| Next changeset 1:3192cb6a88f6 (2017-05-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb |
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PSM2SAM.R PSM2SAM.xml README.md test-data/hg19/exon_anno.RData test-data/hg19/hg19_headers.sam test-data/hg19/hg19_variant_annotation.RData test-data/hg19/procodingseq.RData test-data/hg19/proseq.RData test-data/hg19/test.idpDB test-data/idpicker_hg19_no_variants.sam test-data/idpicker_hg19_with_variants.sam test-data/mm10/Sample_Mouse_pro-B_total.whole_exp.bam test-data/mm10/exon_anno.RData test-data/mm10/mm10_variant_annotation.RData test-data/mm10/procodingseq.RData test-data/mm10/proseq.RData test-data/mm10/test.psm-report test-data/peptideshaker_mm10.sam tool-data/customProDB.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 90ecb65017a0 PSM2SAM.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PSM2SAM.R Wed May 17 20:23:27 2017 -0400 |
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| @@ -0,0 +1,149 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$exon_anno <- make_option('--exon_anno', type='character') +option_list$proteinseq <- make_option('--proteinseq', type='character') +option_list$procodingseq <- make_option('--procodingseq', type='character') +option_list$bam_file <- make_option('--bam', type='character') +option_list$idpDB_file <- make_option('--idpDB', type='character') +option_list$pepXmlTab_file <- make_option('--pepXmlTab', type='character') +option_list$peptideShakerPsmReport_file <- make_option('--peptideShakerPsmReport', type='character') +option_list$variantAnnotation_file <- make_option('--variantAnnotation', type='character') +option_list$searchEngineScore <- make_option('--searchEngineScore', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + + +psm2sam <- function( + exon_anno_file = GalaxyInputFile(required=TRUE), + proteinseq_file = GalaxyInputFile(required=TRUE), + procodingseq_file = GalaxyInputFile(required=TRUE), + bam_file = GalaxyInputFile(required=TRUE), + idpDB_file = GalaxyInputFile(required=FALSE), + pepXmlTab_file = GalaxyInputFile(required=FALSE), + peptideShakerPsmReport_file = GalaxyInputFile(required=FALSE), + variantAnnotation_file = GalaxyInputFile(required=FALSE), + searchEngineScore = GalaxyCharacterParam(required=FALSE) + ) +{ + options(stringsAsFactors = FALSE) + + if (length(bam_file) == 0) + { + stop("BAM file must be specified to provide sequence headers") + } + + outputHeader = grep("^@(?!PG)", readLines(bam_file, n=500, warn=FALSE), value=TRUE, perl=TRUE) + if (length(outputHeader) == 0) + { + stop("failed to read header lines from bam_file") + } + + # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) + download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE) + unzip("customProDB.zip") + devtools::load_all("customProDB-master") + + # load proBAMr from GitHub + download.file("https://github.com/chambm/proBAMr/archive/master.zip", "proBAMr.zip", quiet=TRUE) + unzip("proBAMr.zip") + devtools::load_all("proBAMr-master") + + psmInputLength = length(idpDB_file)+length(pepXmlTab_file)+length(peptideShakerPsmReport_file) + if (psmInputLength == 0) + { + stop("one of the input PSM file parameters must be specified") + } + else if (psmInputLength > 1) + { + stop("only one of the input PSM file parameters can be specified") + } + + if (length(idpDB_file) > 0) + { + if (length(searchEngineScore) == 0) + stop("searchEngineScore parameter must be specified when reading IDPicker PSMs, e.g. 'MyriMatch:MVH'") + passedPSM = readIdpDB(idpDB_file, searchEngineScore) + } + else if (length(pepXmlTab_file) > 0) + { + if (length(searchEngineScore) == 0) + stop("searchEngineScore parameter must be specified when reading pepXmlTab PSMs, e.g. 'mvh'") + passedPSM = readPepXmlTab(pepXmlTab_file, searchEngineScore) + } + else if (length(peptideShakerPsmReport_file) > 0) + { + if (length(searchEngineScore) > 0) + warning("searchEngineScore parameter is ignored when reading PeptideShaker PSM report") + passedPSM = readPeptideShakerPsmReport(peptideShakerPsmReport_file) + } + + load(exon_anno_file) + load(proteinseq_file) + load(procodingseq_file) + + if (length(variantAnnotation_file) > 0) + { + load(variantAnnotation_file) # variantAnnotation list, with members snvprocoding/snvproseq and indelprocoding/indelproseq + + varprocoding = unique(rbind(variantAnnotation$snvprocoding, variantAnnotation$indelprocoding)) + varproseq = unique(rbind(variantAnnotation$snvproseq, variantAnnotation$indelproseq)) + } + else + { + varprocoding = NULL + varproseq = NULL + } + + # add proBAMr program key + outputHeader = c(outputHeader, paste0("@PG\tID:proBAMr\tVN:", packageVersion("proBAMr"))) + + # first write header lines to the output SAM + writeLines(outputHeader, "output.sam") + + # then write the PSM "reads" + PSMtab2SAM(passedPSM, exon, + proteinseq, procodingseq, + varproseq, varprocoding, + outfile = "output.sam", + show_progress = FALSE) + + invisible(NULL) +} + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(psm2sam, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +}) |
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| diff -r 000000000000 -r 90ecb65017a0 PSM2SAM.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PSM2SAM.xml Wed May 17 20:23:27 2017 -0400 |
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| b'@@ -0,0 +1,167 @@\n+<tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2">\n+ <description>Generate SAM files from PSMs.