."%"; - ($bk1, $bk2)=($t[22],$t[23]); - $score=$t[24]; - - }else{ - ($bk1, $bk2)=($t[21],$t[22]); - $score=$t[23]; - } - foreach my $bk ($bk1, $bk2){$bk=~s/\),\(/ /g; $bk=~s/(\(|\))//g; $bk=~s/,/-/g;} - - } - - - push(@sv, $chr_type, $sv_type,$eq_type); - push(@sv,"$chr1\t$start1-$end1"); - push(@sv, $link); - push(@sv,"$chr2\t$start2-$end2", - $nb_pairs,$strand_ratio,$eq_ratio,$insert_ratio, decimal($score,4), $bk1, $bk2); - - - print SV join("\t",@sv)."\n"; - } - - close LINKS; - close SV; - - system "sort -k 9,9nr -k 13,13nr $sv_file > $sv_file.sorted"; - - open SV, "<".$sv_file.".sorted" or die "$0: can't open in the output: $sv_file".".sorted :$!\n"; - my @links=<SV>; - close SV; - - open SV, ">$sv_file" or die "$0: can't write in the output: $sv_file :$!\n"; - - print SV join("\t",@header)."\n"; - print SV @links; - close SV; - - unlink($sv_file.".sorted"); - - print LOG "-- output created: $sv_file\n"; - -} -#------------------------------------------------------------------------------# -sub densityCalculation{ - - my ($chr,$chrID,$file,$tag_length,$window_dist,$step,$mates_file,$mates_file_ref,$density_file,$input_format)=@_; - - my @sfile=split(/\./,$$mates_file[$file]); - my $fchr=$sfile[$#sfile]; - - my $fh = new FileHandle; - - my %density; - my %density_ref; - my @ratio; - my ($cov,$cov_ref); - - #FREQUENCY CALCULATION PROCEDURE - print LOG "# $fchr : Frequency calculation procedure...\n"; - &FreqCalculation(\%density,$chr,$chrID,$tag_length,$window_dist,$step,$$mates_file[$file],$input_format); - &FreqCalculation(\%density_ref,$chr,$chrID,$tag_length,$window_dist,$step,$$mates_file_ref[$file],$input_format); - - #MAKING RATIO AND OUTPUT - print LOG "\# Ratio calculation procedure...\n"; - $density_file=~s/\/mates\//\/density\//; - $fh->open(">".$density_file) or die "$0: can't write in the output ".$density_file." :$!\n"; - - foreach my $k (1..$chr->{nb_chrs}){ - foreach my $frag (1..$chr->{$k}->{nb_frag}){ - - @ratio= ($chr->{$k}->{name}, - (${$chr->{$k}->{$frag}}[0]+1), - (${$chr->{$k}->{$frag}}[1]+1)); - - $cov=(exists $density{$k}{$frag}->{count})? $density{$k}{$frag}->{count}:0; - $cov_ref=(exists $density_ref{$k}{$frag}->{count})? $density_ref{$k}{$frag}->{count}:0; - - push(@ratio,$cov,$cov_ref); - push(@ratio,log($cov/$cov_ref)) if($cov && $cov_ref); - push(@ratio,-log($cov_ref+1)) if(!$cov && $cov_ref); - push(@ratio,log($cov+1)) if($cov && !$cov_ref); - next if(!$cov && !$cov_ref); - - print $fh join("\t",@ratio)."\n"; - } - } - - $fh->close; - print LOG "-- output created: $density_file\n"; - - undef %density; - undef %density_ref; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub FreqCalculation{ - - my ($density,$chr,$chrID,$tag_length,$window_dist,$step,$mates_file,$input_format) = @_; - - my @sfile=split(/\./,$mates_file); - my $fchr=$sfile[$#sfile]; - my $fh = new FileHandle; - - my $nb_windows=0; - my $warn=100000; - my $record=0; - my %pair; - - my ($sumX,$sumX2) = (0,0); - - print LOG "\# Frequency calculation for $mates_file...\n"; - - if ($mates_file =~ /.gz$/) { - $fh->open("gunzip -c $mates_file |") or die "$0: can't open ".$mates_file.":$!\n"; - }elsif($mates_file =~ /.bam$/){ - o$fh->open("$SAMTOOLS_BIN_DIR/samtools view $mates_file |") or die "$0: can't open ".$mates_file.":$!\n";#GALAXY - }else{ - $fh->open("<".$mates_file) or die "$0: can't open ".$mates_file.":$!\n"; - } - - while(<$fh>){ - - my @t=split; - my $mate=$t[0]; - - my ($chr_read1, $chr_read2, $firstbase_read1, $firstbase_read2, $end_order_read1, $end_order_read2,); - - next if(exists $pair{$mate}); - - next if (!readMateFile(\$chr_read1, \$chr_read2, \$firstbase_read1, \$firstbase_read2,\$end_order_read1, \$end_order_read2, \@t, $input_format,$tag_length)); - - next unless (exists $chrID->{$chr_read1} || exists $chrID->{$chr_read2}); - ($chr_read1, $chr_read2)= ($chrID->{$chr_read1},$chrID->{$chr_read2}); - - $pair{$mate}=undef; - $record++; - - my ($coord_start_read1,$coord_end_read1, $coord_start_read2,$coord_end_read2); - - recupCoords($firstbase_read1,\$coord_start_read1,\$coord_end_read1,$tag_length->{$end_order_read1},$input_format); - recupCoords($firstbase_read2,\$coord_start_read2,\$coord_end_read2,$tag_length->{$end_order_read2},$input_format); - - my $length = abs($coord_start_read1-$coord_start_read2); - $sumX += $length; #add to sum and sum^2 for mean and variance calculation - $sumX2 += $length*$length; - - for(my $i=1;$i<=$chr->{$chr_read1}->{'nb_frag'};$i++){ - - if (abs ($coord_start_read1-${$chr->{$chr_read1}->{$i}}[0]) <= $window_dist){ - - &addToDensity($density,$chr_read1,$i,\$nb_windows) - if(overlap($coord_start_read1,$coord_end_read2,${$chr->{$chr_read1}->{$i}}[0],${$chr->{$chr_read1}->{$i}}[1])); - - }else{ - - $i=getNextFrag($coord_start_read1,$i,${$chr->{$chr_read1}->{$i}}[0],$chr->{$chr_read1}->{nb_frag},$window_dist,$step); - } - } - - if($record>=$warn){ - print LOG "-- $warn mate-pairs analysed - $nb_windows points created\n"; - $warn+=100000; - } - } - $fh->close; - - print LOG "-- $fchr : Total : $record mate-pairs analysed - $nb_windows points created\n"; - - if($record>0){ - - my $mu = $sumX/$record; - my $sigma = sqrt($sumX2/$record - $mu*$mu); - print LOG "-- $fchr : mu length = $mu, sigma length = $sigma\n"; - } - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub ratio2segdup{ - - my($id,$density_file,$segdup_file)=@_; - - print LOG "# Converting to circos format...\n"; - - open RATIO, "<$density_file" or die "$0: can't open $density_file :$!\n"; - open SEGDUP, ">$segdup_file" or die "$0: can't write in the output: $segdup_file :$!