sebhtml · plpla · Oct 17, 2012
diff --git a/Illumina_MiSeq/ElectricFancyFox.py b/Illumina_MiSeq/ElectricFancyFox.py
@@ -1,172 +1,177 @@
-#!/usr/bin/env python
-# encoding: utf-8
-# Title: "Electric Fancy Fox . Python"
-# written by sebHTML (S. Boisvert)
-# 2012-06-11
-# reason for creating this software:
-#  the last Illumina(R) MiSeq(R) run failed to convert the data on board
-# because of a faulty cluster density.
-
-"""
-
-The Illumina(R) MiSeq(TM) from Illumina Inc.
-produces a sample sheet file on board, but it is not compatible
-with Illumina(R) CASAVA.
-
-
-
-
-Legal stuff.
-
-ILLUMINA® is a registered trademark of Illumina, Inc.
-
-
-<This is a Illumina(R) MiSeq(R) SampleSheet>
-
-[Header]
-IEMFileVersion,4
-Investigator Name,LR
-Project Name,LSPQ
-Experiment Name,20120606
-Date,6/6/2012
-Workflow,GenerateFASTQ
-Application,FASTQ Only
-Assay,TruSeq DNA/RNA
-Description,
-Chemistry,Default
-
-[Reads]
-151
-151
-
-[Settings]
-
-[Data]
-Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Sample_Project,index,I7_Index_ID,Description,GenomeFolder
-90377-1,,LSPQ20120606,A01,,ATCACG,A001,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-90443-1,,LSPQ20120606,A02,,CGATGT,A002,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-90941-1,,LSPQ20120606,A03,,TTAGGC,A003,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-91375-1,,LSPQ20120606,A04,,TGACCA,A004,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-91378-1,,LSPQ20120606,A05,,ACAGTG,A005,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-91655-1,,LSPQ20120606,A06,,GCCAAT,A006,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-91664-1,,LSPQ20120606,A07,,CAGATC,A007,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-91845-1,,LSPQ20120606,A08,,CTTGTA,A012,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-92375-1,,LSPQ20120606,A09,,AGTCAA,A013,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-93302-1,,LSPQ20120606,A10,,AGTTCC,A014,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-93363-1,,LSPQ20120606,A11,,ATGTCA,A015,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-90494-1,,LSPQ20120606,A12,,CCGTCC,A016,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-90505-1,,LSPQ20120606,B01,,GTCCGC,A018,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-93302-2,,LSPQ20120606,B02,,GTGAAA,A019,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-
-</This is a Illumina(R) MiSeq(R) SampleSheet>
-
-for dual indexes:
-
-Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Sample_Project,index,I7_Index_ID,index2,I5_Index_ID,Description,GenomeFolder
-
-<This is a Illumina(R) CASAVA(R) SampleSheet>
-
-FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
-000000000-A0VER,1,R6_WT,,GCCAAT,,N,PE_indexing,FR,RNA-seq_spr0058_20120604
-000000000-A0VER,1,R6_KOspr0058,,CTTGTA,,N,PE_indexing,FR,RNA-seq_spr0058_20120604
-
-</This is a Illumina(R) CASAVA(R) SampleSheet>
-
-"""
-
-import sys
-
-programName=sys.argv[0]
-
-if len(sys.argv)!=3:
-	print "Usage:"
-	print programName+"	inputMiSeqSampleSheet	outputCASAVASampleSheet"
-	sys.exit(1)
-
-miseqSampleSheet=sys.argv[1]
-
-output=sys.argv[2]
-
-flowcellIdentifier="Unknown"
-lane="1"
-machineOperator="Unknown"
-projectName="Unknown"
-
-started=False
-
-operationCode_Header="[Header]"
-operationCode_Reads="[Reads]"
-operationCode_Settings="[Settings]"
-operationCode_Data="[Data]"
-
-stream=open(output,"w")
-
-print "Welcome to this tool."
