A prototype script and library dependencies to extract a BAM list from a

reasonably well-formed PM's xls{x}-format spreadsheet or tsv file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6036 348d0f76-0448-11de-a6fe-93d51630548a

ivy.xml

@@ -60,6 +60,10 @@
     <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
+    <!-- POI, for reading pipeline files -->
+    <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
+    <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
+
     <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
     <exclude org="javax.servlet" />
     <exclude org="javax.jms" />

python/parse_pm_input.py

@@ -0,0 +1,81 @@
+#
+# Generates BAM lists from Excel and TSV files provided by project managers.  Suitable for input into the pre-QC metrics generation
+# script.
+#
+# To run:
+#   /humgen/gsa-hpprojects/software/bin/jython2.5.2/jython \
+#     -J-classpath $STING_HOME/lib/poi-3.8-beta3.jar:$STING_HOME/lib/poi-ooxml-3.8-beta3.jar:$STING_HOME/lib/poi-ooxml-schemas-3.8-beta3.jar:$STING_HOME/lib/xmlbeans-2.3.0.jar:$STING_HOME/lib/dom4j-1.6.1.jar
+#     parse_pm_input.py > <bam.list>
+#
+from java.io import FileInputStream
+from org.apache.poi.ss.usermodel import Row,Sheet,Workbook,WorkbookFactory
+
+import os,sys
+
+base_path = '/seq/picard_aggregation/%s/%s'
+
+def excel_reader(filename):
+    wb = WorkbookFactory.create(FileInputStream(filename));
+    for sheet_number in range(wb.getNumberOfSheets()):
+        project_column = None
+        sample_column = None
+
+        sheet = wb.getSheetAt(sheet_number);
+
+        for cell in sheet.getRow(0):
+            column_index = cell.getColumnIndex()
+            column_contents = cell.getStringCellValue()
+            if column_contents == 'Project':
+                project_column = column_index
+            if column_contents == 'External ID' or column_contents == 'Individual ID':
+                sample_column = column_index
+
+        if project_column != None and sample_column != None:
+            for row_number in range(1,sheet.getLastRowNum()+1):
+                project = sheet.getRow(row_number).getCell(project_column).getStringCellValue()
+                sample = sheet.getRow(row_number).getCell(sample_column).getStringCellValue()
+                yield project,sample
+            return
+
+def tsv_reader(filename):
+    f = open(filename,'rU')
+    for line in f:
+        tokens =line.split('\t')
+        project = tokens[0].strip()
+        sample = tokens[1].strip()
+        yield project,sample
+    f.close()    
+        
+def create_reader(filename):
+    extension = os.path.splitext(filename)[1]
+    if extension == '.xls' or extension == '.xlsx':
+        return excel_reader(filename)
+    elif extensions == '.tsv' or extension == '.txt':
+        return tsv_reader(filename)
+    else:
+        print 'Unrecognized file extension',extension
+        sys.exit(1)
+
+if len(sys.argv) != 2:
+    print 'USAGE: %s <input file.{xls|xlsx|tsv|txt}>'
+    sys.exit(1)
+if not os.path.exists(sys.argv[1]):
+    print 'Input file %s not found' % sys.argv[1]
+    sys.exit(1)
+
+input_filename = sys.argv[1]
+
+for project,sample in create_reader(input_filename):
+    sample_path = base_path % (project,sample)
+    versions = []
+    for version_path in os.listdir(sample_path):
+        if version_path[0] != 'v':
+            print 'Hit a path name that cannot be parsed: ',version_path
+            sys.exit(1)
+        versions.append(int(version_path[1:]))
+    versions = sorted(versions)
+    bam_file = '%s/v%d/%s.bam' % (sample_path,versions[-1],sample)
+    if not os.path.exists(bam_file):
+        print 'Malformed file: tried to find %s, but no such path exists' % bam_file
+        sys.exit(1)
+    print bam_file