\n"; - - while(<RATIO>){ - chomp; - my ($chr1,$start1,$end1,$ratio)=(split /\t/)[0,1,2,5]; - print SEGDUP "$id$chr1\t$start1\t$end1\t$ratio\n"; - } - - close RATIO; - close SEGDUP; - print LOG "-- output created: $segdup_file\n"; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub ratio2bedfile{ - - my($density_file,$bed_file)=@_; - - print LOG "# Converting to bedGraph format...\n"; - - open RATIO, "<$density_file" or die "$0: can't open $density_file :$!\n"; - open BED, ">$bed_file" or die "$0: can't write in the output: $bed_file :$!\n"; - print BED "track type=bedGraph name=\"$bed_file\" description=\"log ratios for cnv detection\" ". - "visibility=2 color=255,0,0 alwaysZero=\"On\"\n"; - - while(<RATIO>){ - chomp; - my ($chr1,$start1,$end1,$ratio)=(split /\t/)[0,1,2,5]; - $chr1 = "chr".$chr1 unless ($chr1 =~ m/chr/); - print BED "$chr1\t".($start1-1)."\t$end1\t$ratio\n"; - } - - close RATIO; - close BED; - print LOG "-- output created: $bed_file\n"; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub inverseSense{ - - my $mate_sense=$_[0]; - my %reverse=( 'F' => 'R' , 'R' => 'F' , - 'FF' => 'RR', 'RR' => 'FF', - 'FR' => 'RF', 'RF' => 'FR'); - return $reverse{$mate_sense}; -} - -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getNextFrag{ - - my ($read_start,$frag_num,$frag_start,$frag_last,$window_dist,$step)=@_; - - my $how_far = $read_start-$frag_start; - my $nb_windows_toskip; - - if($how_far>0){ - - $nb_windows_toskip=($how_far/$step)-($window_dist/$step); - $nb_windows_toskip=~ s/\..*//; - $nb_windows_toskip=0 if($nb_windows_toskip<0); - return ($frag_num + $nb_windows_toskip); - } - return $frag_last; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getColor{ - - my($count,$hcolor,$format)=@_; - for my $col ( keys % { $hcolor} ) { - return $col if($count>=$hcolor->{$col}->[0] && $count<=$hcolor->{$col}->[1]); - } - return "white" if($format eq "circos"); - return "255,255,255" if($format eq "bed"); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub recupCoords{ - - my($c_hit,$cs_hit,$ce_hit,$tag_length,$input_format)=@_; - my $strand = 'F'; - - if ($c_hit=~s/^\-//) { - $strand='R'; - $$cs_hit=$c_hit; - $$ce_hit=$c_hit-($tag_length-1); - }else{ - $$cs_hit=$c_hit; - $$ce_hit=$c_hit+($tag_length-1); - } - return $strand; - -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub overlap { - my($cs_hit,$ce_hit,$cs_region,$ce_region)=@_; - if( (($cs_hit < $cs_region) && ($ce_hit < $cs_region )) || (($cs_hit > $ce_region) && ($ce_hit > $ce_region )) ) { - return 0; - } - return 1; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub makeLink { - - my ($link,$chr1,$frag1,$chr2,$frag2,$mt,$nb)=@_; - - if($chr1>$chr2){ - ($chr1,$chr2)= ($chr2,$chr1); - ($frag1,$frag2)= ($frag2,$frag1); - } - - if($chr1 == $chr2){ - if($frag1>$frag2){ - ($frag1,$frag2)= ($frag2,$frag1); - } - } - - if(!exists $link->{$chr1}->{$chr2}->{$frag1}->{$frag2}){ - $link->{$chr1}->{$chr2}->{$frag1}->{$frag2}=$mt; - $$nb++; - }elsif($link->{$chr1}->{$chr2}->{$frag1}->{$frag2}!~/(^|,)$mt(,|$)/){ - $link->{$chr1}->{$chr2}->{$frag1}->{$frag2}.=",$mt"; - } -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#fonction of adding the read to the density profile -sub addToDensity { - - my ($density,$chr1,$frag1,$nb)=@_; - - if(!exists $density->{$chr1}->{$frag1}->{count}){ - $density->{$chr1}->{$frag1}->{count}=1; - $$nb++; - }else{ - $density->{$chr1}->{$frag1}->{count}++; - } -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub floor { - my $nb = $_[0]; - $nb=~ s/\..*//; - return $nb; -} -#------------------------------------------------------------------------------# -sub decimal{ - - my $num=shift; - my $digs_to_cut=shift; - - $num=sprintf("%.".($digs_to_cut-1)."f", $num) if ($num=~/\d+\.(\d){$digs_to_cut,}/); - - return $num; -} - -#------------------------------------------------------------------------------# -sub max { - - my($max) = shift(@_); - foreach my $temp (@_) { - $max = $temp if $temp > $max; - } - return($max); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub min { - - my($min) = shift(@_); - foreach my $temp (@_) { - $min = $temp if $temp < $min; - } - return($min); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub sortTablebyIndex{ - my ($tab1,$tab2)=@_; - my @tab3; - - foreach my $i (@$tab1){ - $tab3[$i]=$$tab2[$$tab1[$i]]; - } - return @tab3; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub round { - my $number = shift || 0; - my $dec = 10 ** (shift || 0); - return int( $dec * $number + .5 * ($number <=> 0)) / $dec; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub getUniqueTable{ - - my (@tab)=@_; - my (%saw,@out)=(); - undef %saw; - return sort(grep(!$saw{$_}++, @tab)); -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -sub catFiles { - - unlink("$_[1]") if(exists $_[1]); - system qq( cat "$_" >> "$_[1]" ) for @{$_[0]}; -} -#------------------------------------------------------------------------------# -#------------------------------------------------------------------------------# -#check if the configuration file is correct -sub validateconfiguration{ - - my %conf=%{$_[0]}; - my $list_prgs="@ARGV"; - - my @general_params=qw(input_format mates_orientation read1_length read2_length mates_file cmap_file); - my @detection_params=qw(split_mate_file window_size step_length split_mate_file); - my @filtering_params=qw(split_link_file nb_pairs_threshold strand_filtering split_link_file); - my @circos_params=qw(organism_id colorcode); - my @bed_params=qw(colorcode); - my @compare_params=qw(list_samples file_suffix); - - foreach my $dir ($conf{general}{output_dir},$conf{general}{tmp_dir}){ - - unless (defined($dir)) { - $dir = "."; - } - unless (-d $dir){ - mkdir $dir or die; - } - $dir.