-
-print "I will process the MiSeq sample sheet <"+miseqSampleSheet+"> today."
-stream.write("FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject")
-stream.write("\n")
-
-gotHeader=False
-
-for line in open(miseqSampleSheet):
-	operationCode=line.strip()
-	if operationCode==operationCode_Data:
-		started=True
-		continue
-
-	if line.find("Project Name,")>=0:
-		projectName=line.replace("Project Name,","").strip()
-
-	if not started:
-		continue
-
-	if not gotHeader:
-		gotHeader=True
-		continue
-
-	tokens=line.split(",")
-
-
-# MiSeq format
-# Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Sample_Project,index,I7_Index_ID,Description,GenomeFolder
-# 90377-1,,LSPQ20120606,A01,,ATCACG,A001,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
-
-	sampleName=tokens[1].strip()
-
-	# take the identifier if the name is empty.
-	if sampleName=="":
-		print "Warning: Sample_Name is empty, will use Sample_ID for the sample name"
-		sampleName=tokens[0].strip()
-
-	if sampleName=="":
-		print "Error: sample name is empty."
-		sys.exit(1)
-
-	index=tokens[5].strip()
-
-	if len(tokens)==11:
-		index=tokens[5].strip()+"-"+tokens[7].strip()
-
-
-# CASAVA format
-#FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
-#000000000-A0VER,1,R6_WT,,GCCAAT,,N,PE_indexing,FR,RNA-seq_spr0058_20120604
-
-
-	stream.write(flowcellIdentifier+",")
-	stream.write(lane+",")
-	stream.write(sampleName+",")
-	stream.write(",")
-	stream.write(index+",")
-	stream.write(",")
-	stream.write("N,")
-	stream.write("PE_indexing,")
-	stream.write(machineOperator+",")
-	stream.write(projectName)
-
-	stream.write("\n")
-stream.close()
-
-print "CASAVA Sample sheet file <"+output+"> is now on the disk"
-print "Have a nice day."
+#!/usr/bin/env python
+# encoding: utf-8
+# Title: "Electric Fancy Fox . Python"
+# written by sebHTML (S. Boisvert)
+# updated by plpla (Pier-Luc Plante)
+# 2012-10-17
+# reason for creating this software:
+# the last Illumina(R) MiSeq(R) run failed to convert the data on board
+# because of a faulty cluster density.
+
+"""
+
+The Illumina(R) MiSeq(TM) from Illumina Inc.
+produces a sample sheet file on board, but it is not compatible
+with Illumina(R) CASAVA.
+
+This program was upgraded because of a system upgrade.
+
+
+Legal stuff.
+
+ILLUMINA� is a registered trademark of Illumina, Inc.
+
+
+<This is a Illumina(R) MiSeq(R) SampleSheet>
+
+[Header]
+IEMFileVersion,4
+Investigator Name,LR
+Project Name,LSPQ
+Experiment Name,20120606
+Date,6/6/2012
+Workflow,GenerateFASTQ
+Application,FASTQ Only
+Assay,TruSeq DNA/RNA
+Description,
+Chemistry,Default
+
+[Reads]
+151
+151
+
+[Settings]
+
+[Data]
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Sample_Project,index,I7_Index_ID,Description,GenomeFolder
+90377-1,,LSPQ20120606,A01,,ATCACG,A001,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+90443-1,,LSPQ20120606,A02,,CGATGT,A002,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+90941-1,,LSPQ20120606,A03,,TTAGGC,A003,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+91375-1,,LSPQ20120606,A04,,TGACCA,A004,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+91378-1,,LSPQ20120606,A05,,ACAGTG,A005,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+91655-1,,LSPQ20120606,A06,,GCCAAT,A006,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+91664-1,,LSPQ20120606,A07,,CAGATC,A007,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+91845-1,,LSPQ20120606,A08,,CTTGTA,A012,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