cheripic 1.2.5 → 1.2.6
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- checksums.yaml +4 -4
- data/ChangeLog.md +10 -3
- data/README.md +20 -10
- data/Rakefile +2 -2
- data/galaxy_cheripic_tool.xml +47 -19
- data/lib/cheripic/cmd.rb +40 -14
- data/lib/cheripic/implementer.rb +5 -2
- data/lib/cheripic/options.rb +5 -0
- data/lib/cheripic/variants.rb +84 -77
- data/lib/cheripic/vcf.rb +32 -8
- data/lib/cheripic/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 4b848b1b52f01215fabf404f7387e6f621a2285b
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data.tar.gz: e434cbad53ac982974c30cf2a940668862a6d2bd
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ef7eb0c0008b8d8ed45d6e1deeeb4c59ef187a8af3a92fbc91dba33d91af03b475c337c2e69dcdcb8c34c3cfeea3f9f5d54e42fadba8d0270e0a776c96609c79
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data.tar.gz: beb3fccf28f54a30fc355a93261043d27dfd4d2ebb34043245404608d1608d2185aae57b8263192ca5973caf1a99c9b9b1614187e5d253656efc9ec9fab9aa50
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data/ChangeLog.md
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@@ -6,8 +6,15 @@ All significant changes to this project at each release are documented in this f
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#### Future changes to include
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1. option to take multiple background pileup files
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#### [1.2.6] - 2016-10-26
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1. option to run only using with vcf files as bulk inputs to increase speed of analysis for larger genomes
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#### [1.2.5] - 2016-10-17
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1. Updated methods take bam file (along with a vcf file) or pileup file as inputs of bulks
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2. Replaced output directory with output file name tag, since we only write to one file
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#### [1.2.0] - 2016-08-11
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#### [1.1.0] - 2016-07-26
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first release of the binaries for Linux 64 bit and OSX 64bit
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first release of the binaries for Linux 64 bit and OSX 64bit
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data/README.md
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@@ -45,7 +45,7 @@ Running `cheripic` without any input at command line interface shows following h
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```
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-
Cheripic v1.2.
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Cheripic v1.2.6
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Authors: Shyam Rallapalli and Dan MacLean
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Description: Candidate mutation and closely linked marker selection for non reference genomes
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@@ -53,35 +53,45 @@ Uses bulk segregant data from non-reference sequence genomes
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Inputs:
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1. Needs a reference fasta file of asssembly use for variant analysis
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2. Pileup files for mutant (phenotype of interest) bulks and background (wildtype phenotype) bulks
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3. If
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2. Pileup/Bam files for mutant (phenotype of interest) bulks and background (wildtype phenotype) bulks
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3. If providing bam files, you have to include vcf files for the respective bulks
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4. If polyploid species, include pileup/bam files from one or both parents
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USAGE:
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cheripic <options>
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OPTIONS:
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-f, --assembly=<s> Assembly file in FASTA format
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-F, --input-format=<s> bulk and parent alignment file format types - set either pileup or bam (default: pileup)
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-F, --input-format=<s> bulk and parent alignment file format types - set either pileup or bam or vcf (default: pileup)
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-a, --mut-bulk=<s> Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1
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--mut-bulk-vcf=<s> vcf file for variants from mutant/trait of interest bulk 1 (default: )
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-b, --bg-bulk=<s> Pileup or sorted BAM file alignments from background/wildtype bulk 2
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--
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--bg-bulk-vcf=<s> vcf file for variants from background/wildtype bulk 2 (default: )
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--output=<s> custom name tag to include in the output file name (default: cheripic_results)
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--loglevel=<s> Choose any one of "info / warn / debug" level for logs generated (default: debug)
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--hmes-adjust=<f> factor added to snp count of each contig to adjust for hme score calculations (default: 0.5)
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--htlow=<f> lower level for categorizing heterozygosity (default: 0.2)
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--hthigh=<f> high level for categorizing heterozygosity (default: 0.9)
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--mindepth=<i> minimum read depth
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--mindepth=<i> minimum read depth at a position to consider for variant calls (default: 6)
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--max-d-multiple=<i> multiplication factor for average coverage to calculate maximum read coverage
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if set zero no calculation will be made from bam file.