="/" if($dir!~/\/$/); - } - - unless (defined($conf{general}{num_threads})) { - $conf{general}{num_threads} = 1; - } - $conf{general}{num_threads}=24 if($conf{general}{num_threads}>24); - - if($list_prgs!~/links2compare/){ - - foreach my $p (@general_params){ - die("Error Config : The parameter \"$p\" is not defined\n") if (!defined $conf{general}{$p}); - } - - $conf{general}{input_format}="sam" if($conf{general}{input_format} eq "bam"); - - unless (defined($conf{general}{sv_type})) { - $conf{general}{sv_type} = "all"; - } - - $conf{general}{read_lengths}={ 1=> $conf{general}{read1_length}, 2=> $conf{general}{read2_length}}; - } - - if($list_prgs=~/(linking|cnv)/){ - - foreach my $p (@detection_params){ - die("Error Config : The parameter \"$p\" is not defined\n") if (!defined $conf{detection}{$p}); - } - - die("Error Config : The parameter \"mates_file_ref\" is not defined\n") if($list_prgs=~/cnv/ && !defined $conf{detection}{mates_file_ref}); - - if($conf{detection}{step_length}>$conf{detection}{window_size}){ - die("Error Config : Parameter \"step_length\" should not exceed \"window size\"\n"); - } - - unless (-d $conf{general}{tmp_dir}."/mates"){ - mkdir $conf{general}{tmp_dir}."/mates" or die; - } - - if($list_prgs=~/linking/){ - unless (-d $conf{general}{tmp_dir}."/links"){ - mkdir $conf{general}{tmp_dir}."/links" or die; - } - } - if($list_prgs=~/cnv/){ - unless (-d $conf{general}{tmp_dir}."/density"){ - mkdir $conf{general}{tmp_dir}."/density" or die; - } - } - - } - - if($list_prgs=~/filtering/){ - - foreach my $p (@filtering_params) { - die("Error Config : The filtering parameter \"$p\" is not defined\n") if (!defined $conf{filtering}{$p}); - - } - - if(defined($conf{filtering}{chromosomes})) { - my @chrs=split(",",$conf{filtering}{chromosomes}); - my $exclude=($chrs[0]=~/^\-/)? 1:0; - for my $chrName (@chrs){ - - die("Error Config : The filtering parameter \"chromosomes\" is not valid\n") - if(($chrName!~/^\-/ && $exclude) || ($chrName=~/^\-/ && !$exclude)); - - } - } - - if (( $conf{filtering}{order_filtering} )&& !$conf{filtering}{strand_filtering}) { - die("Error Config : The parameter strand_filtering is set to \"0\" while order_filtering is selected". - "\nChange strand_filtering to \"1\" if you want to use the order filtering\n"); - } - if (( !defined($conf{filtering}{mu_length}) || !defined($conf{filtering}{sigma_length}) )&& $conf{filtering}{order_filtering}) { - die("Error Config : You should set parameters \"mu_length\" and \"sigma_length\" to use order filtering\n"); - } - if (( $conf{filtering}{insert_size_filtering} )&& !$conf{filtering}{strand_filtering}) { - die("Error Config : The parameter strand_filtering is set to \"0\" while insert_size_filtering is selected". - "\nChange strand_filtering to \"1\" if you want to use the insert size filtering\n"); - } - if (( !defined($conf{filtering}{mu_length}) || !defined($conf{filtering}{sigma_length}) )&& $conf{filtering}{insert_size_filtering}) { - die("Error Config : You should set parameters \"mu_length\" and \"sigma_length\" to use discriminate insertions from deletions\n"); - } - - if (!defined($conf{filtering}{indel_sigma_threshold})) { - $conf{filtering}{indel_sigma_threshold} = 2; - } - if (!defined($conf{filtering}{dup_sigma_threshold})) { - $conf{filtering}{dup_sigma_threshold} = 2; - } - if (!defined($conf{filtering}{singleton_sigma_threshold})) { - $conf{filtering}{singleton_sigma_threshold} = 4; - } - - if (!defined($conf{filtering}{nb_pairs_order_threshold})) { - $conf{filtering}{nb_pairs_order_threshold} = 1; - } - - if (!defined($conf{filtering}{final_score_threshold})) { - $conf{filtering}{final_score_threshold} = 0.8; - } - - if ($conf{filtering}{nb_pairs_order_threshold}>$conf{filtering}{nb_pairs_threshold}) { - die("Error Config : Parameter \"nb_pairs_order_threshold\" should not exceed \"nb_pairs_threshold\"\n"); - } - - } - - if($list_prgs=~/2circos$/){ - foreach my $p (@circos_params) { - next if($list_prgs=~/^ratio/ && $p eq "colorcode"); - die("Error Config : The circos parameter \"$p\" is not defined\n") if (!defined $conf{circos}{$p}); - } - } - - if($list_prgs=~/2bed$/){ - foreach my $p (@bed_params) { - die("Error Config : The bed parameter \"$p\" is not defined\n") if (!defined $conf{bed}{$p}); - } - } - - if($list_prgs=~/links2compare/){ - foreach my $p (@compare_params) { - die("Error Config : The compare parameter \"$p\" is not defined\n") if (!defined $conf{compare}{$p}); - } - - unless (defined($conf{compare}{same_sv_type})) { - $conf{compare}{same_sv_type} = 0; - } - - unless (defined($conf{compare}{min_overlap})) { - $conf{compare}{min_overlap} = 1E-9; - } - - if($conf{compare}{circos_output}){ - foreach my $p (@circos_params) { - next if($list_prgs=~/^ratio/ && $p eq "colorcode"); - die("Error Config : The circos parameter \"$p\" is not defined\n") if (!defined $conf{circos}{$p}); - } - } - if($conf{compare}{bed_output}){ - foreach my $p (@bed_params) { - die("Error Config : The bed parameter \"$p\" is not defined\n") if (!defined $conf{bed}{$p}); - } - die("Error Config : The compare parameter \"list_read_lengths\" is not defined\n") if (!defined $conf{compare}{list_read_lengths}); - - my @samples=split(",",$conf{compare}{list_samples}); - my @read_lengths=split(",",$conf{compare}{list_read_lengths}); - for my $i (0..$#samples){ - my @l=split("-",$read_lengths[$i]); - $conf{compare}{read_lengths}{$samples[$i]}={ 1=> $l[0], 2=> $l[1]}; - } - } - } - - -} -#------------------------------------------------------------------------------# -#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#
