Mercurial > repos > artbio > snvtocnv
changeset 8:67213c4eefa6 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
| author | artbio |
|---|---|
| date | Sun, 07 Mar 2021 23:13:08 +0000 |
| parents | e66b91475343 |
| children | f3bacfd9b670 |
| files | sanitize_snv.py segmentation_sequenza.R sequenza_index.xml sequenza_to_hrdtools_input.R snvtocnv.xml |
| diffstat | 5 files changed, 17 insertions(+), 31 deletions(-) [+] |
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--- a/sanitize_snv.py Sun Mar 07 14:21:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -import sys - -handle = open(sys.argv[1], 'r') -out = open(sys.argv[2], 'w') -for line in handle: - if line[0] == '#': - out.write(line) - continue - linelist = line.split('\t') - refcol = linelist[0].split('chr') - infocol = linelist[7].split('INDEL') - if len(infocol) > 1: - continue - if len(refcol) > 1: - refcol = refcol[1] - else: - refcol = refcol[0] - if refcol not in ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', - '11', '12', '13', '14', '15', '16', '17', '18', '19', - '20', '21', '22', 'X', 'Y']: - continue - else: - linelist[0] = refcol - out.write('\t'.join(linelist))
--- a/segmentation_sequenza.R Sun Mar 07 14:21:06 2021 +0000 +++ b/segmentation_sequenza.R Sun Mar 07 23:13:08 2021 +0000 @@ -1,10 +1,13 @@ -options(warn = -1) +options(show.error.messages = F, error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) }) # load packages that are provided in the conda env library(optparse) library(sequenza) library(BiocParallel) library(tidyverse) +library(readr) + option_list <- list( make_option( c("-i", "--input"), @@ -41,8 +44,14 @@ "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22") +Sys.setenv(TZDIR = "/usr/share/zoneinfo/") +Sys.setenv(TZ = "US/Eastern") +options(tz = "US/Eastern") +Sys.timezone(location = TRUE) + + segfile <- sequenza.extract(data_file, - verbose = TRUE, + verbose = FALSE, chromosome.list = chrom_list) ## Estimation of cellularity and ploidy
--- a/sequenza_index.xml Sun Mar 07 14:21:06 2021 +0000 +++ b/sequenza_index.xml Sun Mar 07 23:13:08 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.6.1"> +<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.7.0"> <description> </description> <macros>
--- a/sequenza_to_hrdtools_input.R Sun Mar 07 14:21:06 2021 +0000 +++ b/sequenza_to_hrdtools_input.R Sun Mar 07 23:13:08 2021 +0000 @@ -1,4 +1,5 @@ -options(warn = -1) +options(show.error.messages = F, error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) }) # load packages that are provided in the conda env @@ -61,6 +62,6 @@ print(reformatted) reformatted %>% - write.table(opt$output, quote=F, row.names=F, sep="\t") + write.table(opt$output, quote = F, row.names = F, sep = "\t") message(sprintf("Output written to %s", opt$output))
--- a/snvtocnv.xml Sun Mar 07 14:21:06 2021 +0000 +++ b/snvtocnv.xml Sun Mar 07 23:13:08 2021 +0000 @@ -1,16 +1,16 @@ -<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.6.1"> +<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.7.0"> <description> </description> <macros> <import>macro.xml</import> </macros> <requirements> - <requirement type="package" version="1.6">samtools</requirement> <requirement type="package" version="3.0.0">sequenza-utils</requirement> <requirement type="package" version="3.0.0">r-sequenza</requirement> <requirement type="package" version="1.6.6">r-optparse</requirement> <requirement type="package" version="1.24.0">bioconductor-biocparallel</requirement> <requirement type="package" version="1.3.0">r-tidyverse</requirement> + <requirement type="package" version="2021a=he74cb21_0">tzdata</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error occured" />