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setting this value will override user set max depth (Default: 5)
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--maxdepth=<i> maximum read depth at a position to consider for variant calls
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if set to zero no user max depth will be used (default: 0)
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--min-non-ref-count=<i> minimum read depth supporting non reference base at each position (default: 3)
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--min-indel-count-support=<i> minimum read depth supporting an indel at each position (default: 3)
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--ambiguous-ref-bases
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--ambiguous-ref-bases=<s> including variant at completely ambiguous bases in the reference (default: false)
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-q, --mapping-quality=<i> minimum mapping quality of read covering the position (default: 20)
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-Q, --base-quality=<i> minimum base quality of bases covering the position (default: 15)
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--noise=<f> praportion of reads for a variant to conisder as noise (default: 0.1)
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--cross-type=<s> type of cross used to generated mapping population - back or out (default: back)
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--use-all-contigs
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--include-low-hmes
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-
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--use-all-contigs=<s> option to select all contigs or only contigs containing variants for analysis (default: false)
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--include-low-hmes=<s> option to include or discard variants from contigs with
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low hme-score or bfr score to list in the final output (default: false)
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--polyploidy=<s> Set if the data input is from polyploids (default: false)
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-p, --mut-parent=<s> Pileup or sorted BAM file alignments from mutant/trait of interest parent (default: )
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-r, --bg-parent=<s> Pileup or sorted BAM file alignments from background/wildtype parent (default: )
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-R, --repeats-file=<s> repeat masker output file for the assembly (default: )
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--bfr-adjust=<f> factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05)
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--sel-seq-len=<i> sequence length to print from either side of selected variants (default: 50)
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--examples shows some example commands with explanation
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data/Rakefile
CHANGED
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@@ -61,8 +61,8 @@ def create_package(target)
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package_dir = "packaging/#{package_dest}"
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sh "rm -rf #{package_dir}"
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sh "mkdir #{package_dir}"
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sh "mkdir -p #{package_dir}/lib/app"
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sh "cp
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sh "mkdir -p #{package_dir}/lib/app/bin"
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sh "cp bin/cheripic #{package_dir}/lib/app/bin/"
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sh "cp -R lib #{package_dir}/lib/app/"
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sh "mkdir #{package_dir}/lib/app/ruby"
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sh "tar -xzf packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-#{target}.tar.gz -C #{package_dir}/lib/app/ruby"
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data/galaxy_cheripic_tool.xml
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<tool id="cheripic" name="CHERIPIC" version="1.2.
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<tool id="cheripic" name="CHERIPIC" version="1.2.6">
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<description>CHERIPIC</description>
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<version_command
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<version_command>/full_path_to/cheripic -v</version_command>
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<command>
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<![CDATA[
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-
cheripic
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/full_path_to/cheripic
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--assembly $assembly
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--input-format $input_format
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--mut-bulk $mut_bulk
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--bg-bulk $bg_bulk
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--
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--mut-bulk-vcf $mut_bulk_vcf
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--bg-bulk-vcf $bg_bulk_vcf
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--loglevel $loglevel
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--hmes-adjust $hmes_adjust
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--htlow $ht_low
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--hthigh $ht_high
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--mindepth $min_depth
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--max-d-multiple $max_d_multiple
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--maxdepth $max_depth
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--min-non-ref-count $min_non_ref_count
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--min-indel-count-support $min_indel_count_support
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--ambiguous-ref-bases $ambiguous_ref_bases
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--polyploidy $polyploidy
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--mut-parent $mut_parent
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--bg-parent $bg_parent