--- a/svdetect/SVDetect_run_parallel.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,324 +0,0 @@ -<tool id="svdetect_run_parallel" name="Detect clusters of anomalously mapped pairs"> - -<description>and identify structural variants</description> - -<command interpreter="perl">SVDetect_run_parallel.pl - -#if $getLinks.linking == "linking" -linking -<!-- -out1 '$links_file' --> -#end if -#if $getFilteredLinks.filtering == "filtering" -filtering -<!--- out2 '$flinks_file' --> -#if str($getFilteredLinks.links2SV) == "create" -links2SV --out3 '$sv_file' -#end if -#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2circos) == "create" -links2circos --out4 '$circos_file' -#end if -#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2bed) == "create" -links2bed --out5 '$bed_file' -#end if -#end if --conf '$config_file' --l '$log_file' --N '$sample_name' - -</command> - -<inputs> - <param name="sample_name" type="text" value="sample" label="Sample Name"/> - <param name="mates_file" format="bam" type="data" label="Input BAM file (.ab.bam)"/> - <param name="cmap_file" format="len" type="data" label="Chromosomes list file (.len)" help="Tabulated file format with Chromosome ID (integer from 1), name and length"/> - <param name="mates_orientation" type="select" format="txt" label="Type of sequencing technology and libraries"> - <option value="FR">Illumina paired-ends</option> - <option value="RF">Illumina mate-pairs</option> - <option value="FR">SOLiD paired-ends</option> - <option value="RR">SOLiD mate-pairs</option> - </param> - <param name="read1_length" type="integer" size="10" value="50" label="Read 1 length (bp)" help="Length of the first read in a pair (left read)"/> - <param name="read2_length" type="integer" size="10" value="50" label="Read 2 length (bp)" help="Length of the second read in a pair (right read)"/> - <param name="sv_type" type="select" format="txt" label="Type of SV to detect"> - <option value="all">all types of SVs</option> - <option value="intra">intrachromosomal SVs only</option> - <option value="inter">interchromosomal SVs only</option> - </param> - - <conditional name="getLinks"> - <param name="linking" type="select" label="Linking procedure" help="Detection and isolation of links"> - <option value="linking">Yes</option> - <option value="">No, already done</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="linking"> - <param name="splitmate" label="Do you want to split the original mate file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="True" help="Untick it if already done"/> - <param name="window_size" type="integer" size="20" value="3000" label="Window size (bp)" help="Equal to at least “2µ+2√2σ"/> - <param name="step_length" type="integer" size="20" value="250" label="Step length size (bp)" help="Equal to 1/2 or 1/4 of the window size"/> - </when> - </conditional> - - <conditional name="getFilteredLinks"> - <param name="filtering" type="select" label="Filtering procedure" help="Filtering of links according different parameters and thresholds"> - <option value="filtering">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="filtering"> - - <param name="splitlink" label="Do you want to split the original link file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="False" help="Untick it if (the linking is) already done"/> - <param name="chromosomes" type="text" size="20" label="List of chromosome names to keep or exclude"/> - <param name="nb_pairs_threshold" type="integer" size="20" value="5" label="Minimum number of pairs in a cluster"/> - - <conditional name="filter1"> - <param name="strand_filtering" type="select" label="Strand filtering procedure"> - <option value="strand">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="strand"> - - <conditional name="filter2"> - <param name="order_filtering" type="select" label="Order filtering procedure"> - <option value="order">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="order"> - - <conditional name="filter3"> - <param name="insert_size_filtering" type="select" label="Insert-size filtering procedure"> - <option value="insert">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="insert"> - <param name="indel_sigma_threshold" type="float" size="20" value="3" label="Minimal number of sigma fold for the insert size filtering and to call insertions and deletions"/> - <param name="dup_sigma_threshold" type="float" size="20" value="3" label="minimal number of sigma fold for the insert size filtering to call tandem duplications"/> - <param name="singleton_sigma_threshold" type="float" size="20" value="4" label="Minimal number of sigma fold for the insert size filtering to call singletons" help="for Illumina mate-pairs only"/> - </when> - </conditional> - - <param name="mu_length" type="integer" size="20" value="3000" label="Mean insert size value (µ) of normally mapped mate-pairs, in bp"/> - <param name="sigma_length" type="integer" size="20" value="250" label="Calculated sd value (σ) from the distribution of normally mapped mate-pairs, in bp"/> - <param name="nb_pairs_order_threshold" type="integer" size="20" value="2" label="Minimal number of pairs in a subgroup of paired-end reads for balanced events"/> - </when> - </conditional> - - <param name="final_score_threshold" type="float" size="20" value="1.0" label="Minimal final filtering score for calling SVs" help="A value of 1 means all the pairs in a cluster were consistent between each other after applying filters"/> - </when> - </conditional> - - <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="create" falsevalue="do_not_create" checked="True"/> - - <conditional name="file_conversion"> - <param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs"> - <option value="do_not_convert">No</option> - <option value="convert">Yes</option> - </param> - <when value="do_not_convert"> - <!