</description>\n+ <requirements>\n+ <requirement type="package" version="3.3.1">r-base</requirement>\n+ <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->\n+ <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>\n+ <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>\n+ <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>\n+ <requirement type="package" version="1.11.1">r-devtools</requirement>\n+ <requirement type="package" version="3.98_1.4">r-xml</requirement>\n+ <requirement type="package" version="0.10.11">r-rmysql</requirement>\n+ <requirement type="package" version="1.0.2">r-testthat</requirement>\n+ <requirement type="package" version="0.1.0">r-getoptlong</requirement>\n+ <requirement type="package" version="1.1.2">r-stringi</requirement>\n+ <requirement type="package" version="1.1.0">r-stringr</requirement>\n+ <requirement type="package" version="1.10.0">r-data.table</requirement>\n+ <requirement type="package" version="0.4_10">r-sqldf</requirement>\n+ <requirement type="package" version="0.6_6">r-gsubfn</requirement>\n+ <requirement type="package" version="2.3_47">r-chron</requirement>\n+ <requirement type="package" version="0.3.10">r-proto</requirement>\n+ <requirement type="package" version="1.8.4">r-plyr</requirement>\n+ <requirement type="package" version="1.1_0">r-fastmatch</requirement>\n+ <requirement type="package" version="0.1.0">r-ahocorasicktrie</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Job Failed" />\n+ </stdio>\n+ <command><![CDATA[\n+ Rscript --vanilla \'$__tool_directory__/PSM2SAM.R\'\n+\n+ #if str($input.input_type) == "idpicker":\n+ --idpDB="$input.input_file"\n+ --searchEngineScore="$input.scoreColumn"\n+ #else if str($input.input_type) == "peptideshaker":\n+ --peptideShakerPsmReport="$input.input_file"\n+ #else if str($input.input_type) == "pepxmltab":\n+ --pepXmlTab="$input.input_file"\n+ --searchEngineScore="$input.scoreColumn"\n+ #end if\n+\n+ --bam="$bam_file"\n+\n+ #if str($variantAnnotation_file) != \'None\':\n+ --variantAnnotation="$variantAnnotation_file"\n+ #end if\n+\n+ #if str($genome_annotation.source) == "history":\n+ --exon_anno="$genome_annotation.exonAnno"\n+ --proteinseq="$genome_annotation.proteinSeq"\n+ --procodingseq="$genome_annotation.proCodingSeq"\n+ #else:\n+ #set index_path = $genome_annotation.builtin.fields.path\n+ --exon_anno="$index_path/exon_anno.RData"\n+ --proteinseq="$index_path/proseq.RData"\n+ --procodingseq="$index_path/procodingseq.RData"\n+ #end if\n+ 2>&1\n+]]>\n+ </command>\n+ <inputs>\n+ <conditional name="input">\n+ <param name="input_type" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">\n+ <option value="idpicker">IDPicker idpDB</option>\n+ <option value="peptideshaker">PeptideShaker PSM report</option>\n+ <option value="pepxmltab">PepXmlTab</option>\n+ </param>\n+ <when value="idpicker">\n+ <param name="input_file" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">\n+ <validator type="empty_field" message="This field is required."/>\n+ </param>\n+ <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. "MyriMatch:mvh")" size="60" label="Score Name">\n+ <validator type="empty_field" message="This field is required."/>\n+ </param>\n+ </when>\n+ <when value="peptideshaker"'..b' </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />\n+ <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />\n+ <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />\n+ </when>\n+ </conditional>\n+ <param name="bam_file" type="data" format="bam,sam" help="A SAM or BAM file to extract headers from (i.e. sequence metadata from reference genome)" label="SAM/BAM Headers">\n+ <validator type="empty_field" message="This field is required."/>\n+ </param>\n+ <param name="variantAnnotation_file" type="data" format="RData" help="A variant annotation .RData file from customProDB." label="Variant Annotation" optional="true" />\n+ </inputs>\n+ <outputs>\n+ <data format="sam" name="output_sam" from_work_dir="output.sam" label="${input.input_file.name.rsplit(\'.\',1)[0]}.sam"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_type" value="idpicker" />\n+ <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" />\n+ <param name="scoreColumn" value="Myrimatch:MVH" />\n+ <param name="source" value="history" />\n+ <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" />\n+ <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" />\n+ <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" />\n+ <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" />\n+ <param name="variantAnnotation_file" value="hg19/hg19_variant_annotation.RData" dbkey="hg19" />\n+ <output name="output" file="idpicker_hg19_with_variants.sam" />\n+ </test>\n+ <test>\n+ <param name="input_type" value="idpicker" />\n+ <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" />\n+ <param name="scoreColumn" value="Myrimatch:MVH" />\n+ <param name="source" value="history" />\n+ <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" />\n+ <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" />\n+ <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" />\n+ <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" />\n+ <output name="output" file="idpicker_hg19_no_variants.sam" />\n+ </test>\n+ <!--<test>\n+ <param name="input_type" value="pepxmltab" />\n+ <param name="input_file" value="passedPSM.tab" dbkey="hg19" />\n+ <param name="scoreColumn" value="Myrimatch:MVH" />\n+ <param name="source" value="history" />\n+ <param name="exonAnno" value="gencode/exon_anno.RData" dbkey="hg19" />\n+ <param name="proteinSeq" value="gencode/proseq.RData" dbkey="hg19" />\n+ <param name="proCodingSeq" value="gencode/procodingseq.RData" dbkey="hg19" />\n+ <output name="output" file="pepXmlTab_gencode.sam" />\n+ </test>-->\n+ <test>\n+ <param name="input_type" value="peptideshaker" />\n+ <param name="input_file" value="mm10/test.psm-report" dbkey="mm9" />\n+ <param name="source" value="history" />\n+ <param name="exonAnno" value="mm10/exon_anno.RData" dbkey="mm9" />\n+ <param name="proteinSeq" value="mm10/proseq.RData" dbkey="mm9" />\n+ <param name="proCodingSeq" value="mm10/procodingseq.RData" dbkey="mm9" />\n+ <param name="bam_file" value="mm10/Sample_Mouse_pro-B_total.whole_exp.bam" dbkey="mm9" />\n+ <param name="variantAnnotation_file" value="mm10/mm10_variant_annotation.RData" dbkey="mm9" />\n+ <output name="output" file="peptideshaker_mm10.sam" />\n+ </test>\n+ </tests>\n+ <help>\n+**Description**\n+\n+Generate SAM files from confident peptide-spectrum-matches (PSMs).\n+</help>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 90ecb65017a0 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed May 17 20:23:27 2017 -0400 |