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--repeats-file $repeats_file
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--bfr-adjust $bfr_adjust
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--sel-seq-len $sel_seq_len
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&> output_log.txt
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]]>
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</command>
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<inputs>
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<param name="assembly" type="data" format="fasta" label="Input Assembly file" help="Select Assembly fasta file" />
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<param name="
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<option value="
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<param name="input_format" type="select" optional="true" label="input file format" help="choose between vcf, bam and pileup format" >
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<option value="vcf" selected="true">vcf</option>
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<option value="bam">bam</option>
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<option value="pileup">pileup</option>
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</param>
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<param name="mut_bulk" type="data" label="mutant bulk input file" help="Select mutant bulk input file" />
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<param name="bg_bulk" type="data" label="background bulk input file" help="Select background bulk input file" />
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<param name="mut_bulk_vcf" type="data" optional="true" label="mutant bulk input vcf file" help="Select mutant bulk input vcf file" />
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<param name="bg_bulk_vcf" type="data" optional="true" label="background bulk input vcf file" help="Select background bulk input vcf file" />
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<param name="loglevel" type="select" optional="true" label="analysis log level" help="choose between info, warn and debug levels" >
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<option value="info" selected="true">info</option>
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<option value="warn">warnings</option>
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<option value="debug">debug</option>
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</param>
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label="heterozygosity high limit" help="upper limit to heterozygosity allele fraction" />
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<param name="min_depth" size="4" type="integer" optional="true" value="6" min="1" max="8000"
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label="minimum read coverage" help="minimum read depth to conisder a position for variant calls" />
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<param name="max_d_multiple" size="4" type="integer" optional="true" value="5" min="0" max="100"
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label="multiplication factor avg read coverage" help="multiplication factor for average coverage to calculate maximum read coverage" />
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<param name="max_depth" size="4" type="integer" optional="true" value="0" min="0" max="8000"
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label="maximum read coverage" help="maximum read depth to conisder a position for variant calls" />
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<param name="min_non_ref_count" size="4" type="integer" optional="true" value="3" min="1" max="8000"
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label="minimum alternate read coverage" help="minimum read depth supporting non reference base at each position" />
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<param name="min_indel_count_support" size="4" type="integer" optional="true" value="3" min="1" max="8000"
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help="option to include or discard variants from contigs with low hme-score or bfr score to list in the final output" truevalue="true" falsevalue="false" />
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<param name="polyploidy" type="boolean" optional="true" checked="false" label="polyploid data"
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help="Set if the input data is from polyploids" truevalue="true" falsevalue="false" />
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<param name="
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<param name="
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<param name="mut_parent" type="data" optional="true" format="pileup" label="mutant parent pileup file" help="Select mutant parent pileup file" />
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<param name="bg_parent" type="data" optional="true" format="pileup" label="background parent pileup file" help="Select background parent pileup file" />
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<param name="repeats_file" type="data" optional="true" format="txt" label="Repeat masker output file" help="Repeat masker output file of repeat positions" />
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<param name="bfr_adjust" size="4" type="float" optional="true" value="0.05" min="0.01" max="1.0"
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label="bfr score adjuster" help="factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05)" />
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<param name="sel_seq_len" size="4" type="integer" optional="true" value="50" min="10" max="250"
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label="selected variant seq length out" help="sequence length to print from either side of selected variants (default: 50)" />
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-
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<param name="output" type="text" size="30" value="cheripic_results" label="tag for output filename" help="write a tag to include with output filename" />
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</inputs>
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<outputs>
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<data name="
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<data name="
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<data name="output1" format="txt" from_work_dir="output_log.txt" label="cheripic log file" />