-- do nothing here --> - </when> - <when value="convert"> - <param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="create" falsevalue="do_not_create" checked="True"/> - <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/> - <param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/> - <repeat name="color_code" title="Color-code" min="1" max="7"> - <param name="color" type="select" label="Color"> - <option value="grey">grey</option> - <option value="black">black</option> - <option value="blue">blue</option> - <option value="green">green</option> - <option value="purple">purple</option> - <option value="orange">orange</option> - <option value="red">red</option> - </param> - <param name="interval" type="text" value="1,3" label="Interval"/> - </repeat> - </when> - </conditional> - </when> - </conditional> -</inputs> - - -<outputs> - <!--<data format="txt" name="links_file" label="svdetect.links"> - <filter>getLinks['linking']=="linking"</filter> - </data> - <data format="txt" name="flinks_file" label="svdetect.links.filtered"> - <filter>getFilteredLinks['filtering']=="filtering"</filter> - </data>--> - <data format="sv" name="sv_file" label="${sample_name}.sv"> - <filter>( - getFilteredLinks['filtering']=="filtering" and - getFilteredLinks['links2SV'] is True - ) - </filter> - </data> - <data format="segdup" name="circos_file" label="${sample_name}.segdup"> - <filter>( - getFilteredLinks['filtering']=="filtering" and - getFilteredLinks['file_conversion']['file_conversion_select']=="convert" and - getFilteredLinks['file_conversion']['links2circos'] is True - ) - </filter> - </data> - <data format="bed" name="bed_file" label="${sample_name}.bed"> - <filter>( - getFilteredLinks['filtering']=="filtering" and - getFilteredLinks['file_conversion']['file_conversion_select']=="convert" and - getFilteredLinks['file_conversion']['links2bed'] is True - ) - </filter> - </data> - <data format="txt" name="log_file" label="${sample_name}.svdetect_run.log"/> -</outputs> - - - -<configfiles> - <configfile name="config_file"> -<general> -input_format = bam -sv_type = ${sv_type} -mates_orientation=${mates_orientation} -read1_length=${read1_length} -read2_length=${read2_length} -mates_file=${mates_file} -cmap_file=${cmap_file} -tmp_dir=$__new_file_path__/svdetect/tmp -output_dir=$__new_file_path__/svdetect -num_threads=8 -</general> - -#if $getLinks.linking == "linking" -<detection> -#if str($getLinks.splitmate) == "split" -split_mate_file=1 -#else -split_mate_file=0 -#end if -window_size=${getLinks.window_size} -step_length=${getLinks.step_length} -</detection> -#end if - -#if $getFilteredLinks.filtering == "filtering" -<filtering> -#if str($getFilteredLinks.splitlink) == "split" -split_link_file=1 -#else -split_link_file=0 -#end if -#if str($getFilteredLinks.chromosomes) != "" -chromosomes=${getFilteredLinks.chromosomes} -#end if -nb_pairs_threshold=${getFilteredLinks.nb_pairs_threshold} -#if $getFilteredLinks.filter1.strand_filtering == "strand" -strand_filtering=1 -final_score_threshold=${getFilteredLinks.filter1.final_score_threshold} -#if $getFilteredLinks.filter1.filter2.order_filtering == "order" -order_filtering=1 -mu_length=${getFilteredLinks.filter1.filter2.mu_length} -sigma_length=${getFilteredLinks.filter1.filter2.sigma_length} -nb_pairs_order_threshold=${getFilteredLinks.filter1.filter2.nb_pairs_order_threshold} -#if $getFilteredLinks.filter1.filter2.filter3.insert_size_filtering == "insert" -insert_size_filtering=1 -indel_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.indel_sigma_threshold} -dup_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.dup_sigma_threshold} -singleton_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.singleton_sigma_threshold} -#else -insert_size_filtering=0 -#end if -#else -order_filtering=0 -#end if -#else -strand_filtering=0 -#end if -</filtering> -#end if - -#if $getFilteredLinks.filtering == "filtering" -#if $getFilteredLinks.file_conversion.file_conversion_select == "convert" -#if str($getFilteredLinks.file_conversion.links2circos) == "create" -<circos> -organism_id=${getFilteredLinks.file_conversion.organism_id} -<colorcode> -#for $color_repeat in $getFilteredLinks.file_conversion.color_code -${color_repeat.color}=${color_repeat.interval} -#end for -</colorcode> -</circos> -#end if -#if str($getFilteredLinks.file_conversion.links2bed) == "create" -<bed> -<colorcode> -#for $color_repeat in $getFilteredLinks.file_conversion.color_code -#if str($color_repeat.color)== "grey" -190,190,190=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "black" -0,0,0=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "blue" -0,0,255=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "green" -0,255,0=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "purple" -153,50,205=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "orange" -255,140,0=${color_repeat.interval} -#end if -#if str($color_repeat.color)== "red" -255,0,0=${color_repeat.interval} -#end if -#end for -</colorcode> -</bed> -#end if -#end if -#end if - </configfile> -</configfiles> - - <help> -**What it does** - -SVDetect - Version : 0.8b - -Parallel version (nCPU=8) - -SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies - -This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. -SVDetect is compatible with SOLiD and Illumina (>=1.3) reads. - -Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. - - </help> - -</tool>
