From bf0c77528411976b18e1a26677f6eeb99dce87d0 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 26 Feb 2018 16:09:05 +0100
Subject: [PATCH] rework input functions
---
Snakefile | 26 +++++++++++++-------------
1 file changed, 13 insertions(+), 13 deletions(-)
diff --git a/Snakefile b/Snakefile
index d5b3431..ebd1e63 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,4 +1,5 @@
import json
+from functools import partial
from os.path import join, basename
from os import mkdir
@@ -82,31 +83,30 @@ except OSError:
pass
-def get_r1(wildcards):
+def get_r(strand, wildcards):
+ """Get fastq files on a single strand for a sample"""
s = SAMPLE_CONFIG['samples'].get(wildcards.sample)
- r1 = []
+ rs = []
for l in sorted(s['libraries'].keys()):
- r1.append(s['libraries'][l]['R1'])
- return r1
+ rs.append(s['libraries'][l][strand])
+ return rs
-
-def get_r2(wildcards):
- s = SAMPLE_CONFIG['samples'].get(wildcards.sample)
- r2 = []
- for l in sorted(s['libraries'].keys()):
- r2.append(s['libraries'][l]['R2'])
- return r2
+get_r1 = partial(get_r, "R1")
+get_r2 = partial(get_r, "R2")
def get_bedpath(wildcards):
- return [x for x in BEDS if basename(x) == wildcards.bed][0]
+ """Get absolute path of a bed file"""
+ return next(x for x in BEDS if basename(x) == wildcards.bed)
def get_refflatpath(wildcards):
- return [x for x in REFFLATS if basename(x) == wildcards.refflat][0]
+ """Get absolute path of a refflat file"""
+ return next(x for x in REFFLATS if basename(x) == wildcards.refflat)
def sample_gender(wildcards):
+ """Get sample gender"""
sam = SAMPLE_CONFIG['samples'].get(wildcards.sample)
return sam.get("gender", "null")
--
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