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| @@ -0,0 +1,58 @@ +GalaxyP - PSM2SAM +=================== + +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/psm_to_sam> +* Tool ID: `psm_to_sam` + + +Description +----------- + +The interpretation of proteomics data is significantly enhanced by genomic annotation. +Using proBAMr, peptide-spectrum-matches can be easily reannotated using user-specified gene annotation +schemes and assembled into both protein and gene identifications. Using the genome as a common reference, +proBAMr facilitates seamless proteomics and proteogenomics data integration. ProBAM files can be readily +visualized in genome browsers and thus bring proteomics data analysis to a general audience beyond the +proteomics community. + +See: + +* <https://www.bioconductor.org/packages/release/bioc/html/proBAMr.html> + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: + +<https://github.com/galaxyproteomics> + + +License +------- + +Copyright (c) 2017 Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* Matt Chambers <matt.chambers42@gmail.com> + +* Xiaojing Wang <xiaojing.wang@bcm.edu> + Baylor Medical College |
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| @@ -0,0 +1,95 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr10 LN:135534747 +@SQ SN:chr11 LN:135006516 +@SQ SN:chr11_gl000202_random LN:40103 +@SQ SN:chr12 LN:133851895 +@SQ SN:chr13 LN:115169878 +@SQ SN:chr14 LN:107349540 +@SQ SN:chr15 LN:102531392 +@SQ SN:chr16 LN:90354753 +@SQ SN:chr17_ctg5_hap1 LN:1680828 +@SQ SN:chr17 LN:81195210 +@SQ SN:chr17_gl000203_random LN:37498 +@SQ SN:chr17_gl000204_random LN:81310 +@SQ SN:chr17_gl000205_random LN:174588 +@SQ SN:chr17_gl000206_random LN:41001 +@SQ SN:chr18 LN:78077248 +@SQ SN:chr18_gl000207_random LN:4262 +@SQ SN:chr19 LN:59128983 +@SQ SN:chr19_gl000208_random LN:92689 +@SQ SN:chr19_gl000209_random LN:159169 +@SQ SN:chr1 LN:249250621 +@SQ SN:chr1_gl000191_random LN:106433 +@SQ SN:chr1_gl000192_random LN:547496 +@SQ SN:chr20 LN:63025520 +@SQ SN:chr21 LN:48129895 +@SQ SN:chr21_gl000210_random LN:27682 +@SQ SN:chr22 LN:51304566 +@SQ SN:chr2 LN:243199373 +@SQ SN:chr3 LN:198022430 +@SQ SN:chr4_ctg9_hap1 LN:590426 +@SQ SN:chr4 LN:191154276 +@SQ SN:chr4_gl000193_random LN:189789 +@SQ SN:chr4_gl000194_random LN:191469 +@SQ SN:chr5 LN:180915260 +@SQ SN:chr6_apd_hap1 LN:4622290 +@SQ SN:chr6_cox_hap2 LN:4795371 +@SQ SN:chr6_dbb_hap3 LN:4610396 +@SQ SN:chr6 LN:171115067 +@SQ SN:chr6_mann_hap4 LN:4683263 +@SQ SN:chr6_mcf_hap5 LN:4833398 +@SQ SN:chr6_qbl_hap6 LN:4611984 +@SQ SN:chr6_ssto_hap7 LN:4928567 +@SQ SN:chr7 LN:159138663 +@SQ SN:chr7_gl000195_random LN:182896 +@SQ SN:chr8 LN:146364022 +@SQ SN:chr8_gl000196_random LN:38914 +@SQ SN:chr8_gl000197_random LN:37175 +@SQ SN:chr9 LN:141213431 +@SQ SN:chr9_gl000198_random LN:90085 +@SQ SN:chr9_gl000199_random LN:169874 +@SQ SN:chr9_gl000200_random LN:187035 +@SQ SN:chr9_gl000201_random LN:36148 +@SQ SN:chrM LN:16571 +@SQ SN:chrUn_gl000211 LN:166566 +@SQ SN:chrUn_gl000212 LN:186858 +@SQ SN:chrUn_gl000213 LN:164239 +@SQ SN:chrUn_gl000214 LN:137718 +@SQ SN:chrUn_gl000215 LN:172545 +@SQ SN:chrUn_gl000216 LN:172294 +@SQ SN:chrUn_gl000217 LN:172149 +@SQ SN:chrUn_gl000218 LN:161147 +@SQ SN:chrUn_gl000219 LN:179198 +@SQ SN:chrUn_gl000220 LN:161802 +@SQ SN:chrUn_gl000221 LN:155397 +@SQ SN:chrUn_gl000222 LN:186861 +@SQ SN:chrUn_gl000223 LN:180455 +@SQ SN:chrUn_gl000224 LN:179693 +@SQ SN:chrUn_gl000225 LN:211173 +@SQ SN:chrUn_gl000226 LN:15008 +@SQ SN:chrUn_gl000227 LN:128374 +@SQ SN:chrUn_gl000228 LN:129120 +@SQ SN:chrUn_gl000229 LN:19913 +@SQ SN:chrUn_gl000230 LN:43691 +@SQ SN:chrUn_gl000231 LN:27386 +@SQ SN:chrUn_gl000232 LN:40652 +@SQ SN:chrUn_gl000233 LN:45941 +@SQ SN:chrUn_gl000234 LN:40531 +@SQ SN:chrUn_gl000235 LN:34474 +@SQ SN:chrUn_gl000236 LN:41934 +@SQ SN:chrUn_gl000237 LN:45867 +@SQ SN:chrUn_gl000238 LN:39939 +@SQ SN:chrUn_gl000239 LN:33824 +@SQ SN:chrUn_gl000240 LN:41933 +@SQ SN:chrUn_gl000241 LN:42152 +@SQ SN:chrUn_gl000242 LN:43523 +@SQ SN:chrUn_gl000243 LN:43341 +@SQ SN:chrUn_gl000244 LN:39929 +@SQ SN:chrUn_gl000245 LN:36651 +@SQ SN:chrUn_gl000246 LN:38154 +@SQ SN:chrUn_gl000247 LN:36422 +@SQ SN:chrUn_gl000248 LN:39786 +@SQ SN:chrUn_gl000249 LN:38502 +@SQ SN:chrX LN:155270560 +@SQ SN:chrY LN:59373566 +@PG ID:proBAMr VN:2.0.0 |
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| diff -r 000000000000 -r 90ecb65017a0 test-data/idpicker_hg19_no_variants.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/idpicker_hg19_no_variants.sam Wed May 17 20:23:27 2017 -0400 |
| b |
| b'@@ -0,0 +1,752 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:chr10\tLN:135534747\n+@SQ\tSN:chr11\tLN:135006516\n+@SQ\tSN:chr11_gl000202_random\tLN:40103\n+@SQ\tSN:chr12\tLN:133851895\n+@SQ\tSN:chr13\tLN:115169878\n+@SQ\tSN:chr14\tLN:107349540\n+@SQ\tSN:chr15\tLN:102531392\n+@SQ\tSN:chr16\tLN:90354753\n+@SQ\tSN:chr17_ctg5_hap1\tLN:1680828\n+@SQ\tSN:chr17\tLN:81195210\n+@SQ\tSN:chr17_gl000203_random\tLN:37498\n+@SQ\tSN:chr17_gl000204_random\tLN:81310\n+@SQ\tSN:chr17_gl000205_random\tLN:174588\n+@SQ\tSN:chr17_gl000206_random\tLN:41001\n+@SQ\tSN:chr18\tLN:78077248\n+@SQ\tSN:chr18_gl000207_random\tLN:4262\n+@SQ\tSN:chr19\tLN:59128983\n+@SQ\tSN:chr19_gl000208_random\tLN:92689\n+@SQ\tSN:chr19_gl000209_random\tLN:159169\n+@SQ\tSN:chr1\tLN:249250621\n+@SQ\tSN:chr1_gl000191_random\tLN:106433\n+@SQ\tSN:chr1_gl000192_random\tLN:547496\n+@SQ\tSN:chr20\tLN:63025520\n+@SQ\tSN:chr21\tLN:48129895\n+@SQ\tSN:chr21_gl000210_random\tLN:27682\n+@SQ\tSN:chr22\tLN:51304566\n+@SQ\tSN:chr2\tLN:243199373\n+@SQ\tSN:chr3\tLN:198022430\n+@SQ\tSN:chr4_ctg9_hap1\tLN:590426\n+@SQ\tSN:chr4\tLN:191154276\n+@SQ\tSN:chr4_gl000193_random\tLN:189789\n+@SQ\tSN:chr4_gl000194_random\tLN:191469\n+@SQ\tSN:chr5\tLN:180915260\n+@SQ\tSN:chr6_apd_hap1\tLN:4622290\n+@SQ\tSN:chr6_cox_hap2\tLN:4795371\n+@SQ\tSN:chr6_dbb_hap3\tLN:4610396\n+@SQ\tSN:chr6\tLN:171115067\n+@SQ\tSN:chr6_mann_hap4\tLN:4683263\n+@SQ\tSN:chr6_mcf_hap5\tLN:4833398\n+@SQ\tSN:chr6_qbl_hap6\tLN:4611984\n+@SQ\tSN:chr6_ssto_hap7\tLN:4928567\n+@SQ\tSN:chr7\tLN:159138663\n+@SQ\tSN:chr7_gl000195_random\tLN:182896\n+@SQ\tSN:chr8\tLN:146364022\n+@SQ\tSN:chr8_gl000196_random\tLN:38914\n+@SQ\tSN:chr8_gl000197_random\tLN:37175\n+@SQ\tSN:chr9\tLN:141213431\n+@SQ\tSN:chr9_gl000198_random\tLN:90085\n+@SQ\tSN:chr9_gl000199_random\tLN:169874\n+@SQ\tSN:chr9_gl000200_random\tLN:187035\n+@SQ\tSN:chr9_gl000201_random\tLN:36148\n+@SQ\tSN:chrM\tLN:16571\n+@SQ\tSN:chrUn_gl000211\tLN:166566\n+@SQ\tSN:chrUn_gl000212\tLN:186858\n+@SQ\tSN:chrUn_gl000213\tLN:164239\n+@SQ\tSN:chrUn_gl000214\tLN:137718\n+@SQ\tSN:chrUn_gl000215\tLN:172545\n+@SQ\tSN:chrUn_gl000216\tLN:172294\n+@SQ\tSN:chrUn_gl000217\tLN:172149\n+@SQ\tSN:chrUn_gl000218\tLN:161147\n+@SQ\tSN:chrUn_gl000219\tLN:179198\n+@SQ\tSN:chrUn_gl000220\tLN:161802\n+@SQ\tSN:chrUn_gl000221\tLN:155397\n+@SQ\tSN:chrUn_gl000222\tLN:186861\n+@SQ\tSN:chrUn_gl000223\tLN:180455\n+@SQ\tSN:chrUn_gl000224\tLN:179693\n+@SQ\tSN:chrUn_gl000225\tLN:211173\n+@SQ\tSN:chrUn_gl000226\tLN:15008\n+@SQ\tSN:chrUn_gl000227\tLN:128374\n+@SQ\tSN:chrUn_gl000228\tLN:129120\n+@SQ\tSN:chrUn_gl000229\tLN:19913\n+@SQ\tSN:chrUn_gl000230\tLN:43691\n+@SQ\tSN:chrUn_gl000231\tLN:27386\n+@SQ\tSN:chrUn_gl000232\tLN:40652\n+@SQ\tSN:chrUn_gl000233\tLN:45941\n+@SQ\tSN:chrUn_gl000234\tLN:40531\n+@SQ\tSN:chrUn_gl000235\tLN:34474\n+@SQ\tSN:chrUn_gl000236\tLN:41934\n+@SQ\tSN:chrUn_gl000237\tLN:45867\n+@SQ\tSN:chrUn_gl000238\tLN:39939\n+@SQ\tSN:chrUn_gl000239\tLN:33824\n+@SQ\tSN:chrUn_gl000240\tLN:41933\n+@SQ\tSN:chrUn_gl000241\tLN:42152\n+@SQ\tSN:chrUn_gl000242\tLN:43523\n+@SQ\tSN:chrUn_gl000243\tLN:43341\n+@SQ\tSN:chrUn_gl000244\tLN:39929\n+@SQ\tSN:chrUn_gl000245\tLN:36651\n+@SQ\tSN:chrUn_gl000246\tLN:38154\n+@SQ\tSN:chrUn_gl000247\tLN:36422\n+@SQ\tSN:chrUn_gl000248\tLN:39786\n+@SQ\tSN:chrUn_gl000249\tLN:38502\n+@SQ\tSN:chrX\tLN:155270560\n+@SQ\tSN:chrY\tLN:59373566\n+@PG\tID:proBAMr\tVN:2.0.0\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR08 0.1.3165\t4\t*\t0\t255\t*M\t*\t0\t0\t\t*\tXA:Z:2\tNH:i:1\tXL:i:1\tXP:Z:AAAPAPVSEAVSR\tXR:Z:AAAPAPVSEAVSR\tXC:i:2\tXS:f:28.7324\tXQ:f:7.658424e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:U\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR08 0.1.3231\t4\t*\t0\t255\t*M\t*\t0\t0\t\t*\tXA:Z:2\tNH:i:1\tXL:i:1\tXP:Z:AAAPAPVSEAVSR\tXR:Z:AAAPAPVSEAVSR\tXC:i:2\tXS:f:34.2375\tXQ:f:7.045235e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:U\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR06 0.1.5198\t16\tchr17\t39680208\t255\t39M\t*\t0\t0\tCATGGTTAGCTTCTCGTTGCCCGCCAGCAGCCCGTCGGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AALEDTLAETEAR\tXR:Z:AALEDTLAETEAR\tXC:i:2\tXS:f:49.4039\tXQ:f:5.627961e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR06 0.1.5260\t16\tchr17\t39680208\t255\t39M\t*\t0\t0\tCATGGTTAGCTTCTCGTTGCCCGCCAGCAGCCCGTCGGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AALEDTLAETEAR\tXR:Z:AALEDTLAETEAR\tXC:i:2\tXS:f:43.6036\tXQ:f:6.336773e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCG'..b'255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:46.9182\tXQ:f:6.898008e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR11 0.1.2646\t16\tchr2\t85625240\t255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:59.8479\tXQ:f:4.543858e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.1100\t16\tchr2\t85625240\t255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:36.2767\tXQ:f:6.915431e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.2567\t16\tchr2\t85625240\t255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:38.6069\tXQ:f:6.769638e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.4801\t0\tchr12\t6647298\t255\t33M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASK\tXR:Z:VVDLMAHMASK\tXC:i:2\tXS:f:48.9717\tXQ:f:5.157285e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.4863\t0\tchr12\t6647298\t255\t33M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASK\tXR:Z:VVDLMAHMASK\tXC:i:2\tXS:f:42.2369\tXQ:f:5.979038e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4904\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:41.5452\tXQ:f:6.690421e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4966\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:45.2893\tXQ:f:6.215797e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.5035\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:49.2959\tXQ:f:5.707892e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.5107\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:47.64\tXQ:f:5.917798e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR05 0.1.4342\t0\tchr16\t29791447\t255\t27M\t*\t0\t0\tGTGTGGAGCGACTATGTGGGTGGTCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VWSDYVGGR\tXR:Z:VWSDYVGGR\tXC:i:2\tXS:f:41.0668\tXQ:f:6.496164e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR05 0.1.4414\t0\tchr16\t29791447\t255\t27M\t*\t0\t0\tGTGTGGAGCGACTATGTGGGTGGTCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VWSDYVGGR\tXR:Z:VWSDYVGGR\tXC:i:2\tXS:f:32.2425\tXQ:f:7.736297e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4754\t0\tchr5\t132424825\t255\t29M400N22M\t*\t0\t0\tTGGAATTCTCCAGCTGAAGAAGGGTCAAGTGACTGTGAAGTCTTTTCCAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:WNSPAEEGSSDCEVFSK\tXR:Z:WNSPAEEGSSDCEVFSK\tXC:i:2\tXS:f:50.5021\tXQ:f:5.554988e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4820\t0\tchr5\t132424825\t255\t29M400N22M\t*\t0\t0\tTGGAATTCTCCAGCTGAAGAAGGGTCAAGTGACTGTGAAGTCTTTTCCAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:WNSPAEEGSSDCEVFSK\tXR:Z:WNSPAEEGSSDCEVFSK\tXC:i:2\tXS:f:56.7369\tXQ:f:4.764629e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.3091\t16\tchr2\t85628423\t255\t30M199N6M\t*\t0\t0\tGTTGCCCTCCTTCAGAGCAGGCTTGGGGCCCAGGAC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:YQEGGVESAFHK\tXR:Z:YQEGGVESAFHK\tXC:i:2\tXS:f:39.9334\tXQ:f:6.894736e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.3160\t16\tchr2\t85628423\t255\t30M199N6M\t*\t0\t0\tGTTGCCCTCCTTCAGAGCAGGCTTGGGGCCCAGGAC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:YQEGGVESAFHK\tXR:Z:YQEGGVESAFHK\tXC:i:2\tXS:f:34.2558\tXQ:f:7.614462e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n' |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/idpicker_hg19_with_variants.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/idpicker_hg19_with_variants.sam Wed May 17 20:23:27 2017 -0400 |
| b |