--- a/svdetect/circos_graph.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,290 +0,0 @@ -<tool id="circos_graph" name="Circos" version="1.1.0"> - -<description>plots</description> - -<command interpreter="perl">circos/bin/circos - --conf '$circos_config_file' --outputfile '${outputfile}.dat' --png - -> '$log_file' - -; - -rm '$outputfile'; ln -s '${outputfile}.png' '$outputfile' - -</command> - - -<inputs> - <param name="graph_name" type="text" size="20" value="graph1" label="Graph name"/> - - <param name="karyotype" type="select" format="txt" label="Type of model organism"> - <option value="data/karyotype.human_hg19.txt">Human (homo sapiens, hs) -hg19-</option> - <option value="data/karyotype.human.txt">Human (homo sapiens, hs) -hg18-</option> - <option value="data/2/karyotype.mouse.txt">Mouse (Mus Musculus, mm)</option> - <option value="data/2/karyotype.dog.txt">Dog (Canis familiaris, cf)</option> - <option value="data/2/karyotype.rt.txt">Rat (Rattus norvegicus, rn)</option> - <option value="data/karyotype.yeast.txt">Yeast (Saccharomyces Cerevisiae, sc) -SGD-</option> - - </param> - <param name="chromosomes_units" type="integer" size="50" value="1000000" label="Chromosomes units"/> - <param name="chromosomes" type="text" size="100" value="" label="List of chromosome names to keep or exclude" help="ex: hs2;hs3 or -hsX;-hsY"> - <sanitizer> - <valid initial="string.printable"> - <add value=";"/> - </valid> - </sanitizer> - </param> - <param name="link_file" format="segdup" type="data" label="Input link file (.segdup)"/> -</inputs> - -<outputs> - <data format="txt" name="log_file" label="${graph_name}.circos.log"/> - <data format="png" name="outputfile" label="${graph_name}.png"/> -</outputs> - - - -<configfiles> - <configfile name="ideogram_config_file"> - -<ideogram> - -<spacing> - -default = 5u -break = 1u - -axis_break_at_edge = yes -axis_break = yes -axis_break_style = 2 - -<break_style 1> -stroke_color = black -fill_color = blue -thickness = 0.25r -stroke_thickness = 2 -</break> - -<break_style 2> -stroke_color = black -stroke_thickness = 3p -thickness = 1.5r -</break> - -</spacing> - -## thickness (px) of chromosome ideogram -thickness = 100p -stroke_thickness = 2 -## ideogram border color -stroke_color = black -fill = yes -## the default chromosome color is set here and any value -## defined in the karyotype file overrides it -fill_color = black - -## fractional radius position of chromosome ideogram within image -radius = 0.85r -show_label = yes -label_with_tag = yes -label_font = condensedbold -label_radius = dims(ideogram,radius) + 0.075r -label_size = 60p - -## cytogenetic bands -band_stroke_thickness = 2 - -## show_bands determines whether the outline of cytogenetic bands -## will be seen -show_bands = yes -## in order to fill the bands with the color defined in the karyotype -## file you must set fill_bands -fill_bands = yes - -</ideogram> - - </configfile> - - <configfile name="ticks_config_file"> - -show_ticks = yes -show_tick_labels = yes - -<ticks> -radius = dims(ideogram,radius_outer) -multiplier = 1e-6 - -<tick> -spacing = 0.5u -size = 2p -thickness = 2p -color = grey -show_label = no -label_size = 12p -label_offset = 0p -format = %.2f -</tick> - -<tick> -spacing = 1u -size = 3p -thickness = 2p -color = dgrey -show_label = no -label_size = 12p -label_offset = 0p -format = %.2f -</tick> - -<tick> -spacing = 5u -size = 5p -thickness = 2p -color = black -show_label = yes -label_size = 16p -label_offset = 0p -format = %d -</tick> - -<tick> -spacing = 10u -size = 8p -thickness = 2p -color = black -show_label = yes -label_size = 20p -label_offset = 5p -format = %d -</tick> -</ticks> - </configfile> - - - <configfile name="circos_config_file"> -<colors> -<<include etc/colors.conf>> -</colors> - -<fonts> -<<include etc/fonts.conf>> -</fonts> - -<<include $ideogram_config_file>> -<<include $ticks_config_file>> - -karyotype = $karyotype - -<image> -24bit = yes -##png = yes -##svg = no -## radius of inscribed circle in image -radius = 1500p -background = white -## by default angle=0 is at 3 o'clock position -angle_offset = -90 -#angle_orientation = counterclockwise - -auto_alpha_colors = yes -auto_alpha_steps = 5 -</image> - -chromosomes_units= $chromosomes_units - -#if str($chromosomes)=="" -chromosomes_display_default = yes -#else -chromosomes_display_default = no -chromosomes = $chromosomes -#end if - -<links> - -z = 0 -radius = 0.95r -bezier_radius = 0.2r - -<link segdup> -show = yes -color = dgrey_a5 -thickness = 2 -file = $link_file -record_limit = 1000 -</link> - -</links> - - -anglestep = 0.5 -minslicestep = 10 -beziersamples = 40 -debug = no -warnings = no -imagemap = no - -units_ok = bupr -units_nounit = n - </configfile> -</configfiles> - - <help> -**What it does** - -Circos - -Manual documentation available at the http://circos.ca/ - - -**Example of link segdup file** - -segdup file:: - - 1 hs1 1077096 1078746 color=red - 1 hs1 1080923 1082805 color=red - 2 hs1 1137684 1137961 color=red - 2 hs3 1138138 1138423 color=red - 3 hs11 1169417 1170000 color=red - 3 hs11 1170025 1170975 color=red - 4 hs11 1222480 1224271 color=green - 4 hs11 1223328 1225675 color=green - 5 hs12 1223336 1225812 color=grey - 5 hs13 1224709 1227633 color=grey - 6 hs11 1223621 1226460 color=red - 6 hs11 1224918 1227633 color=red - 7 hs11 1399510 1401513 color=white - 7 hs11 1401628 1403697 color=white - 8 hs15 1652045 1653746 color=red - 8 hs15 1657167 1658940 color=red - 9 hs11 165333 165887 color=white - 9 hs11 165981 168016 color=white - 10 hs11 1702700 1702841 color=red - 10 hs11 1702903 1703057 color=red - 11 hs11 1912272 1915186 color=white - 11 hs11 1937111 1939824 color=white - 12 hs11 1983211 1983355 color=red - 12 hs11 1983591 1983748 color=red - 13 hs11 2913657 2913898 color=white - 13 hs11 2914048 2914341 color=white - 14 hs11 3090593 3090749 color=purple - 14 hs11 3090709 3090864 color=purple - 15 hs21 3466365 3466434 color=red - 15 hs21 3466554 3466620 color=red - 16 hsX 3603073 3603321 color=white - 16 hsX 3603295 3603520 color=white - - - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of Circos. - - - </help> - -</tool>
