From 97fd01f393c2354f4dc52f0700a951399b92a8fc Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:42:56 +0200
Subject: [PATCH] Changed to make it compatible for new file structure
---
.../flexiprep/scripts/summarize_flexiprep.py | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
index ce0723be8..cdf952472 100755
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
@@ -116,7 +116,7 @@ def clip2dict(sample, samplea, sampleb, lib_type, run_dir):
def get_sync_stats(sample):
stats = {}
- with open_result(sample + '.clipsync.stats') as src:
+ with open_result(sample + '.clip.sync.stats') as src:
sync_txt = src.read()
stats['num_reads_discarded_1'] = int(re.search(re_disc_1, sync_txt).group(1))
@@ -146,15 +146,19 @@ def clip2dict(sample, samplea, sampleb, lib_type, run_dir):
return clip_stats
-def sickle2dict(run_name, lib_type, run_dir):
+def sickle2dict(run_name, qc_mode, lib_type, run_dir):
trim_stats = {}
+ if qc_mode == 'trim':
+ stat_mark = '.trim.stats'
+ else:
+ stat_mark = '.clip.sync.trim.stats'
if lib_type == 'paired':
re_paired_kept = re.compile(r'paired records kept: \d+ \((\d+) pairs\)')
re_disc = re.compile(r'single records discarded: \d+ \(from PE1: (\d+), from PE2: (\d+)\)')
re_disc_paired = re.compile(r'paired records discarded: \d+ \((\d+) pairs\)')
- with open(os.path.join(run_dir, run_name + '.filtersync.stats')) as src:
+ with open(os.path.join(run_dir, run_name + stat_mark)) as src:
sickle_txt = src.read()
discarda = int(re.search(re_disc, sickle_txt).group(1))
@@ -170,7 +174,7 @@ def sickle2dict(run_name, lib_type, run_dir):
else:
re_kept = re.compile(r'records kept: (\d+)')
re_disc = re.compile(r'records discarded: (\d+)')
- with open(os.path.join(run_dir, run_name + '.filtersync.stats')) as src:
+ with open(os.path.join(run_dir, run_name + stat_mark)) as src:
sickle_txt = src.read()
trim_stats['num_reads_kept'] = int(re.search(re_kept, sickle_txt).group(1))
@@ -399,7 +403,7 @@ def summarize_flexiprep(run_name, qc_mode, samplea, sampleb, outf, run_dir):
sumd['stats']['clip'] = clip2dict(run_name, samplea, sampleb, lib_type, run_dir)
if 'trim' in qc_mode:
- sumd['stats']['trim'] = sickle2dict(run_name, lib_type, run_dir)
+ sumd['stats']['trim'] = sickle2dict(run_name, qc_mode, lib_type, run_dir)
dict2json(sumd, outf)
--
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