# HG changeset patch # User galaxyp # Date 1489515278 14400 # Node ID 8ccfff69dd57a1058f4d313a82880a64536bee4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66 diff -r 000000000000 -r 8ccfff69dd57 COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. diff -r 000000000000 -r 8ccfff69dd57 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,54 @@ +GalaxyP - CustomProDB +=================== + +* Home: +* Galaxy Tool Shed: +* Tool ID: `customProDB` + + +Description +----------- + +Generate customized FASTA files based on the transcriptome or exome sequencing of an individual sample. + +See: + +* + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: + + + + +License +------- + +Copyright (c) 2016 Vanderbilt University and 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 . + +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 + + +Authors +------- + +Authors and contributors: + +* Matt Chambers + Vanderbilt University Medical Center + +* Xiaojing Wang + Vanderbilt University Medical Center diff -r 000000000000 -r 8ccfff69dd57 customProDB.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customProDB.R Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,113 @@ +#!/usr/bin/env Rscript + +initial.options <- commandArgs(trailingOnly = FALSE) +script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)])) + +## 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$bam <- make_option('--bam', type='character') +option_list$bai <- make_option('--bai', type='character') +option_list$vcf <- make_option('--vcf', type='character') +option_list$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$ids <- make_option('--ids', type='character') +option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character') +option_list$cosmic <- make_option('--cosmic', type='character') +option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE) +option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') +#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE) +#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE) +option_list$outputFile <- make_option('--outputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + + +customProDB <- function( + bam_file = GalaxyInputFile(required=TRUE), + bai_file = GalaxyInputFile(required=TRUE), + vcf_file = GalaxyInputFile(required=TRUE), + exon_anno_file = GalaxyInputFile(required=TRUE), + proteinseq_file = GalaxyInputFile(required=TRUE), + procodingseq_file = GalaxyInputFile(required=TRUE), + ids_file = GalaxyInputFile(required=TRUE), + dbsnpinCoding_file = GalaxyInputFile(required=FALSE), + cosmic_file = GalaxyInputFile(required=FALSE), + annotationFromHistory = GalaxyLogicalParam(required=FALSE), + rpkmCutoff = GalaxyNumericParam(required=TRUE), + #outputIndels = GalaxyLogicalParam(required=FALSE), + #outputNovelJunctions = GalaxyLogicalParam(required=FALSE), + outputFile = GalaxyOutput("FASTA","fasta")) +{ + file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/")) + file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/")) + file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/")) + file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/")) + + if (length(dbsnpinCoding_file) > 0) + { + file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/")) + labelrsid = T + } + else + { + labelrsid = F + } + + if (length(cosmic_file) > 0) + { + file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/")) + cosmic = T + } + else + { + cosmic = F + } + + bamLink = "input.bam" + file.symlink(bam_file, bamLink) + file.symlink(bai_file, paste(bamLink, ".bai", sep="")) + + suppressPackageStartupMessages(library(customProDB)) + + easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), + rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", + nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic) +} + + +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(customProDB, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +}) diff -r 000000000000 -r 8ccfff69dd57 customProDB.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customProDB.xml Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,121 @@ + + Generate protein FASTAs from exosome or transcriptome data + + bioconductor-customprodb + bioconductor-rgalaxy + + + + + 1 +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** + +Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). + + 10.1093/bioinformatics/btt543 + @misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub +repository}, + year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}} + + diff -r 000000000000 -r 8ccfff69dd57 test-data/exon_anno.RData Binary file test-data/exon_anno.RData has changed diff -r 000000000000 -r 8ccfff69dd57 test-data/ids.RData Binary file test-data/ids.RData has changed diff -r 000000000000 -r 8ccfff69dd57 test-data/procodingseq.RData Binary file test-data/procodingseq.RData has changed diff -r 000000000000 -r 8ccfff69dd57 test-data/proseq.RData Binary file test-data/proseq.RData has changed diff -r 000000000000 -r 8ccfff69dd57 test-data/test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.vcf Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,87 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.17 (r973:277) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test +chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15 +chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36 +chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30 +chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99 +chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21 +chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16 +chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87 +chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33 +chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39 +chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21 +chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81 +chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99 +chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99 +chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81 +chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99 +chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27 +chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57 +chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54 +chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39 +chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99 +chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28 +chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34 +chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21 +chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99 +chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99 +chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99 +chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78 +chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99 +chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34 +chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51 +chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27 +chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55 +chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99 +chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21 +chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62 +chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16 +chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21 +chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61 +chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39 +chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45 +chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51 +chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70 +chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21 +chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99 +chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21 +chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21 +chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82 +chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99 +chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99 +chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26 +chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40 +chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33 +chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50 +chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8 +chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21 +chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99 +chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75 +chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96 +chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99 +chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99 +chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99 diff -r 000000000000 -r 8ccfff69dd57 test-data/test1_sort.bam Binary file test-data/test1_sort.bam has changed diff -r 000000000000 -r 8ccfff69dd57 test-data/test1_sort.bam.bai Binary file test-data/test1_sort.bam.bai has changed diff -r 000000000000 -r 8ccfff69dd57 test-data/test_indel.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_indel.fasta Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,4 @@ +>NP_001120983_954:CT>C |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a| +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLACLAPKTAVYPCDSLDVFLSSSSFYMAMTKTLYCWEIPGAVKRLGPGPVQHSTTSFTHSLMTREAGVKSESFIFWNRYALTVKPVGSGRKLMNQAWTRTKIQCQLLLNIRSVLLCVF +>NP_001120983_4552:GAA>GA |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a| +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNEQNQSSLKNQMKTKRKRQKKLLILKRTY diff -r 000000000000 -r 8ccfff69dd57 test-data/test_rpkm.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_rpkm.fasta Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,6 @@ +>NP_004439 |121102.4845|NM_004448|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform a precursor +MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV +>NP_000170 |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983 |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV diff -r 000000000000 -r 8ccfff69dd57 test-data/test_snv.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_snv.fasta Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,4 @@ +>NP_000170_T139I,E956D |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPIRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLDKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983_R1432*,V1804D |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTK diff -r 000000000000 -r 8ccfff69dd57 tool-data/customProDB.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/customProDB.loc.sample Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,18 @@ +#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): +# +# +# +#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 +# +#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. +# diff -r 000000000000 -r 8ccfff69dd57 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Mar 14 14:14:38 2017 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+