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<data name="output2" format="txt" from_work_dir="cheripic_results_selected_hme_variants.txt" label="selected hmes variants" />
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<data name="output3" format="txt" from_work_dir="cheripic_results_selected_bfr_variants.txt" label="selected bfr variants" >
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<filter>polyploidy == "true"</filter>
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</data>
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</outputs>
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<tests>
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@@ -154,15 +173,22 @@ All of the options have a default value. You can change any of them. All of the
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OPTIONS:
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-f, --assembly Assembly file in FASTA format
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-
-F, --input-format bulk and parent alignment file format types - set either pileup or bam (default: pileup)
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-F, --input-format bulk and parent alignment file format types - set either pileup or bam or vcf (default: pileup)
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-a, --mut-bulk Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1
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--mut-bulk-vcf vcf file for variants from mutant/trait of interest bulk 1
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-b, --bg-bulk Pileup or sorted BAM file alignments from background/wildtype bulk 2
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-
--
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--bg-bulk-vcf vcf file for variants from background/wildtype bulk 2
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--output custom name tag to include in the output file name (default: cheripic_results)
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--loglevel Choose any one of "info / warn / debug" level for logs generated (default: debug)
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--hmes-adjust factor added to snp count of each contig to adjust for hme score calculations (default: 0.5)
|
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--htlow lower level for categorizing heterozygosity (default: 0.2)
|
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--hthigh high level for categorizing heterozygosity (default: 0.9)
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-
--mindepth minimum read depth
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+
--mindepth minimum read depth at a position to consider for variant calls (default: 6)
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--max-d-multiple multiplication factor for average coverage to calculate maximum read coverage
|
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+
if set zero no calculation will be made from bam file.
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+
setting this value will override user set max depth (Default: 5)
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+
--maxdepth maximum read depth at a position to consider for variant calls
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+
if set to zero no user max depth will be used (default: 0)
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--min-non-ref-count minimum read depth supporting non reference base at each position (default: 3)
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--min-indel-count-support minimum read depth supporting an indel at each position (default: 3)
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--ambiguous-ref-bases including variant at completely ambiguous bases in the reference
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|
@@ -171,10 +197,12 @@ OPTIONS:
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--noise praportion of reads for a variant to conisder as noise (default: 0.1)
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--cross-type type of cross used to generated mapping population - back or out (default: back)
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--use-all-contigs option to select all contigs or only contigs containing variants for analysis
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-
--include-low-hmes option to include or discard variants from contigs with
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+
--include-low-hmes option to include or discard variants from contigs with
|
|
201
|
+
low hme-score or bfr score to list in the final output
|
|
175
202
|
--polyploidy Set if the data input is from polyploids
|
|
176
203
|
-p, --mut-parent Pileup or sorted BAM file alignments from mutant/trait of interest parent (default: )
|
|
177
204
|
-r, --bg-parent Pileup or sorted BAM file alignments from background/wildtype parent (default: )
|
|
205
|
+
-R, --repeats-file repeat masker output file for the assembly (default: )
|
|
178
206
|
--bfr-adjust factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05)
|
|
179
207
|
--sel-seq-len sequence length to print from either side of selected variants (default: 50)
|
|
180
208
|
|
|
@@ -190,7 +218,7 @@ Shyam Rallapalli
|
|
|
190
218
|
</help>
|
|
191
219
|
|
|
192
220
|
<citations>
|
|
193
|
-
<citation type="doi">
|
|
221
|
+
<citation type="doi">spaceholder</citation>
|
|
194
222
|
</citations>
|
|
195
223
|
|
|
196
224
|
</tool>
|
data/lib/cheripic/cmd.rb
CHANGED
|
@@ -45,7 +45,7 @@ module Cheripic
|
|
|
45
45
|
opt :assembly, 'Assembly file in FASTA format',
|
|
46
46
|
:short => '-f',
|
|
47
47
|
:type => String
|
|
48
|
-
opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam',
|
|
48
|
+
opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam or vcf',
|
|
49
49
|
:short => '-F',
|
|
50
50
|
:type => String,
|
|
51
51
|
:default => 'pileup'
|
|
@@ -53,16 +53,18 @@ module Cheripic
|
|
|
53
53
|
:short => '-a',
|
|
54
54
|
:type => String
|
|
55
55
|
opt :mut_bulk_vcf, 'vcf file for variants from mutant/trait of interest bulk 1',
|
|
56
|
-
:type => String
|
|
56
|
+
:type => String,
|
|
57
|
+
:default => ''
|
|
57
58
|
opt :bg_bulk, 'Pileup or sorted BAM file alignments from background/wildtype bulk 2',
|
|
58
59
|
:short => '-b',
|
|
59
60
|
:type => String
|
|
60
61
|
opt :bg_bulk_vcf, 'vcf file for variants from background/wildtype bulk 2',
|
|
61
|
-
:type => String
|
|
62
|
+
:type => String,
|
|
63
|
+
:default => ''
|
|
62
64
|
opt :output, 'custom name tag to include in the output file name',
|
|