| b'@@ -0,0 +1,752 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:chr10\tLN:135534747\n+@SQ\tSN:chr11\tLN:135006516\n+@SQ\tSN:chr11_gl000202_random\tLN:40103\n+@SQ\tSN:chr12\tLN:133851895\n+@SQ\tSN:chr13\tLN:115169878\n+@SQ\tSN:chr14\tLN:107349540\n+@SQ\tSN:chr15\tLN:102531392\n+@SQ\tSN:chr16\tLN:90354753\n+@SQ\tSN:chr17_ctg5_hap1\tLN:1680828\n+@SQ\tSN:chr17\tLN:81195210\n+@SQ\tSN:chr17_gl000203_random\tLN:37498\n+@SQ\tSN:chr17_gl000204_random\tLN:81310\n+@SQ\tSN:chr17_gl000205_random\tLN:174588\n+@SQ\tSN:chr17_gl000206_random\tLN:41001\n+@SQ\tSN:chr18\tLN:78077248\n+@SQ\tSN:chr18_gl000207_random\tLN:4262\n+@SQ\tSN:chr19\tLN:59128983\n+@SQ\tSN:chr19_gl000208_random\tLN:92689\n+@SQ\tSN:chr19_gl000209_random\tLN:159169\n+@SQ\tSN:chr1\tLN:249250621\n+@SQ\tSN:chr1_gl000191_random\tLN:106433\n+@SQ\tSN:chr1_gl000192_random\tLN:547496\n+@SQ\tSN:chr20\tLN:63025520\n+@SQ\tSN:chr21\tLN:48129895\n+@SQ\tSN:chr21_gl000210_random\tLN:27682\n+@SQ\tSN:chr22\tLN:51304566\n+@SQ\tSN:chr2\tLN:243199373\n+@SQ\tSN:chr3\tLN:198022430\n+@SQ\tSN:chr4_ctg9_hap1\tLN:590426\n+@SQ\tSN:chr4\tLN:191154276\n+@SQ\tSN:chr4_gl000193_random\tLN:189789\n+@SQ\tSN:chr4_gl000194_random\tLN:191469\n+@SQ\tSN:chr5\tLN:180915260\n+@SQ\tSN:chr6_apd_hap1\tLN:4622290\n+@SQ\tSN:chr6_cox_hap2\tLN:4795371\n+@SQ\tSN:chr6_dbb_hap3\tLN:4610396\n+@SQ\tSN:chr6\tLN:171115067\n+@SQ\tSN:chr6_mann_hap4\tLN:4683263\n+@SQ\tSN:chr6_mcf_hap5\tLN:4833398\n+@SQ\tSN:chr6_qbl_hap6\tLN:4611984\n+@SQ\tSN:chr6_ssto_hap7\tLN:4928567\n+@SQ\tSN:chr7\tLN:159138663\n+@SQ\tSN:chr7_gl000195_random\tLN:182896\n+@SQ\tSN:chr8\tLN:146364022\n+@SQ\tSN:chr8_gl000196_random\tLN:38914\n+@SQ\tSN:chr8_gl000197_random\tLN:37175\n+@SQ\tSN:chr9\tLN:141213431\n+@SQ\tSN:chr9_gl000198_random\tLN:90085\n+@SQ\tSN:chr9_gl000199_random\tLN:169874\n+@SQ\tSN:chr9_gl000200_random\tLN:187035\n+@SQ\tSN:chr9_gl000201_random\tLN:36148\n+@SQ\tSN:chrM\tLN:16571\n+@SQ\tSN:chrUn_gl000211\tLN:166566\n+@SQ\tSN:chrUn_gl000212\tLN:186858\n+@SQ\tSN:chrUn_gl000213\tLN:164239\n+@SQ\tSN:chrUn_gl000214\tLN:137718\n+@SQ\tSN:chrUn_gl000215\tLN:172545\n+@SQ\tSN:chrUn_gl000216\tLN:172294\n+@SQ\tSN:chrUn_gl000217\tLN:172149\n+@SQ\tSN:chrUn_gl000218\tLN:161147\n+@SQ\tSN:chrUn_gl000219\tLN:179198\n+@SQ\tSN:chrUn_gl000220\tLN:161802\n+@SQ\tSN:chrUn_gl000221\tLN:155397\n+@SQ\tSN:chrUn_gl000222\tLN:186861\n+@SQ\tSN:chrUn_gl000223\tLN:180455\n+@SQ\tSN:chrUn_gl000224\tLN:179693\n+@SQ\tSN:chrUn_gl000225\tLN:211173\n+@SQ\tSN:chrUn_gl000226\tLN:15008\n+@SQ\tSN:chrUn_gl000227\tLN:128374\n+@SQ\tSN:chrUn_gl000228\tLN:129120\n+@SQ\tSN:chrUn_gl000229\tLN:19913\n+@SQ\tSN:chrUn_gl000230\tLN:43691\n+@SQ\tSN:chrUn_gl000231\tLN:27386\n+@SQ\tSN:chrUn_gl000232\tLN:40652\n+@SQ\tSN:chrUn_gl000233\tLN:45941\n+@SQ\tSN:chrUn_gl000234\tLN:40531\n+@SQ\tSN:chrUn_gl000235\tLN:34474\n+@SQ\tSN:chrUn_gl000236\tLN:41934\n+@SQ\tSN:chrUn_gl000237\tLN:45867\n+@SQ\tSN:chrUn_gl000238\tLN:39939\n+@SQ\tSN:chrUn_gl000239\tLN:33824\n+@SQ\tSN:chrUn_gl000240\tLN:41933\n+@SQ\tSN:chrUn_gl000241\tLN:42152\n+@SQ\tSN:chrUn_gl000242\tLN:43523\n+@SQ\tSN:chrUn_gl000243\tLN:43341\n+@SQ\tSN:chrUn_gl000244\tLN:39929\n+@SQ\tSN:chrUn_gl000245\tLN:36651\n+@SQ\tSN:chrUn_gl000246\tLN:38154\n+@SQ\tSN:chrUn_gl000247\tLN:36422\n+@SQ\tSN:chrUn_gl000248\tLN:39786\n+@SQ\tSN:chrUn_gl000249\tLN:38502\n+@SQ\tSN:chrX\tLN:155270560\n+@SQ\tSN:chrY\tLN:59373566\n+@PG\tID:proBAMr\tVN:2.0.0\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR08 0.1.3165\t0\tchr5\t96086300\t255\t39M\t*\t0\t0\tGCCGCTGCTCCAGCTCCTGTGTCGGAGGCTGTGTCTCGG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AAAPAPVSEAVSR\tXR:Z:AAAPAPVSEAVCR\tXC:i:2\tXS:f:28.7324\tXQ:f:7.658424e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:V\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR08 0.1.3231\t0\tchr5\t96086300\t255\t39M\t*\t0\t0\tGCCGCTGCTCCAGCTCCTGTGTCGGAGGCTGTGTCTCGG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AAAPAPVSEAVSR\tXR:Z:AAAPAPVSEAVCR\tXC:i:2\tXS:f:34.2375\tXQ:f:7.045235e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:V\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR06 0.1.5198\t16\tchr17\t39680208\t255\t39M\t*\t0\t0\tCATGGTTAGCTTCTCGTTGCCCGCCAGCAGCCCGTCGGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AALEDTLAETEAR\tXR:Z:AALEDTLAETEAR\tXC:i:2\tXS:f:49.4039\tXQ:f:5.627961e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR06 0.1.5260\t16\tchr17\t39680208\t255\t39M\t*\t0\t0\tCATGGTTAGCTTCTCGTTGCCCGCCAGCAGCCCGTCGGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AAL'..b'255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:46.9182\tXQ:f:6.898008e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR11 0.1.2646\t16\tchr2\t85625240\t255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:59.8479\tXQ:f:4.543858e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.1100\t16\tchr2\t85625240\t255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:36.2767\tXQ:f:6.915431e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.2567\t16\tchr2\t85625240\t255\t36M\t*\t0\t0\tGCGGTGCTGCACAGGCCGCTCTCCCAGCAGCGTGTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VSDATGQMNLTK\tXR:Z:VSDATGQMNLTK\tXC:i:2\tXS:f:38.6069\tXQ:f:6.769638e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.4801\t0\tchr12\t6647298\t255\t33M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASK\tXR:Z:VVDLMAHMASK\tXC:i:2\tXS:f:48.9717\tXQ:f:5.157285e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR12 0.1.4863\t0\tchr12\t6647298\t255\t33M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASK\tXR:Z:VVDLMAHMASK\tXC:i:2\tXS:f:42.2369\tXQ:f:5.979038e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4904\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:41.5452\tXQ:f:6.690421e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4966\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:45.2893\tXQ:f:6.215797e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.5035\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:49.2959\tXQ:f:5.707892e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.5107\t0\tchr12\t6647298\t255\t36M\t*\t0\t0\tGTGGTGGACCTCATGGCCCACATGGCCTCCAAGGAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VVDLMAHMASKE\tXR:Z:VVDLMAHMASKE\tXC:i:2\tXS:f:47.64\tXQ:f:5.917798e-04\tXM:Z:-\tXN:i:1\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR05 0.1.4342\t0\tchr16\t29791447\t255\t27M\t*\t0\t0\tGTGTGGAGCGACTATGTGGGTGGTCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VWSDYVGGR\tXR:Z:VWSDYVGGR\tXC:i:2\tXS:f:41.0668\tXQ:f:6.496164e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121012_A0218_4E_R_FR05 0.1.4414\t0\tchr16\t29791447\t255\t27M\t*\t0\t0\tGTGTGGAGCGACTATGTGGGTGGTCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VWSDYVGGR\tXR:Z:VWSDYVGGR\tXC:i:2\tXS:f:32.2425\tXQ:f:7.736297e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4754\t0\tchr5\t132424825\t255\t29M400N22M\t*\t0\t0\tTGGAATTCTCCAGCTGAAGAAGGGTCAAGTGACTGTGAAGTCTTTTCCAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:WNSPAEEGSSDCEVFSK\tXR:Z:WNSPAEEGSSDCEVFSK\tXC:i:2\tXS:f:50.5021\tXQ:f:5.554988e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.4820\t0\tchr5\t132424825\t255\t29M400N22M\t*\t0\t0\tTGGAATTCTCCAGCTGAAGAAGGGTCAAGTGACTGTGAAGTCTTTTCCAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:WNSPAEEGSSDCEVFSK\tXR:Z:WNSPAEEGSSDCEVFSK\tXC:i:2\tXS:f:56.7369\tXQ:f:4.764629e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.3091\t16\tchr2\t85628423\t255\t30M199N6M\t*\t0\t0\tGTTGCCCTCCTTCAGAGCAGGCTTGGGGCCCAGGAC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:YQEGGVESAFHK\tXR:Z:YQEGGVESAFHK\tXC:i:2\tXS:f:39.9334\tXQ:f:6.894736e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n+TCGA-AA-A00E-01A-31_W_VU_20121013_A0218_4E_R_FR10 0.1.3160\t16\tchr2\t85628423\t255\t30M199N6M\t*\t0\t0\tGTTGCCCTCCTTCAGAGCAGGCTTGGGGCCCAGGAC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:YQEGGVESAFHK\tXR:Z:YQEGGVESAFHK\tXC:i:2\tXS:f:34.2558\tXQ:f:7.614462e-04\tXM:Z:-\tXN:i:0\tXT:i:2\tXG:Z:N\n' |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/mm10/Sample_Mouse_pro-B_total.whole_exp.bam |
