From e6c009a1ab92689977be66bd0eb721739f1bbff6 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Sun, 7 Oct 2018 09:48:13 +0200
Subject: [PATCH] Switch from v0.3 to latest git version of C++ code, requires
a workaround to fix the bps column of segmentation output.
---
Snake.config.json | 4 ++--
Snakefile | 24 ++++++++++++++++++++++--
2 files changed, 24 insertions(+), 4 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 5091f09..83dfd24 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -2,8 +2,8 @@
"chromosomes" : ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX"],
"reference" : "/MMCI/TM/scratch/ref/GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
- "mosaicatcher" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/build/mosaic",
- "plot_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/qc.R",
+ "mosaicatcher" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/git/build/mosaic",
+ "plot_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/git/R/qc.R",
"samtools" : "samtools",
"bcftools" : "bcftools",
diff --git a/Snakefile b/Snakefile
index 80b43c5..3f83e4e 100644
--- a/Snakefile
+++ b/Snakefile
@@ -490,7 +490,7 @@ rule segmentation:
input:
"counts/{sample}/{window}_{file_name}.txt.gz"
output:
- "segmentation/{sample}/{window,\d+}_{file_name}.txt"
+ "segmentation/{sample}/{window,\d+}_{file_name}.txt.fixme"
log:
"log/segmentation/{sample}/{window}_{file_name}.log"
params:
@@ -506,6 +506,16 @@ rule segmentation:
{input} > {log} 2>&1
"""
+# TODO: This is a workaround because latest versions of "mosaic segment" don't compute the "bps"
+# TODO: column properly. Remove once fixed in the C++ code.
+rule fix_segmentation:
+ input:
+ "segmentation/{sample}/{window}_{file_name}.txt.fixme"
+ output:
+ "segmentation/{sample}/{window,\d+}_{file_name}.txt"
+ shell:
+ 'awk \'BEGIN {{OFS="\\t"}} {{if ($1=="{wildcards.sample}") $12=int(($14-1)/100000); print}}\' {input} > {output}'
+
# Pick a few segmentations and prepare the input files for SV classification
rule prepare_segments:
input:
@@ -523,7 +533,7 @@ rule segment_one_cell:
input:
"counts-per-cell/{sample}/{cell}/{window}_{file_name}.txt.gz"
output:
- "segmentation-per-cell/{sample}/{cell}/{window,\d+}_{file_name}.txt"
+ "segmentation-per-cell/{sample}/{cell}/{window,\d+}_{file_name}.txt.fixme"
log:
"log/segmentation-per-cell/{sample}/{cell}/{window}_{file_name}.log"
params:
@@ -539,6 +549,16 @@ rule segment_one_cell:
{input} > {log} 2>&1
"""
+# TODO: This is a workaround because latest versions of "mosaic segment" don't compute the "bps"
+# TODO: column properly. Remove once fixed in the C++ code.
+rule fix_segmentation_one_cell:
+ input:
+ "segmentation-per-cell/{sample}/{cell}/{window}_{file_name}.txt.fixme"
+ output:
+ "segmentation-per-cell/{sample}/{cell}/{window,\d+}_{file_name}.txt"
+ shell:
+ 'awk \'BEGIN {{OFS="\\t"}} {{if ($1=="{wildcards.sample}") $12=int(($14-1)/100000); print}}\' {input} > {output}'
+
rule segmentation_selection:
input:
counts="counts/{sample}/{window}_{file_name}.txt.gz",
--
GitLab