From cec4f52e31d22d3b27e8c2d34cc2103f5b3d2036 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 14 Mar 2012 10:58:44 +0000
Subject: [PATCH] cleaner code
SVN: 24724
---
.../dist/etc/data-set-handler-alignment.py | 93 ++++++++++++++++---
1 file changed, 80 insertions(+), 13 deletions(-)
diff --git a/deep_sequencing_unit/dist/etc/data-set-handler-alignment.py b/deep_sequencing_unit/dist/etc/data-set-handler-alignment.py
index 97fad7cf8a9..52530a1fef8 100755
--- a/deep_sequencing_unit/dist/etc/data-set-handler-alignment.py
+++ b/deep_sequencing_unit/dist/etc/data-set-handler-alignment.py
@@ -9,15 +9,25 @@ TOTAL_READS, MAPPED_READS
Obviously you need a working samtools binary
+Uses 'flagstat' and 'view -H'
+
Note:
print statements go to: ~openbis/sprint/datastore_server/log/startup_log.txt
'''
import os
+import fnmatch
+import re
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
-FOLDER='/net/bs-dsu-data/array0/dsu/dss/incoming-jython-alignment/'
+FOLDER='/links/shared/dsu-dss/dss/incoming-jython-alignment/'
SAMTOOLS='/usr/local/dsu/samtools/samtools'
+BAM_PATTERN='*.bam'
+
+matches = []
+searchStrings = ['@PG']
+programList = []
# Create a "transaction" -- a way of grouping operations together so they all
# happen or none of them do.
@@ -30,27 +40,76 @@ dataSet.setMeasuredData(False)
incomingPath = incoming.getAbsolutePath()
# Get the incoming name
+# expected:
+# Project_110907_SN792_0059_AC012FACXX_3/Sample_BSSE-DSU-1662/BSSE-DSU-1662_CGATGTA_L003_R1_001_sorted.bam
name = incoming.getName()
-# expected incoming Name, e.g.:ETHZ_BSSE_110429_63558AAXX_1_sorted.bam
-split=name.split("_")
-sample=split[2]+ '_'+ split[3] + ':' + split[4]
+split=name.split('_')
+if (len(split) == 6):
+ incoming_sample=split[1]+ '_'+ split[2] + '_' + split[3] + '_' + split[4]+ ':' + split[-1]
+if (len(split) ==4):
+ incoming_sample=split[1]+ '_'+ split[2] + ':' + split[-1]
+
+
+# Looking for BAMS:
+for root, dirnames, filenames in os.walk(FOLDER + name):
+ for filename in fnmatch.filter(filenames, BAM_PATTERN):
+ matches.append(os.path.join(root, filename))
+
+# -----------------------------------------------------------------------------
+
+def listSearch (myList, searchString):
+ '''
+ Searches for a given String in a list.
+ Only lines matching the start of a line a considerd as a match
+ '''
+ matches = []
+ for i in range (0, len(myList)):
+ if(re.match(searchString, myList[i])):
+ matches.append(myList[i])
+ return (matches)
+
+# -----------------------------------------------------------------------------
+
+def programParameters (programList):
+ '''
+ Extracts the aligner datils from the bam header
+ '''
+ elements = {}
+ for program in range(0, len(programList)):
+ line = programList[program].split('\t')
+
+ for element in range (1, len(line)):
+ key, value = line[element].split(":")
+ elements[key] = value
+
+ return elements
+
# Extract values from a samtools view and set the results as DataSet properties
# Command: samtools view -H ETHZ_BSSE_110429_63558AAXX_1_sorted.bam
-arguments = SAMTOOLS + ' view -H ' + FOLDER + name
-#print('Arguments: '+ arguments)
+
+arguments = SAMTOOLS + ' view -H ' + matches[0]
+print('Arguments: '+ arguments)
cmdResult=os.popen(arguments).read()
-properties=cmdResult.split("\n")[-2].split('\t')
-aligner=(properties[1].split(':')[1].upper() + '_' + properties[2].split(':')[1])
-command=properties[3]
-arguments = SAMTOOLS + ' flagstat ' + FOLDER + name
+properties=cmdResult.split("\n")
+for s in range (0, len(searchStrings)):
+ programList = listSearch (properties, searchStrings[s])
+print(programList)
+
+e = programParameters (programList)
+
+dataSet.setPropertyValue("ALIGNMENT_SOFTWARE", e['ID'])
+dataSet.setPropertyValue("VERSION", e['VN'])
+dataSet.setPropertyValue("ISSUED_COMMAND", e['CL'])
+
+
+arguments = SAMTOOLS + ' flagstat ' + matches[0]
+
cmdResult=os.popen(arguments).read()
totalReads=cmdResult.split('\n')[0].split(' ')[0]
mappedReads=cmdResult.split('\n')[2].split(' ')[0]
-dataSet.setPropertyValue("ALIGNMENT_SOFTWARE", aligner)
-dataSet.setPropertyValue("ISSUED_COMMAND", command)
dataSet.setPropertyValue("SAMTOOLS_FLAGSTAT", cmdResult)
dataSet.setPropertyValue("TOTAL_READS", totalReads)
dataSet.setPropertyValue("MAPPED_READS", mappedReads)
@@ -63,8 +122,16 @@ search_service = transaction.getSearchService()
# Search for the sample
sc = SearchCriteria()
-sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
+sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, incoming_sample));
foundSamples = search_service.searchForSamples(sc)
if foundSamples.size() > 0:
dataSet.setSample(foundSamples[0])
+
+ # Search for parent data set of the same sample
+ dataSetSc = SearchCriteria()
+ dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, 'FASTQ_GZ'))
+ dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
+ foundDataSets = search_service.searchForDataSets(dataSetSc)
+ if foundDataSets.size() > 0:
+ dataSet.setParentDatasets([ds.getDataSetCode() for ds in foundDataSets])
--
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