| b |
| Binary file test-data/mm10/Sample_Mouse_pro-B_total.whole_exp.bam has changed |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/mm10/exon_anno.RData |
| b |
| Binary file test-data/mm10/exon_anno.RData has changed |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/mm10/mm10_variant_annotation.RData |
| b |
| Binary file test-data/mm10/mm10_variant_annotation.RData has changed |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/mm10/procodingseq.RData |
| b |
| Binary file test-data/mm10/procodingseq.RData has changed |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/mm10/proseq.RData |
| b |
| Binary file test-data/mm10/proseq.RData has changed |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/mm10/test.psm-report --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm10/test.psm-report Wed May 17 20:23:27 2017 -0400 |
| [ |
| b'@@ -0,0 +1,98 @@\n+\tProtein(s)\tSequence\tAAs Before\tAAs After\tPosition\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n+11738\tNP_001001491\tAEGDAAALNR\tEK\tRI\t45\tiTRAQ-AEGDAAALNR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.2874.2874.2 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=2874"""\t\t1291.5035\t566.2957153\t2+\t2+\t1130.580185\t0\t-2.919656107\t\t\t\t99.88636364\tConfident\n+13101\tNP_001001491\tAEGDAAALNR\tEK\tRI\t45\tiTRAQ-AEGDAAALNR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.3039.3039.2 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=3039"""\t\t1324.9681\t566.2960815\t2+\t2+\t1130.580185\t0\t-2.27298007\t\t\t\t99.88558352\tConfident\n+27886\tNP_001001491\tAEGDAAALNRR\tEK\tIQ\t45\tiTRAQ-AEGDAAALNRR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f9.mgf\t"Mo_Tai_iTRAQ_f9.3005.3005.2 File:""Mo_Tai_iTRAQ_f9.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=3005"""\t\t1192.457\t644.3468628\t2+\t2+\t1286.681296\t0\t-1.647315671\t\t\t\t100\tConfident\n+30717\tNP_001001491\tAEGDAAALNRR\tEK\tIQ\t45\tiTRAQ-AEGDAAALNRR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f9.mgf\t"Mo_Tai_iTRAQ_f9.2994.2994.3 File:""Mo_Tai_iTRAQ_f9.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=2994"""\t\t1190.325\t429.8999329\t3+\t3+\t1286.681296\t0\t-2.579165366\t\t\t\t100\tConfident\n+19687\tNP_001001491\tIQALQQQADDAEDR\tRK\tAQ\t14\tiTRAQ-IQALQQQADDAEDR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f4.mgf\t"Mo_Tai_iTRAQ_f4.7011.7011.2 File:""Mo_Tai_iTRAQ_f4.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=7011"""\t\t2711.4201\t872.9315796\t2+\t2+\t1743.85094\t0\t-1.336512473\t\t\t\t100\tConfident\n+23947\tNP_001001491\tIQALQQQADDAEDRAQGLQR\tRK\tEL\t14\tiTRAQ-IQALQQQADDAEDRAQGLQR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f6.mgf\t"Mo_Tai_iTRAQ_f6.13161.13161.3 File:""Mo_Tai_iTRAQ_f6.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=13161"""\t\t3545.8174\t800.0770264\t3+\t3+\t2397.211847\t0\t-1.082158182\t\t\t\t100\tConfident\n+24911\tNP_001001491\tIQALQQQADDAEDRAQGLQR\tRK\tEL\t14\tiTRAQ-IQALQQQADDAEDRAQGLQR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f6.mgf\t"Mo_Tai_iTRAQ_f6.13120.13120.3 File:""Mo_Tai_iTRAQ_f6.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=13120"""\t\t3534.407\t800.4118042\t3+\t3+\t2397.211847\t1\t-0.674423593\t\t\t\t100\tConfident\n+10327\tNP_001001491\tLVILEGELK\tRK\tRA\t133\tiTRAQ-LVILEGELK<iTRAQ>-COOH\t\t"iTRAQ 4-plex of K(9), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.16441.16441.2 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=16441"""\t\t4575.6012\t651.4170532\t2+\t2+\t1300.820972\t0\t-1.088967567\t\t\t\t100\tConfident\n+13102\tNP_001001491\tMEILEMQLK\tEK\tEA\t105\tiTRAQ-MEILEMQLK<iTRAQ>-COOH\t\t"iTRAQ 4-plex of K(9), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.17009.17009.2 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=17009"""\t\t4761.3408\t711.8983154\t2+\t2+\t1421.786578\t0\t-3.160590367\t\t\t\t100\tConfident\n+13229\tNP_001001491\tMEILEMQLK\tEK\tEA\t105\tiTRAQ-M<ox>EILEMQLK<iTRAQ>-COOH\tOxidation of M(1)\t"iTRAQ 4-plex of K(9), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.13232.13232.2 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=13232"""\t\t3655.5182\t719.8991089\t2+\t2+\t1437.781493\t0\t1.508715328\tOxidation of M (1: Very Confident)\t"Oxidation of M (1: 99.97303193913477, 6: 0.026968060865238112)"\tOxidation of M (1: 99.105733824303)\t98.63481229\tConfident\n+23704\tNP_001001491\tSLEAASEK\tLK\tYS\t170\tiTRAQ-SLEAASEK<iTRAQ>-COOH\t\t"iTRAQ 4-plex of K(8), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f6.mgf\t"Mo_Tai_iTRAQ_f6.3605.3605.2 File:""Mo_Tai_iTRAQ_f6.raw"", NativeID:""'..b'ntrollerType=0 controllerNumber=1 scan=6125"""\t\t2938.7087\t663.355896\t3+\t3+\t1987.045617\t0\t0.121561461\t\t\t\t100\tConfident\n+13463\t"NP_758514_D63E,N95S,K98N,P110A,R153M,G330V,Y622F,N750D_pre-pro-B"\tIDNAVNVR\tEK\tTR\t749\tiTRAQ-IDNAVNVR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.4170.4170.2 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=4170"""\t\t1586.551\t522.7996826\t2+\t2+\t1043.584542\t0\t0.258874289\t\t\t\t88.44393593\tConfident\n+6145\t"NP_780438_rs33607691:V277D,rs29538383:G332V,rs33341352:I831V,rs33115192:L871P,rs33099876:H1543R,T2185K,rs33128516:V2322A_pro-B"\tSVAQTTPVAGSQSLSSGTVAK\tSR\tST\t2320\tiTRAQ-SVAQTTPVAGSQSLSSGTVAK<iTRAQ>-COOH\t\t"iTRAQ 4-plex of K(21), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f3.mgf\t"Mo_Tai_iTRAQ_f3.5021.5021.3 File:""Mo_Tai_iTRAQ_f3.