From 16f1c49611b28291fb45afe765accc8f13ec69b3 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Fri, 3 Aug 2018 13:36:18 +0200
Subject: [PATCH] Fix: pindel detect all variants type grouped
---
snakecnv/svsnakemake_utils.py | 13 ++++++++-----
snakecnv/tools/pindel.snk | 16 ++++++++++------
2 files changed, 18 insertions(+), 11 deletions(-)
diff --git a/snakecnv/svsnakemake_utils.py b/snakecnv/svsnakemake_utils.py
index f4b96de..cc46fb1 100644
--- a/snakecnv/svsnakemake_utils.py
+++ b/snakecnv/svsnakemake_utils.py
@@ -69,12 +69,15 @@ class SnakemakeUtils:
return inputs
def get_pindel_chr_batches(self, wildcards):
- inputs = []
+ inputs = {"D": [],
+ "INV": [],
+ "TD": []}
for batch in self.chr_batches[wildcards.chrom]:
- inputs.append("{batch}/pindel/{chrom}_{svtype}/{chrbatch}/pindel_{chrom}_{svtype}.gz".format(
- batch=wildcards.batch, chrom=wildcards.chrom, chrbatch="-".join(map(str, batch)),
- svtype=wildcards.svtype
- ))
+ for svtype in inputs:
+ inputs[svtype].append("{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_{svtype}.gz".format(
+ batch=wildcards.batch, chrom=wildcards.chrom, chrbatch="-".join(map(str, batch)),
+ svtype=svtype
+ ))
return inputs
diff --git a/snakecnv/tools/pindel.snk b/snakecnv/tools/pindel.snk
index 4e1e6d7..74c5197 100644
--- a/snakecnv/tools/pindel.snk
+++ b/snakecnv/tools/pindel.snk
@@ -30,9 +30,9 @@ rule pindel:
genome = REFERENCE,
fai = REFERENCE + ".fai"
output:
- "{batch}/pindel/{chrom}_{svtype}/{chrbatch}/pindel_{chrom}_D.gz",
- "{batch}/pindel/{chrom}_{svtype}/{chrbatch}/pindel_{chrom}_INV.gz",
- "{batch}/pindel/{chrom}_{svtype}/{chrbatch}/pindel_{chrom}_TD.gz",
+ "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_D.gz",
+ "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_INV.gz",
+ "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_TD.gz",
threads:
get_threads("pindel", 4)
log:
@@ -50,7 +50,7 @@ rule pindel:
"""
for svtype in D TD INV RP SI LI BP CloseEndMapped INT_final;
do
- gzip -f {wildcards.batch}/pindel/{wildcards.chrom}_{wildcards.svtype}/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
+ gzip -f {wildcards.batch}/pindel/{wildcards.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
done
"""
@@ -58,12 +58,16 @@ rule mergepindelbatches:
input:
unpack(snakemake_utils.get_pindel_chr_batches)
output:
- "{batch}/pindel/pindel_{chrom}_{svtype}.gz"
+ D="{batch}/pindel/pindel_{chrom}_D.gz",
+ INV="{batch}/pindel/pindel_{chrom}_INV.gz",
+ TD="{batch}/pindel/pindel_{chrom}_TD.gz"
log:
stdout = "{batch}/logs/pindel/{chrom}_{svtype}.o",
stderr = "{batch}/logs/pindel/{chrom}_{svtype}.e",
threads:
1
shell:
- "mergepindelbatches.py {output} {input} 1>{log.stdout} 2>{log.stderr}; "
+ "mergepindelbatches.py {output.D} {input.D} 1>{log.stdout} 2>{log.stderr}; "
+ "mergepindelbatches.py {output.INV} {input.INV} 1>>{log.stdout} 2>>{log.stderr}; "
+ "mergepindelbatches.py {output.TD} {input.TD} 1>>{log.stdout} 2>>{log.stderr}; "
"rm -rf {wildcards.batch}/pindel/{wildcards.chrom}_{wildcards.svtype}"
\ No newline at end of file
--
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