+92375-1,,LSPQ20120606,A09,,AGTCAA,A013,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+93302-1,,LSPQ20120606,A10,,AGTTCC,A014,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+93363-1,,LSPQ20120606,A11,,ATGTCA,A015,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+90494-1,,LSPQ20120606,A12,,CCGTCC,A016,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+90505-1,,LSPQ20120606,B01,,GTCCGC,A018,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+93302-2,,LSPQ20120606,B02,,GTGAAA,A019,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+
+</This is a Illumina(R) MiSeq(R) SampleSheet>
+
+for dual indexes before update:
+
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Sample_Project,index,I7_Index_ID,index2,I5_Index_ID,Description,GenomeFolder
+
+for dual indexes after Illumina(R) MiSeq(R) upgrade:
+
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+
+<This is a Illumina(R) CASAVA(R) SampleSheet>
+
+FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
+000000000-A0VER,1,R6_WT,,GCCAAT,,N,PE_indexing,FR,RNA-seq_spr0058_20120604
+000000000-A0VER,1,R6_KOspr0058,,CTTGTA,,N,PE_indexing,FR,RNA-seq_spr0058_20120604
+
+</This is a Illumina(R) CASAVA(R) SampleSheet>
+
+"""
+
+import sys
+
+programName=sys.argv[0]
+
+if len(sys.argv)!=3:
+	print "Usage:"
+	print programName+" inputMiSeqSampleSheet outputCASAVASampleSheet"
+	sys.exit(1)
+
+miseqSampleSheet=sys.argv[1]
+
+output=sys.argv[2]
+
+flowcellIdentifier="Unknown"
+lane="1"
+machineOperator="Unknown"
+projectName="Unknown"
+
+started=False
+
+operationCode_Header="[Header]"
+operationCode_Reads="[Reads]"
+operationCode_Settings="[Settings]"
+operationCode_Data="[Data]"
+
+stream=open(output,"w")
+
+print "Welcome to this tool."
+
+print "I will process the MiSeq sample sheet <"+miseqSampleSheet+"> today."
+stream.write("FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject")
+stream.write("\n")
+
+gotHeader=False
+
+for line in open(miseqSampleSheet):
+	operationCode=line.strip()
+	if operationCode==operationCode_Data:
+		started=True
+		continue
+
+	if line.find("Project Name,")>=0:
+		projectName=line.replace("Project Name,","").strip()
+
+	if not started:
+		continue
+
+	if not gotHeader:
+		gotHeader=True
+		continue
+
+	tokens=line.split(",")
+
+
+# MiSeq format
+# Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Sample_Project,index,I7_Index_ID,Description,GenomeFolder
+# 90377-1,,LSPQ20120606,A01,,ATCACG,A001,,PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
+
+	sampleName=tokens[1].strip()
+
+# take the identifier if the name is empty.
+	if sampleName=="":
+		print "Warning: Sample_Name is empty, will use Sample_ID for the sample name"
+		sampleName=tokens[0].strip()
+
+	if sampleName=="":
+		print "Error: sample name is empty."
+		sys.exit(1)
+
+	index=tokens[5].strip()
+
+	if len(tokens)==10:
+		index=tokens[5].strip()+"-"+tokens[7].strip()
+
+
+# CASAVA format
+#FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
+#000000000-A0VER,1,R6_WT,,GCCAAT,,N,PE_indexing,FR,RNA-seq_spr0058_20120604
+
+
+	stream.write(flowcellIdentifier+",")
+	stream.write(lane+",")
+	stream.write(sampleName+",")
+	stream.write(",")
+	stream.write(index+",")
+	stream.write(",")
+	stream.write("N,")
+	stream.write("PE_indexing,")
+	stream.write(machineOperator+",")
+	stream.write(projectName)
+
+	stream.write("\n")
+stream.close()
+
+print "CASAVA Sample sheet file <"+output+"> is now on the disk"
+print "Have a nice day."