63
65
|
:default => 'cheripic_results'
|
|
64
66
|
opt :loglevel, 'Choose any one of "info / warn / debug" level for logs generated',
|
|
65
|
-
:default => '
|
|
67
|
+
:default => 'info'
|
|
66
68
|
opt :hmes_adjust, 'factor added to snp count of each contig to adjust for hme score calculations',
|
|
67
69
|
:type => Float,
|
|
68
70
|
:default => 0.5
|
|
@@ -79,8 +81,8 @@ module Cheripic
|
|
|
79
81
|
if set zero no calculation will be made from bam file.\nsetting this value will override user set max depth",
|
|
80
82
|
:type => Integer,
|
|
81
83
|
:default => 5
|
|
82
|
-
opt :maxdepth,
|
|
83
|
-
if set to zero no user max depth will be used
|
|
84
|
+
opt :maxdepth, 'maximum read depth at a position to consider for variant calls
|
|
85
|
+
if set to zero no user max depth will be used',
|
|
84
86
|
:type => Integer,
|
|
85
87
|
:default => 0
|
|
86
88
|
opt :min_non_ref_count, 'minimum read depth supporting non reference base at each position',
|
|
@@ -90,8 +92,8 @@ if set to zero no user max depth will be used",
|
|
|
90
92
|
:type => Integer,
|
|
91
93
|
:default => 3
|
|
92
94
|
opt :ambiguous_ref_bases, 'including variant at completely ambiguous bases in the reference',
|
|
93
|
-
:type =>
|
|
94
|
-
:default => false
|
|
95
|
+
:type => String,
|
|
96
|
+
:default => 'false'
|
|
95
97
|
opt :mapping_quality, 'minimum mapping quality of read covering the position',
|
|
96
98
|
:short => '-q',
|
|
97
99
|
:type => Integer,
|
|
@@ -107,15 +109,15 @@ if set to zero no user max depth will be used",
|
|
|
107
109
|
:type => String,
|
|
108
110
|
:default => 'back'
|
|
109
111
|
opt :use_all_contigs, 'option to select all contigs or only contigs containing variants for analysis',
|
|
110
|
-
:type =>
|
|
111
|
-
:default => false
|
|
112
|
+
:type => String,
|
|
113
|
+
:default => 'false'
|
|
112
114
|
opt :include_low_hmes, 'option to include or discard variants from contigs with
|
|
113
115
|
low hme-score or bfr score to list in the final output',
|
|
114
|
-
:type =>
|
|
115
|
-
:default => false
|
|
116
|
+
:type => String,
|
|
117
|
+
:default => 'false'
|
|
116
118
|
opt :polyploidy, 'Set if the data input is from polyploids',
|
|
117
|
-
:type =>
|
|
118
|
-
:default => false
|
|
119
|
+
:type => String,
|
|
120
|
+
:default => 'false'
|
|
119
121
|
opt :mut_parent, 'Pileup or sorted BAM file alignments from mutant/trait of interest parent',
|
|
120
122
|
:short => '-p',
|
|
121
123
|
:type => String,
|
|
@@ -187,11 +189,35 @@ low hme-score or bfr score to list in the final output',
|
|
|
187
189
|
|
|
188
190
|
# calls other methods to check if command line inputs are valid
|
|
189
191
|
def check_arguments
|
|
192
|
+
convert_boolean_strings
|
|
190
193
|
check_output
|
|
191
194
|
check_log_level
|
|
195
|
+
check_input_entry
|
|
192
196
|
check_input_types
|
|
193
197
|
end
|
|
194
198
|
|
|
199
|
+
# convert true or false options to boolean
|
|
200
|
+
def convert_boolean_strings
|
|
201
|
+
%i{ambiguous_ref_bases use_all_contigs include_low_hmes polyploidy}.each do | symbol |
|
|
202
|
+
if @options.key?(symbol)
|
|
203
|
+
@options[symbol] = @options[symbol] == 'false' ? false : true
|
|
204
|
+
end
|
|
205
|
+
end
|
|
206
|
+
end
|
|
207
|
+
|
|
208
|
+
# set file given option to false if input is nil or None or ''
|
|
209
|
+
def check_input_entry
|
|
210
|
+
%i{assembly mut_bulk bg_bulk mut_bulk_vcf bg_bulk_vcf mut_parent bg_parent repeats_file}.each do | symbol |
|
|
211
|
+
if @options.key?(symbol)
|
|
212
|
+
if @options[symbol] == 'None'
|
|
213
|
+
param = (symbol.to_s + '_given').to_sym
|
|
214
|
+
@options[symbol] = ''
|
|
215
|
+
@options.delete(param)
|
|
216
|
+
end
|
|
217
|
+
end
|
|
218
|
+
end
|
|
219
|
+
end
|
|
220
|
+
|
|
195
221
|
# checks input files based on bulk file type
|
|
196
222
|
def check_input_types
|
|
197
223
|
inputfiles = {}
|
data/lib/cheripic/implementer.rb
CHANGED
|
@@ -54,6 +54,7 @@ module Cheripic
|
|
|
54
54
|
sel_seq_len}
|
|
55
55
|
settings = inputs.select { |k| set2.include?(k) }
|
|
56
56
|
Options.update(settings)
|
|
57
|
+
logger.debug "parameter values set\n#{Options.current_values.to_yaml}"
|
|
57
58
|
@vars_extracted = false
|
|
58
59
|
@has_run = false
|
|
59
60
|
end
|
|
@@ -74,19 +75,21 @@ module Cheripic
|
|
|
74
75
|
end
|
|
75
76
|
# print selected variants that could be potential markers or mutation
|
|
76
77
|
out_file = File.open(@options[pos_type], 'w')
|
|
77
|
-
out_file.puts "Score\tAlleleFreq\tseq_id\tposition\tref_base\tcoverage\tbases\tbase_quals\tsequence_left\tAlt_seq\tsequence_right"
|
|
78
|
+
out_file.puts "Score\tAlleleFreq\tlength\tseq_id\tposition\tref_base\tcoverage\tbases\tbase_quals\tsequence_left\tAlt_seq\tsequence_right"
|
|
78
79
|
regions = Regions.new(@options.assembly)
|
|
79
80
|
@variants.send(pos_type).each_key do | frag |
|
|
80
81
|
contig_obj = @variants.assembly[frag]
|
|
81
82
|
if pos_type == :hmes_frags
|
|
82
83
|
positions = contig_obj.hm_pos.keys
|
|
84
|
+
score = contig_obj.hme_score
|
|
83
85
|
else
|
|
84
86
|
positions = contig_obj.hemi_pos.keys
|
|
87
|
+
score = contig_obj.bfr_score
|
|
85
88
|
end
|
|
86
89
|
positions.each do | pos |
|
|
87
90
|
pileup = @variants.pileups[frag].mut_bulk[pos]
|
|
88
91
|
seqs = regions.fetch_seq(frag,pos)
|
|
89
|
-
out_file.puts "#{
|
|
92
|
+
out_file.puts "#{score}\t#{contig_obj.hm_pos[pos]}\t#{contig_obj.length}\t#{pileup.to_s.chomp}\t#{seqs[0]}\t#{pileup.consensus}\t#{seqs[1]}"
|
|
90
93
|
end
|
|
91
94
|
end
|
|
92
95
|
out_file.close
|
data/lib/cheripic/options.rb
CHANGED
data/lib/cheripic/variants.rb
CHANGED
|
@@ -4,35 +4,6 @@ require 'forwardable'
|
|
|
4
4
|
|
|
5
5
|
module Cheripic
|
|
6
6
|
|
|
7
|
-
require 'bio-samtools'
|
|
8
|
-
require 'bio/db/sam'
|
|
9
|
-
require 'open3'
|
|
10
|
-
|
|
11
|
-
# An extension of Bio::DB::Sam object to modify depth method
|
|
12
|
-
class Bio::DB::Sam
|
|
13
|
-
|
|
14
|
-
# A method to retrieve depth information from bam object
|
|
15
|
-
# @param opts [Hash] a hash of following input options
|
|
16
|
-
# b [File] list of positions or regions in BED format
|
|
17
|
-
# l [INT] minQLen
|
|
18
|
-
# q [INT] base quality threshold
|
|
19
|
-
# Q [INT] mapping quality threshold
|
|
20
|
-
# r [chr:from-to] region
|
|
21
|
-
# @returns a block with each line reporting sequence_name, position and depth
|
|
22
|
-
def depth(opts={})
|
|
23
|
-
command = form_opt_string(self.samtools, 'depth', opts)
|
|
24
|
-
# capture returns string output, so careful not to give whole genome or big contigs for depth analysis
|
|
25
|
-
stdout, stderr, status = Open3.capture3(command)
|
|
26
|
-
unless status.success?