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=5021"""\t\t2533.4843\t755.4138794\t3+\t3+\t2263.226323\t0\t-2.874598484\t\t\t\t100\tConfident\n+23143\t"NP_780447_S111P,rs45654505:F593L,rs50064568:E599G,rs52047355:E603G,rs33627173:S724A,rs32921804:V750A,rs13467382:I966S,rs32857057:M1129T,rs27893949:L1186M,rs27893948:I1245M,rs6191517:A1591S,rs29562616:N1678T,rs27893945:V1779L,rs27893944:P1805S,rs45724362:V1810M,rs33396584:E1925D,rs27893943:L2004F,rs27893942:M2031T,rs32859763:N2059K_pro-B"\tETDIFASASK\tVK\tSE\t2000\tiTRAQ-ETDIFASASK<iTRAQ>-COOH\t\t"iTRAQ 4-plex of K(10), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f6.mgf\t"Mo_Tai_iTRAQ_f6.10298.10298.2 File:""Mo_Tai_iTRAQ_f6.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=10298"""\t\t2781.6354\t678.8642578\t2+\t2+\t1355.717629\t0\t-2.700603449\t\t\t\t100\tConfident\n+673\t"NP_795953_rs13474901:S1420P,rs30093916:L1427F_pro-B"\tVLPGHPEPLFK\tAK\tDA\t1418\tiTRAQ-VLPGHPEPLFK<iTRAQ>-COOH\t\t"iTRAQ 4-plex of K(11), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f8.mgf\t"Mo_Tai_iTRAQ_f8.11078.11078.3 File:""Mo_Tai_iTRAQ_f8.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=11078"""\t\t3309.9327\t507.9709473\t3+\t3+\t1520.895869\t0\t-3.186613455\t\t\t\t100\tConfident\n+12323\t"NP_796277_T273A,R333K,rs27245866:E393G,P491S_pro-B"\tYLEPLPTSPNSR\tSK\tSL\t481\tiTRAQ-Y<iTRAQ>LEPLPTSPNSR-COOH\tiTRAQ 4-plex of Y(1)\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f5.mgf\t"Mo_Tai_iTRAQ_f5.16647.16647.3 File:""Mo_Tai_iTRAQ_f5.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=16647"""\t\t4640.253\t554.6449585\t3+\t3+\t1660.902804\t0\t6.155146283\tiTRAQ 4-plex of Y (1: Very Confident)\tiTRAQ 4-plex of Y (1: 100.0)\tiTRAQ 4-plex of Y (1: 84.98129342597541)\t93.68421053\tConfident\n+17711\t"NP_851009_S35I,D48V,rs13465512:N694S_pro-B"\tAEVSELPSVVR\tIR\tDL\t687\tiTRAQ-AEVSELPSVVR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f4.mgf\t"Mo_Tai_iTRAQ_f4.8550.8550.2 File:""Mo_Tai_iTRAQ_f4.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=8550"""\t\t3121.4644\t665.8776245\t2+\t2+\t1328.742164\t1\t-3.624411708\t\t\t\t100\tConfident\n+19079\t"NP_851009_S35I,D48V,rs13465512:N694S_pro-B"\tAEVSELPSVVR\tIR\tDL\t687\tiTRAQ-AEVSELPSVVR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f4.mgf\t"Mo_Tai_iTRAQ_f4.8535.8535.2 File:""Mo_Tai_iTRAQ_f4.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=8535"""\t\t3117.3078\t665.3777466\t2+\t2+\t1328.742164\t0\t-0.919951623\t\t\t\t99.60238569\tConfident\n+19194\t"NP_851009_S35I,D48V,rs13465512:N694S_pro-B"\tAEVSELPSVVR\tIR\tDL\t687\tiTRAQ-AEVSELPSVVR-COOH\t\tiTRAQ 4-plex of peptide N-term(1)\tMo_Tai_iTRAQ_f4.mgf\t"Mo_Tai_iTRAQ_f4.8639.8639.2 File:""Mo_Tai_iTRAQ_f4.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=8639"""\t\t3147.8209\t665.3759766\t2+\t2+\t1328.742164\t0\t-3.580121597\t\t\t\t99.80694981\tConfident\n+21888\t"NP_955518_R136L,E321A,S461L,rs30309127:S732C,Q789H,P909T,I967S,D1083A,R1105L_pre-pro-B"\tDMLPCFPAGL\tLK\tVK\t314\tiTRAQ-DMLPC<cmm>FPAGL-COOH\t\t"Carbamidomethylation of C(5), iTRAQ 4-plex of peptide N-term(1)"\tMo_Tai_iTRAQ_f4.mgf\t"Mo_Tai_iTRAQ_f4.7295.7295.2 File:""Mo_Tai_iTRAQ_f4.raw"", NativeID:""controllerType=0 controllerNumber=1 scan=7295"""\t\t2786.8987\t632.8096924\t2+\t2+\t1263.611351\t0\t-5.150641126\t\t\t\t99.80620155\tConfident\n' |
| b |
| diff -r 000000000000 -r 90ecb65017a0 test-data/peptideshaker_mm10.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptideshaker_mm10.sam Wed May 17 20:23:27 2017 -0400 |
| b |
| b'@@ -0,0 +1,181 @@\n+@SQ\tSN:chr1\tLN:195471971\n+@SQ\tSN:chr10\tLN:130694993\n+@SQ\tSN:chr11\tLN:122082543\n+@SQ\tSN:chr12\tLN:120129022\n+@SQ\tSN:chr13\tLN:120421639\n+@SQ\tSN:chr14\tLN:124902244\n+@SQ\tSN:chr15\tLN:104043685\n+@SQ\tSN:chr16\tLN:98207768\n+@SQ\tSN:chr17\tLN:94987271\n+@SQ\tSN:chr18\tLN:90702639\n+@SQ\tSN:chr19\tLN:61431566\n+@SQ\tSN:chr1_GL456210_random\tLN:169725\n+@SQ\tSN:chr1_GL456211_random\tLN:241735\n+@SQ\tSN:chr1_GL456212_random\tLN:153618\n+@SQ\tSN:chr1_GL456213_random\tLN:39340\n+@SQ\tSN:chr1_GL456221_random\tLN:206961\n+@SQ\tSN:chr2\tLN:182113224\n+@SQ\tSN:chr3\tLN:160039680\n+@SQ\tSN:chr4\tLN:156508116\n+@SQ\tSN:chr4_GL456216_random\tLN:66673\n+@SQ\tSN:chr4_GL456350_random\tLN:227966\n+@SQ\tSN:chr4_JH584292_random\tLN:14945\n+@SQ\tSN:chr4_JH584293_random\tLN:207968\n+@SQ\tSN:chr4_JH584294_random\tLN:191905\n+@SQ\tSN:chr4_JH584295_random\tLN:1976\n+@SQ\tSN:chr5\tLN:151834684\n+@SQ\tSN:chr5_GL456354_random\tLN:195993\n+@SQ\tSN:chr5_JH584296_random\tLN:199368\n+@SQ\tSN:chr5_JH584297_random\tLN:205776\n+@SQ\tSN:chr5_JH584298_random\tLN:184189\n+@SQ\tSN:chr5_JH584299_random\tLN:953012\n+@SQ\tSN:chr6\tLN:149736546\n+@SQ\tSN:chr7\tLN:145441459\n+@SQ\tSN:chr7_GL456219_random\tLN:175968\n+@SQ\tSN:chr8\tLN:129401213\n+@SQ\tSN:chr9\tLN:124595110\n+@SQ\tSN:chrM\tLN:16299\n+@SQ\tSN:chrUn_GL456239\tLN:40056\n+@SQ\tSN:chrUn_GL456359\tLN:22974\n+@SQ\tSN:chrUn_GL456360\tLN:31704\n+@SQ\tSN:chrUn_GL456366\tLN:47073\n+@SQ\tSN:chrUn_GL456367\tLN:42057\n+@SQ\tSN:chrUn_GL456368\tLN:20208\n+@SQ\tSN:chrUn_GL456370\tLN:26764\n+@SQ\tSN:chrUn_GL456372\tLN:28664\n+@SQ\tSN:chrUn_GL456378\tLN:31602\n+@SQ\tSN:chrUn_GL456379\tLN:72385\n+@SQ\tSN:chrUn_GL456381\tLN:25871\n+@SQ\tSN:chrUn_GL456382\tLN:23158\n+@SQ\tSN:chrUn_GL456383\tLN:38659\n+@SQ\tSN:chrUn_GL456385\tLN:35240\n+@SQ\tSN:chrUn_GL456387\tLN:24685\n+@SQ\tSN:chrUn_GL456389\tLN:28772\n+@SQ\tSN:chrUn_GL456390\tLN:24668\n+@SQ\tSN:chrUn_GL456392\tLN:23629\n+@SQ\tSN:chrUn_GL456393\tLN:55711\n+@SQ\tSN:chrUn_GL456394\tLN:24323\n+@SQ\tSN:chrUn_GL456396\tLN:21240\n+@SQ\tSN:chrUn_JH584304\tLN:114452\n+@SQ\tSN:chrX\tLN:171031299\n+@SQ\tSN:chrX_GL456233_random\tLN:336933\n+@SQ\tSN:chrY\tLN:91744698\n+@SQ\tSN:chrY_JH584300_random\tLN:182347\n+@SQ\tSN:chrY_JH584301_random\tLN:259875\n+@SQ\tSN:chrY_JH584302_random\tLN:155838\n+@SQ\tSN:chrY_JH584303_random\tLN:158099\n+@PG\tID:proBAMr\tVN:2.0.0\n+Mo_Tai_iTRAQ_f6 0.1.11861\t0\tchr3\t51446679\t255\t63M\t*\t0\t0\tGCTGCTGCTGACGTTTATAGAGGATTACAAGAGAGGAATCCTGAAAATTGGGCCTATTACAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AAADVYRGLQERNPENWAYYK\tXR:Z:DAADVYRGLQERNPENWAYYK\tXC:i:4\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of Y(6), iTRAQ 4-plex of K(21), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f6 0.1.17618\t16\tchr7\t28894639\t255\t21M772N45M\t*\t0\t0\tCGGACGGAGTGGTCGGACCCGATACTGCACCTCTTACTGGCCGTCCCACTACGACTCAAGTTGGCC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:ACLTSLGYDVENDRQGDAEFNR\tXR:Z:ACLISLGYDVENDRQGDAEFNR\tXC:i:3\tXS:f:NA\tXQ:f:0e+00\tXM:Z:Carbamidomethylation