--- a/varscan/tool_dependencies.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="VarScan" version="2.3.5"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.5.jar</action> - <action type="move_file"> - <source>VarScan.v2.3.5.jar</source> - <destination>$INSTALL_DIR/jars</destination> - </action> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> -</tool_dependency>
--- a/varscan/varscan_mpileup.pl Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,116 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Cwd; - -die qq( -Bad numbr of inputs - -) if(!@ARGV); - -my $options =""; -my $file=""; -my $command=""; -my $output=""; -my $working_dir = cwd(); -my $temp_vcf = "$working_dir/temp"; -my $log=""; - -foreach my $input (@ARGV) -{ - my @tmp = split "::", $input; - if($tmp[0] eq "COMMAND") - { - $command = $tmp[1]; - } - elsif($tmp[0] eq "INPUT") - { - $file = $tmp[1]; - } - elsif($tmp[0] eq "OPTION") - { - $options = "$options ${tmp[1]}"; - } - elsif($tmp[0] eq "OUTPUT") - { - $output = $tmp[1]; - } - elsif($tmp[0] eq "LOG") - { - $log = $tmp[1]; - } - else - { - die("Unknown Input: $input\n"); - } -} - -system ("$command $file $options 1>$temp_vcf 2>$log"); - -vs2vcf($temp_vcf, $output); - - -sub vs2vcf -{ - - # - # G l o b a l v a r i a b l e s - # - my $version = '0.1'; - - # - # Read in file - # - my $input = shift; - my $output = shift; - my $chr_ord = shift; - open(IN, $input) or die "Can't open $input': $!\n"; - open(OUT, ">$output") or die "Can't create $output': $!\n"; - my %output; - - while ( <IN> ) - { - if ( /^#/ ) - { - print OUT; - next; - } - chomp; - my $line = $_; - - my @flds = split ( "\t", $line ); - my $ref = $flds[3]; - my $alt = $flds[4]; - # - # Deletion of bases - # - if ( $alt =~ /^\-/ ) - { - ($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref); - } - - # - # Insertion of bases - # - if ( $alt =~ /^\+/ ) - { - $flds[4] = $ref.substr($alt,1); - } - print OUT join( "\t", @flds),"\n" unless defined $chr_ord; - $output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord; - } - close(IN); - # if chromosome order given return in sorted order - if(defined $chr_ord) - { - for my $chrom (@{ $chr_ord }) - { - for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) - { - print OUT $output{$chrom}{$pos}; - } - } - } - close(OUT); -} -
--- a/varscan/varscan_mpileup.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,124 +0,0 @@ -<tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5"> - <description> - mutation caller for targeted, exome, and whole-genome resequencing - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - - varscan_mpileup.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command" - "INPUT::$in_file" - "OUTPUT::$output" - "LOG::$log" - "OPTION::--min-coverage $min_coverage" - "OPTION::--min-reads2 $min_reads2" - "OPTION::--min-avg-qual $min_avg_qual" - "OPTION::--min-var-freq $min_var_freq" - "OPTION::--min-freq-for-hom $min_freq_for_hom" - "OPTION::--p-value $p_value" - "OPTION::--strand-filter $strand_filter" - "OPTION::--output-vcf 1" - - #if ($vcf_sample_list): - "OPTION::--vcf-sample-list $vcf_sample_list" - #end if - "OPTION::--variants $variants" - - - - </command> - - <inputs> - - <param name="exe_command" type="select" label="Command" help="" optional="false"> - <option value="mpileup2snp" >mpileup2snp</option> - <option value="mpileup2indel">mpileup2indel</option> - <option value="mpileup2cns">mpileup2cns</option> - </param> - <param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" /> - <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/> - <param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/> - <param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/> - <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/> - <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/> - <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/> - <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/> - <param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" /> - <param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/> - - - </inputs> - <outputs> - <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/> - <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/> - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup file - The SAMtools mpileup file - - -**Parameters** - -:: - - commands - mpileup2snp Identify SNPs from an mpileup file - mpileup2indel Identify indels an mpileup file - mpileup2cns Call consensus and variants from an mpileup file - - min-coverage - Minimum read depth at a position to make a call [8] - - min-reads2 - Minimum supporting reads at a position to call variants [2] - - min-avg-qual - Minimum base quality at a position to count a read [15] - - min-var-freq - Minimum variant allele frequency threshold [0.01] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - p-value - Default p-value threshold for calling variants [99e-02] - - strand-filter - Ignore variants with >90% support on one strand [1] - - output-vcf - If set to 1, outputs in VCF format - - vcf-sample-list - For VCF output, a list of sample names in order, one per line - - variants - Report only variant (SNP/indel) positions [0] - - - - </help> -</tool> -
