drop box script for handling bam files

SVN: 22857

deep_sequencing_unit/dist/etc/data-set-handler-alignment.py

+'''
+This is handling bowtie-BAM files and extracts some properties from the BAM header and
+the samtools flagstat command. The results are formatted and attached  as a property
+to the openBIS DataSet.
+Prerequisites are the DataSetType: ALIGNMENT and
+the following properties assigned to the DataSetType mentioned above:
+ALIGNMENT_SOFTWARE, ISSUED_COMMAND, SAMTOOLS_FLAGSTAT,
+TOTAL_READS, MAPPED_READS
+
+Obviously you need a working samtools binary
+
+Note: 
+print statements go to: ~openbis/sprint/datastore_server/log/startup_log.txt
+'''
+
+import os
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+FOLDER='/net/bs-dsu-data/array0/dsu/dss/incoming-jython-alignment/'
+SAMTOOLS='/usr/local/dsu/samtools/samtools'
+
+# Create a "transaction" -- a way of grouping operations together so they all
+# happen or none of them do.
+transaction = service.transaction()
+ 
+# Create a data set and set type
+dataSet = transaction.createNewDataSet("ALIGNMENT")
+dataSet.setMeasuredData(False)
+
+incomingPath = incoming.getAbsolutePath()
+
+# Get the incoming name 
+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] 
+
+# 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)
+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
+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)
+ 
+# Add the incoming file into the data set
+transaction.moveFile(incomingPath, dataSet)
+
+# Get the search service
+search_service = transaction.getSearchService()
+
+# Search for the sample
+sc = SearchCriteria()
+sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
+foundSamples = search_service.searchForSamples(sc)
+
+if foundSamples.size() > 0:
+  dataSet.setSample(foundSamples[0])