of C(2), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f5 0.1.2874\t0\tchr8\t72138588\t255\t30M\t*\t0\t0\tGCTGAAGGAGATGCAGCCGCTCTCAACCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AEGDAAALNR\tXR:Z:AEGDAAALNR\tXC:i:2\tXS:f:NA\tXQ:f:1.136364e-03\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f5 0.1.3039\t0\tchr8\t72138588\t255\t30M\t*\t0\t0\tGCTGAAGGAGATGCAGCCGCTCTCAACCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AEGDAAALNR\tXR:Z:AEGDAAALNR\tXC:i:2\tXS:f:NA\tXQ:f:1.144165e-03\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f9 0.1.3005\t0\tchr8\t72138588\t255\t33M\t*\t0\t0\tGCTGAAGGAGATGCAGCCGCTCTCAACCGCCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AEGDAAALNRR\tXR:Z:AEGDAAALNRR\tXC:i:2\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f9 0.1.2994\t0\tchr8\t72138588\t255\t33M\t*\t0\t0\tGCTGAAGGAGATGCAGCCGCTCTCAACCGCCGC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AEGDAAALNRR\tXR:Z:AEGDAAALNRR\tXC:i:3\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f8 0.1.7186\t0\tchr14\t47289613\t255\t39M\t*\t0\t0\tGCTGAAAACAATAGTAAAAATGTAGATGTATGGCCTAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:AENNSKNVDVWPK\tXR:Z:AENNSKNVDVRPK\tXC:i:3\tXS:f:NA\tXQ:f:2.845188e-01\tXM:Z:iTRAQ 4-plex of K(6, 13),'..b'_Tai_iTRAQ_f3 0.1.5705\t0\tchr2\t120022722\t255\t27M\t*\t0\t0\tACAGAGTCTCGGAGCATCTCATCACGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TESRSISSR\tXR:Z:TESQSISSR\tXC:i:2\tXS:f:NA\tXQ:f:1.481481e-01\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f4 0.1.6840\t0\tchr2\t120022722\t255\t27M\t*\t0\t0\tACAGAGTCTCGGAGCATCTCATCACGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TESRSISSR\tXR:Z:TESQSISSR\tXC:i:2\tXS:f:NA\tXQ:f:2.667984e-01\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f5 0.1.7198\t0\tchr8\t72147249\t255\t19M4474N5M\t*\t0\t0\tACAATCGATGACCTGGAAGAAAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TIDDLEEK\tXR:Z:TIDDLEEK\tXC:i:2\tXS:f:NA\tXQ:f:2.262038e-01\tXM:Z:iTRAQ 4-plex of K(8), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f6 0.1.8513\t0\tchr8\t72147249\t255\t19M4474N5M\t*\t0\t0\tACAATCGATGACCTGGAAGAAAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TIDDLEEK\tXR:Z:TIDDLEEK\tXC:i:2\tXS:f:NA\tXQ:f:6.17284e-03\tXM:Z:iTRAQ 4-plex of K(8), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f6 0.1.8367\t0\tchr8\t72147249\t255\t19M4474N5M\t*\t0\t0\tACAATCGATGACCTGGAAGAAAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TIDDLEEK\tXR:Z:TIDDLEEK\tXC:i:2\tXS:f:NA\tXQ:f:3.04878e-03\tXM:Z:iTRAQ 4-plex of K(8), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:N\n+Mo_Tai_iTRAQ_f5 0.1.3743\t16\tchr8\t4268354\t255\t24M\t*\t0\t0\tTGGTAGCTTAGTCTTTGACACGCA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TIESETVR\tXR:Z:SIESETVR\tXC:i:2\tXS:f:NA\tXQ:f:9.578107e-02\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f4 0.1.3241\t16\tchr8\t4268354\t255\t24M\t*\t0\t0\tTGGTAGCTTAGTCTTTGACACGCA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TIESETVR\tXR:Z:SIESETVR\tXC:i:2\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f4 0.1.1279\t0\tchr10\t108252887\t255\t38M400N1M\t*\t0\t0\tACTCCCCCGGGTTCCTCCTCCGCAGGCACACAGAGCAGG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TPPGSSSAGTQSR\tXR:Z:TPPGSSSAGTQSS\tXC:i:2\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f6 0.1.16412\t0\tchr8\t71358978\t255\t75M\t*\t0\t0\tACCCCAGTGGTCCAAGACCTGGAGCTGGGGGCTCTCTCCGAGGAGGCTGCAGGTGGCGACGAGGACCGAGAAAAG\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TPVVQDLELGALSEEAAGGDEDREK\tXR:Z:TPVVQDLELGALPEEAAGGDEDREK\tXC:i:3\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of K(25), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f6 0.1.12166\t0\tchr10\t115409133\t255\t54M\t*\t0\t0\tACAAGTTCGCCGTCTCCAGCAAACTCAGATGTGGAAATGGATGGGATTGGTAGA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:TSSPSPANSDVEMDGIGR\tXR:Z:TSSSSPANSDVEMDGIGR\tXC:i:3\tXS:f:NA\tXQ:f:1.810345e-01\tXM:Z:Oxidation of M(13), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f8 0.1.11915\t16\tchr1\t133624604\t255\t45M\t*\t0\t0\tCACCGCCCCTTCGGCCACGAGTGACGATATAGTCCGCAGTGAGCC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VAGKPVLTAISGVTR\tXR:Z:VAGKPVLTAVSGVTR\tXC:i:3\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of K(4), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f8 0.1.11078\t0\tchr9\t103346927\t255\t33M\t*\t0\t0\tGTGTTACCTGGTCATCCAGAACCTTTATTTAAA\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VLPGHPEPLFK\tXR:Z:VLSGHPEPLLK\tXC:i:3\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of K(11), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f9 0.1.7554\t16\tchr3\t138959073\t255\t39M\t*\t0\t0\tCACTTATCGTTGTTTCTCCTGCTGCAACGGCTCGAATTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VNSNKEDDVAELK\tXR:Z:VDSNKEDDVAELK\tXC:i:3\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of K(5, 13), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f8 0.1.14638\t16\tchr14\t54514786\t255\t90M\t*\t0\t0\tCATGGGAACCACCGGGGTCTCCTGGACTCTCTACTACATTAACGCTTACGGGGCTGATGTGTGTGTCTCCTCATGTCACCTCTTCTCTTT\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:VPLVAPEDLRDDVIANAPTTHTEEYSGEEK\tXR:Z:VPLVAPEDLRDDVIENAPTTHTEEYSGEEK\tXC:i:4\tXS:f:NA\tXQ:f:0e+00\tXM:Z:iTRAQ 4-plex of K(30), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n+Mo_Tai_iTRAQ_f5 0.1.16647\t16\tchr2\t132870426\t255\t36M\t*\t0\t0\tATGGAACTTGGGAACGGATGAAGTGGTTTGAGGTCC\t*\tXA:Z:0\tNH:i:1\tXL:i:1\tXP:Z:YLEPLPTSPNSR\tXR:Z:YLEPLPTSPNPR\tXC:i:3\tXS:f:NA\tXQ:f:6.315789e-02\tXM:Z:iTRAQ 4-plex of Y(1), iTRAQ 4-plex of peptide N-term(1)\tXN:i:NA\tXT:i:NA\tXG:Z:V\n' |
| b |
| diff -r 000000000000 -r 90ecb65017a0 tool-data/customProDB.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/customProDB.loc.sample Wed May 17 20:23:27 2017 -0400 |
| b |
| @@ -0,0 +1,19 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#mm10 mm10 Mouse (Mus musculus): mm10 /path/to/genome/mm10/mm10.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r 000000000000 -r 90ecb65017a0 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed May 17 20:23:27 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all customProDB annotations under genome directory --> + <table name="customProDB" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/customProDB.loc" /> + </table> +</tables> |