|
|
27
|
-
logger.error "resulted in exit code #{status.exitstatus} using #{command}"
|
|
28
|
-
logger.error "stderr output is: #{stderr}"
|
|
29
|
-
raise CheripicError
|
|
30
|
-
end
|
|
31
|
-
# return stdout
|
|
32
|
-
stdout
|
|
33
|
-
end
|
|
34
|
-
|
|
35
|
-
end
|
|
36
7
|
|
|
37
8
|
# Custom error handling for Variants class
|
|
38
9
|
class VariantsError < CheripicError; end
|
|
@@ -110,6 +81,8 @@ module Cheripic
|
|
|
110
81
|
logger.info "processing #{input} file"
|
|
111
82
|
if @params.input_format == 'pileup'
|
|
112
83
|
extract_pileup(infile, input)
|
|
84
|
+
elsif @params.input_format == 'vcf'
|
|
85
|
+
extract_vcfs(infile, input)
|
|
113
86
|
else
|
|
114
87
|
extract_bam_pileup(infile, input)
|
|
115
88
|
end
|
|
@@ -119,35 +92,21 @@ module Cheripic
|
|
|
119
92
|
@pileups_analyzed = true
|
|
120
93
|
end
|
|
121
94
|
|
|
122
|
-
#
|
|
123
|
-
# @param
|
|
124
|
-
#
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
data.split("\n").each do |line|
|
|
136
|
-
info = line.split("\t")
|
|
137
|
-
depths << info[2].to_i
|
|
138
|
-
end
|
|
139
|
-
variance = 0
|
|
140
|
-
mean_depth = depths.reduce(0, :+) / len.to_f
|
|
141
|
-
depths.each do |value|
|
|
142
|
-
variance += (value.to_f - mean_depth)**2
|
|
95
|
+
# Input vcf file is read and positions are selected that pass the thresholds
|
|
96
|
+
# @param vcffile [String] path to the pileup file to read
|
|
97
|
+
# @param sym [Symbol] Symbol of the pileup file used to write selected variants
|
|
98
|
+
# pileup information to respective ContigPileups object
|
|
99
|
+
def extract_vcfs(vcffile, sym)
|
|
100
|
+
# read vcf file and process each variant
|
|
101
|
+
File.foreach(vcffile) do |line|
|
|
102
|
+
next if line =~ /^#/
|
|
103
|
+
v = Bio::DB::Vcf.new(line)
|
|
104
|
+
unless v.alt == '.'
|
|
105
|
+
pileup_string = Vcf.to_pileup(v)
|
|
106
|
+
pileup = Pileup.new(pileup_string)
|
|
107
|
+
store_pileup_info(pileup, sym)
|
|
143
108
|
end
|
|
144
|
-
all_depths << mean_depth
|
|
145
|
-
contig_obj.sd_depth = Math.sqrt(variance)
|
|
146
|
-
contig_obj.mean_depth = mean_depth
|
|
147
109
|
end
|
|
148
|
-
# setting max depth as 3 times the average depth
|
|
149
|
-
mean_coverage = all_depths.reduce(0, :+) / @assembly.length.to_f
|
|
150
|
-
Options.maxdepth = Options.max_d_multiple * mean_coverage
|
|
151
110
|
end
|
|
152
111
|
|
|
153
112
|
# Input pileup file is read and positions are selected that pass the thresholds
|
|
@@ -159,8 +118,7 @@ module Cheripic
|
|
|
159
118
|
File.foreach(pileupfile) do |line|
|
|
160
119
|
pileup = Pileup.new(line)
|
|
161
120
|
if pileup.is_var
|
|
162
|
-
|
|
163
|
-
contig_obj.send(sym).store(pileup.pos, pileup)
|
|
121
|
+
store_pileup_info(pileup, sym)
|
|
164
122
|
end
|
|
165
123
|
end
|
|
166
124
|
end
|
|
@@ -175,44 +133,93 @@ module Cheripic
|
|
|
175
133
|
bamobject = Bio::DB::Sam.new(:bam=>bamfile, :fasta=>@params.assembly)
|
|
176
134
|
bamobject.index unless bamobject.indexed?
|
|
177
135
|
|
|
136
|
+
# or calculate from bamfile
|
|
137
|
+
set_max_depth(bamobject, bamfile) if Options.max_d_multiple > 0 and sym == :mut_bulk
|
|
178
138
|
# check if user has set max depth or set to zero to ignore
|
|
179
139
|
max_d = Options.maxdepth
|
|
180
|
-
|
|
181
|
-
if Options.max_d_multiple > 0
|
|
182
|
-
set_max_depth(bamobject, bamfile)
|
|
183
|
-
max_d = Options.maxdepth
|
|
184
|
-
logger.info "max depth used for #{sym} file\t#{max_d}"
|
|
185
|
-
end
|
|
140
|
+
logger.info "max depth used for #{sym} file\t#{max_d}"
|
|
186
141
|
|
|
187
142
|
@vcf_hash.each_key do | id |
|
|
188
143
|
positions = @vcf_hash[id][:het].keys
|
|
189
144
|
positions << @vcf_hash[id][:hom].keys
|
|
190
145
|
positions.flatten!
|
|
191
146
|
next if positions.empty?
|
|
192
|
-
contig_obj = @pileups[id]
|
|
193
147
|
positions.each do | pos |
|
|
194
148
|
command = "#{bamobject.samtools} mpileup -r #{id}:#{pos}-#{pos} -Q #{bq} -q #{mq} -B -f #{@params.assembly} #{bamfile}"
|
|
195
|
-
stdout
|
|
196
|
-
unless status.success?