--- a/varscan/varscan_somatic.pl Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -#!/usr/bin/perl - - -use strict; -use Cwd; - -die qq( -Bad numbr of inputs - -) if(!@ARGV); - -my $options =""; -my $normal=""; -my $command=""; -my $tumor=""; -my $output=""; -my $working_dir = cwd(); -my $snp = "$working_dir/output.snp.vcf"; -my $indels = "$working_dir/output.indel.vcf"; - -foreach my $input (@ARGV) -{ - my @tmp = split "::", $input; - if($tmp[0] eq "COMMAND") - { - $command = $tmp[1]; - } - if($tmp[0] eq "NORMAL") - { - $normal = $tmp[1]; - } - elsif($tmp[0] eq "TUMOR") - { - $tumor = $tmp[1]; - } - elsif($tmp[0] eq "OPTION") - { - $options = "$options ${tmp[1]}"; - } - elsif($tmp[0] eq "OUTPUT") - { - $output = $tmp[1]; - } - - else - { - die("Unknown Input: $input\n"); - } -} - -system ("$command $normal $tumor $options "); -system("grep -v '^\#' $indels | grep -v '^chrom position' >> $snp"); - -my @chr_ord = chromosome_order($tumor); - -vs2vcf($snp, $output,\@chr_ord); - - -sub vs2vcf -{ - - # - # G l o b a l v a r i a b l e s - # - my $version = '0.1'; - - # - # Read in file - # - my $input = shift; - my $output = shift; - my $chr_ord = shift; - open(IN, $input) or die "Can't open $input': $!\n"; - open(OUT, ">$output") or die "Can't create $output': $!\n"; - my %output; - - while ( <IN> ) - { - if ( /^#/ ) - { - print OUT; - next; - } - chomp; - my $line = $_; - - my @flds = split ( "\t", $line ); - my $ref = $flds[3]; - my $alt = $flds[4]; - # - # Deletion of bases - # - if ( $alt =~ /^\-/ ) - { - ($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref); - } - - # - # Insertion of bases - # - if ( $alt =~ /^\+/ ) - { - $flds[4] = $ref.substr($alt,1); - } - print OUT join( "\t", @flds),"\n" unless defined $chr_ord; - $output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord; - } - close(IN); - # if chromosome order given return in sorted order - if(defined $chr_ord) - { - for my $chrom (@{ $chr_ord }) - { - for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) - { - print OUT $output{$chrom}{$pos}; - } - } - } - close(OUT); -} - - -sub chromosome_order -{ - my $input = shift; - # calculate flagstats - my $COMM = "samtools view -H $input | grep '^\@SQ'"; - my @SQ = `$COMM`; - chomp @SQ; - for(my $i = 0; $i <= $#SQ; $i++) - { - $SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/; - } - return(@SQ); -} - -
--- a/varscan/varscan_somatic.xml Fri Sep 13 02:11:51 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -<tool id="varscan_somatic" name="VarScan Somatic" version="2.3.5"> - <description> - somatic mutation caller for cancer genomics - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - varscan_somatic.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" - "NORMAL::$normal" - "TUMOR::$tumor" - "OUTPUT::$output" - - "OPTION::--min-coverage $min_coverage" - "OPTION::--min-coverage-normal $min_coverage_normal" - "OPTION::--min-coverage-tumor $min_coverage_tumor" - - "OPTION::--min-var-freq $min_var_freq" - "OPTION::--min-freq-for-hom $min_freq_for_hom" - - "OPTION::--normal-purity $normal_purity" - "OPTION::--tumor-purity $tumor_purity" - - "OPTION::--p-value $p_value" - "OPTION::--somatic-p-value $somatic_p_value" - - "OPTION::--strand-filter $strand_filter" - "OPTION::--validation $validation" - "OPTION::--output-vcf 1" - - - - </command> - - <inputs> - - <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" /> - <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" /> - - <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/> - <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/> - <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/> - - <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/> - <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/> - - <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/> - <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/> - - - <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/> - <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/> - - <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/> - <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/> - - </inputs> - <outputs> - <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/> - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup normal file - The SAMtools mpileup file for normal - mpileup tumor file - The SAMtools mpileup file for tumor - - -**Parameters** - -:: - - min-coverage - Minimum read depth at a position to make a call [8] - - min-coverage-normal - Minimum coverage in normal to call somatic [8] - - min-coverage-tumor - Minimum coverage in tumor to call somatic [6] - - min-var-freq - Minimum variant frequency to call a heterozygote [0.10] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - normal-purity - Estimated purity (non-tumor content) of normal sample [1.00] - - tumor-purity - Estimated purity (tumor content) of tumor sample [1.00] - - p-value - Default p-value threshold for calling variants [0.99] - - somatic-p-value - P-value threshold to call a somatic site [0.05] - - strand-filter - If set to 1, removes variants with >90% strand bias - - validation - If set to 1, outputs all compared positions even if non-variant - - output-vcf - If set to 1, outputs in VCF format [Default] - - - - </help> -</tool> -