From 1c7e1b7e33528afa4174d9e6e6337570324398c4 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Thu, 1 Nov 2018 14:02:48 +0100
Subject: [PATCH] Change rule filter_calls to retain all calls that overlap
with any merged call
---
Snakefile | 5 +++--
utils/apply_filter.py | 32 ++++++++++++++++++++++++++++++++
2 files changed, 35 insertions(+), 2 deletions(-)
create mode 100755 utils/apply_filter.py
diff --git a/Snakefile b/Snakefile
index bdbcbe7..b501014 100644
--- a/Snakefile
+++ b/Snakefile
@@ -617,11 +617,12 @@ rule mosaiClassifier_make_call:
rule filter_calls:
input:
- calls = "sv_calls/{sample}/{window}_fixed_norm.{bpdens}/simpleCalls_llr{llr}_poppriors{pop_priors}_haplotags{use_haplotags}_gtcutoff{gtcutoff}_regfactor{regfactor}_filterFALSE.txt"
+ inputcalls = "sv_calls/{sample}/{window}_fixed_norm.{bpdens}/simpleCalls_llr{llr}_poppriors{pop_priors}_haplotags{use_haplotags}_gtcutoff{gtcutoff}_regfactor{regfactor}_filterFALSE.txt",
+ mergedcalls = "postprocessing/merge/{sample}/{window}_fixed_norm.{bpdens}/simpleCalls_llr{llr}_poppriors{pop_priors}_haplotags{use_haplotags}_gtcutoff{gtcutoff}_regfactor{regfactor}.txt",
output:
calls = "sv_calls/{sample}/{window}_fixed_norm.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+_scedist[0-9\\.]+}/simpleCalls_llr{llr}_poppriors{pop_priors,(TRUE|FALSE)}_haplotags{use_haplotags,(TRUE|FALSE)}_gtcutoff{gtcutoff,[0-9\\.]+}_regfactor{regfactor,[0-9]+}_filterTRUE.txt"
shell:
- 'utils/filter_MosaiCatcher_calls.pl {input.calls} | awk \'BEGIN {{OFS="\\t"}} (NR==1) || ($16=="PASS") {{$16=""; print}}\' > {output.calls}'
+ 'utils/apply_filter.py {input.inputcalls} {input.mergedcalls} > {output.calls}'
rule mosaiClassifier_calc_probs:
diff --git a/utils/apply_filter.py b/utils/apply_filter.py
new file mode 100755
index 0000000..5e58aa4
--- /dev/null
+++ b/utils/apply_filter.py
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+"""
+Retains calls that overlap with a call after filtering and merging.
+That is, output all calls in the input sets that are present in the
+provided merged set.
+"""
+
+import sys
+from argparse import ArgumentParser
+import pandas as pd
+
+def main():
+ parser = ArgumentParser(prog='apply_filter.py', description=__doc__)
+
+ parser.add_argument('inputcalls', metavar='INPUTCALLS', help='Input call set')
+ parser.add_argument('mergedcalls', metavar='MERGEDCALLS', help='Merged calls used to decide which input calls to retain')
+
+ args = parser.parse_args()
+
+ input_calls = pd.read_csv(args.inputcalls, sep='\t')
+ merged_calls = pd.read_csv(args.mergedcalls, sep=', ', engine='python')
+
+ input_calls['selected'] = False
+ for chrom, start, end in merged_calls[['chrom','start','end']].values:
+ input_calls.loc[(input_calls.chrom==chrom) & (input_calls.start<end) & (input_calls.end>start), 'selected'] = True
+
+ output_calls = input_calls[input_calls.selected].drop(columns=['selected'])
+ output_calls.to_csv(sys.stdout, sep='\t', index=False)
+
+if __name__ == '__main__':
+ main()
--
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