|
|
197
|
-
logger.error "resulted in exit code #{status.exitstatus} using #{command}"
|
|
198
|
-
logger.error "stderr output is: #{stderr}"
|
|
199
|
-
raise CheripicError
|
|
200
|
-
end
|
|
201
|
-
stdout.chomp!
|
|
149
|
+
stdout = capture_command(command)
|
|
202
150
|
if stdout == '' or stdout.split("\t")[3].to_i == 0 or stdout =~ /^\t0/
|
|
203
151
|
logger.info "pileup data empty for\t#{id}\t#{pos}"
|
|
204
152
|
else
|
|
205
153
|
pileup = Pileup.new(stdout)
|
|
206
|
-
|
|
207
|
-
logger.info "pileup coverage is higher than max\t#{pileup.to_s}"
|
|
208
|
-
next
|
|
209
|
-
end
|
|
210
|
-
contig_obj.send(sym).store(pos, pileup)
|
|
154
|
+
store_pileup_info(pileup, sym)
|
|
211
155
|
end
|
|
212
156
|
end
|
|
213
157
|
end
|
|
214
158
|
end
|
|
215
159
|
|
|
160
|
+
# Bam object is read and each contig mean and std deviation of depth calculated
|
|
161
|
+
# @param bamobject [Bio::DB::Sam]
|
|
162
|
+
# Open3 capture returns string output, so careful not to give whole genome or big contigs for depth analysis
|
|
163
|
+
def set_max_depth(bamobject, bamfile)
|
|
164
|
+
logger.info "processing #{bamfile} file for depth"
|
|
165
|
+
all_depths = []
|
|
166
|
+
bq = Options.base_quality
|
|
167
|
+
mq = Options.mapping_quality
|
|
168
|
+
@assembly.each_key do | id |
|
|
169
|
+
contig_obj = @assembly[id]
|
|
170
|
+
len = contig_obj.length
|
|
171
|
+
command = "#{bamobject.samtools} depth -r #{id} -Q #{bq} -q #{mq} #{bamfile}"
|
|
172
|
+
data = capture_command(command)
|
|
173
|
+
if data == ''
|
|
174
|
+
logger.info "depth data empty for\t#{id}"
|
|
175
|
+
next
|
|
176
|
+
end
|
|
177
|
+
depths = []
|
|
178
|
+
data.split("\n").each do |line|
|
|
179
|
+
info = line.split("\t")
|
|
180
|
+
depths << info[2].to_i
|
|
181
|
+
end
|
|
182
|
+
variance = 0
|
|
183
|
+
mean_depth = depths.reduce(0, :+) / len.to_f
|
|
184
|
+
depths.each do |value|
|
|
185
|
+
variance += (value.to_f - mean_depth)**2
|
|
186
|
+
end
|
|
187
|
+
all_depths << mean_depth
|
|
188
|
+
contig_obj.sd_depth = Math.sqrt(variance)
|
|
189
|
+
contig_obj.mean_depth = mean_depth
|
|
190
|
+
end
|
|
191
|
+
# setting max depth as 3 times the average depth
|
|
192
|
+
mean_coverage = all_depths.reduce(0, :+) / @assembly.length.to_f
|
|
193
|
+
Options.maxdepth = Options.max_d_multiple * mean_coverage
|
|
194
|
+
end
|
|
195
|
+
|
|
196
|
+
def capture_command(command)
|
|
197
|
+
stdout, stderr, status = Open3.capture3(command)
|
|
198
|
+
unless status.success?
|
|
199
|
+
logger.error "resulted in exit code #{status.exitstatus} using #{command}"
|
|
200
|
+
logger.error "stderr output is: #{stderr}"
|
|
201
|
+
raise CheripicError
|
|
202
|
+
end
|
|
203
|
+
stdout.chomp
|
|
204
|
+
end
|
|
205
|
+
|
|
206
|
+
# stores pileup information provided to respective contig_pileup object using sym input
|
|
207
|
+
# @param pileup [Pileup] Pileup objects
|
|
208
|
+
# @param sym [Symbol] Symbol of the input file used to write selected variants
|
|
209
|
+
# pileup information stored to respective ContigPileups object
|
|
210
|
+
def store_pileup_info(pileup, sym)
|
|
211
|
+
# discarding variants with higher than max depth only for mut_bulk
|
|
212
|
+
if sym == :mut_bulk
|
|
213
|
+
unless Options.maxdepth == 0 or pileup.coverage <= Options.maxdepth
|
|
214
|
+
logger.info "pileup coverage is higher than max\t#{pileup.ref_name}\t#{pileup.pos}\t#{pileup.coverage}"
|
|
215
|
+
return nil
|
|
216
|
+
end
|
|
217
|
+
end
|
|
218
|
+
contig_obj = @pileups[pileup.ref_name]
|
|
219
|
+
contig_obj.send(sym).store(pileup.pos, pileup)
|
|
220
|
+
nil
|
|
221
|
+
end
|
|
222
|
+
|
|
216
223
|
# Once pileup files are analysed and variants are extracted from each bulk;
|
|
217
224
|
# bulks are compared to identify and isolate variants for downstream analysis.
|
|
218
225
|
# If polyploidy set to trye and mut_parent and bg_parent bulks are provided
|
data/lib/cheripic/vcf.rb
CHANGED
|
@@ -9,33 +9,38 @@ module Cheripic
|
|
|
9
9
|
|
|
10
10
|
class Vcf
|
|
11
11
|
|
|
12
|
-
def self.
|
|
12
|
+
def self.get_allele_depth(vcf_obj)
|
|
13
13
|
# check if the vcf is from samtools (has DP4 and AF1 fields in INFO)
|
|
14
14
|
if vcf_obj.info.key?('DP4')
|
|
15
15
|
freq = vcf_obj.info['DP4'].split(',')
|
|
16
|
-
|
|
16
|
+
ref = freq[0].to_f + freq[1].to_f
|
|
17
17
|
alt = freq[2].to_f + freq[3].to_f
|
|
18
|
-
allele_freq = alt / depth
|
|
19
|
-
# allele_freq = vcf_obj.non_ref_allele_freq
|
|
20
18
|
# check if the vcf is from VarScan (has RD, AD and FREQ fields in FORMAT)
|
|
21
19
|
elsif vcf_obj.samples['1'].key?('RD')
|
|
20
|
+
ref = vcf_obj.samples['1']['RD'].to_f
|
|
22
21
|
alt = vcf_obj.samples['1']['AD'].to_f
|
|
23
|
-
depth = vcf_obj.samples['1']['RD'].to_f + alt
|
|
24
|
-
allele_freq = alt / depth
|
|
25
22
|
# check if the vcf is from GATK (has AD and GT fields in FORMAT)
|
|
26
23
|
elsif vcf_obj.samples['1'].key?('AD') and vcf_obj.samples['1']['AD'].include?(',')
|
|
27
24
|
freq = vcf_obj.samples['1']['AD'].split(',')
|
|
28
|
-
|
|
25
|
+
ref = freq[0].to_i
|
|
26
|
+
alt = freq[1].to_i
|
|
29
27
|
# check if the vcf has has AF fields in INFO
|
|
30
28
|
elsif vcf_obj.info.key?('AF')
|
|
31
29
|
allele_freq = vcf_obj.info['AF'].to_f
|
|
30
|
+
depth = vcf_obj.info['DP'].to_i
|
|
31
|
+
alt = (depth * allele_freq).round
|
|
32
|
+
ref = depth - alt
|
|
32
33
|
else
|
|
33
34
|
raise VcfError.new 'not a supported vcf format (VarScan, GATK, Bcftools(Samtools), Vcf 4.0, 4.1 and 4.2)' +
|
|
34
35
|
" and check that it is one sample vcf\n"
|
|
35
36
|
end
|
|
36
|
-
|
|
37
|
+
[ref, alt]
|
|
37
38
|
end
|
|
38
39
|
|
|
40
|
+
def self.get_allele_freq(vcf_obj)
|
|
41
|
+
ref, alt = get_allele_depth(vcf_obj)
|
|
42
|
+
alt.to_f/(ref + alt)
|
|
43
|
+
end
|
|
39
44
|
|
|
40
45
|
##Input: vcf file
|
|
41
46
|
##Ouput: lists of hm and ht SNPS and hash of all fragments with variants
|
|
@@ -78,6 +83,25 @@ module Cheripic
|
|
|
78
83
|
var_pos_mut
|
|
79
84
|
end
|
|
80
85
|
|
|
86
|
+
def self.to_pileup(v)
|
|
87
|
+
ref, alt = Vcf.get_allele_depth(v)
|
|
88
|
+
depth = ref + alt
|
|
89
|
+
alt_bases = '' + v.alt
|
|
90
|
+
ref_len = v.ref.length
|
|
91
|
+
alt_len = v.alt.length
|
|
92
|
+
if ref_len > alt_len
|
|
93
|
+
seq = v.ref[alt_len..-1]
|
|
94
|
+
alt_bases = '-' + seq.length.to_s + seq
|
|
95
|
+
v.ref = v.ref[0]
|
|
96
|
+
elsif ref_len < alt_len
|
|
97
|
+
seq = v.alt[ref_len..-1]
|
|
98
|
+
alt_bases = '+' + seq.length.to_s + seq
|
|
99
|
+
end
|
|
100
|
+
bases = ('.' * ref) + ( alt_bases * alt)
|
|
101
|
+
quality = 'D' * depth
|
|
102
|
+
[v.chrom, v.pos, v.ref, depth, bases, quality].join("\t")
|
|
103
|
+
end
|
|
104
|
+
|
|
81
105
|
end
|
|
82
106
|
|
|
83
107
|
end
|
data/lib/cheripic/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: cheripic
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.2.
|
|
4
|
+
version: 1.2.6
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Shyam Rallapalli
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: exe
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2016-10-
|
|
11
|
+
date: 2016-10-26 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: yell
|