sam2fastx.py updated

fastq2fasta.py

@@ -10,95 +10,81 @@
 import argparse, gzip, os, sys
 from datetime import datetime
 
-'''def report(read,fastaOut,qualsOut,phred):
-  """ """
-  id,seq,spacer,quals = read
-  
-  #store fasta
-  fastaOut.write( '>%s\n%s\n' % ( id[1:],seq ) )
-  
-  #store quals
-  if qualsOut:
-    formattedQuals = ' '.join( str( ord(q)-phred ) for q in quals ) 
-    qualsOut.write( '>%s\n%s\n' % ( id[1:],formattedQuals ) )
-
-#def fastq2fasta( inFn,outFn,outQuals,phred,verbose ):'''
-
 def report(read, output, minLen, qualityTh, offset):
-	""" """
-	id,seq,spacer,quals = read
-	#cut @ Ns
-	if 'N' in seq:
-		iN = seq.index('N')
-		if iN<minLen:
-			return
-		seq = seq[:iN]
+    """ """
+    id,seq,spacer,quals = read
+    #cut @ Ns
+    if 'N' in seq:
+        iN = seq.index('N')
+        if iN<minLen:
+            return
+        seq = seq[:iN]
 
-	#cut @ low quality
-	if qualityTh:
-		qualsL = []
-		for i in range(len(seq)):
-			q = quals[i]
-			if ord(q)-offset < qualityTh:
-				break
-			qualsL.append(q)
-		#skip if too short	
-		if i<minLen:
-			return
-		#trim seq
-		seq = seq[:i+1]
+    #cut @ low quality
+    if qualityTh:
+        qualsL = []
+        for i in range(len(seq)):
+            q = quals[i]
+            if ord(q)-offset < qualityTh:
+                    break
+            qualsL.append(q)
+        #skip if too short	
+        if i<minLen:
+            return
+        #trim seq
+        seq = seq[:i+1]
+
+    #store fasta				
+    output.write('>%s\n%s\n' % (id[1:], "\n".join(seq[i:i+100] for i in range(0,len(seq),100))))
 
-	#store fasta				
-	output.write('>%s\n%s\n' % (id[1:], "\n".join(seq[i:i+100] for i in range(0,len(seq),100))))
-
 def fastq2fasta(input, output, minLen, qualityTh, offset, verbose):
-	"""
-	"""
-	#parse fastq    
-	read = []
-	for line in input:
-		#skip empty lines
-		line = line.strip()
-		if not line:
-	  		continue
-		#store read info
-		read.append(line)
-		#report reads
-		if len(read)==4:
-	  		report(read, output, minLen, qualityTh, offset)
-	  		read = []
+    """
+    """
+    #parse fastq    
+    read = []
+    for line in input:
+        #skip empty lines
+        line = line.strip()
+        if not line:
+            continue
+        #store read info
+        read.append(line)
+        #report reads
+        if len(read)==4:
+            report(read, output, minLen, qualityTh, offset)
+            read = []
 
 def main():
-
-	usage   = "%(prog)s [options] -v " 
-	parser  = argparse.ArgumentParser( usage=usage,description=desc,epilog=epilog )
 
-	parser.add_argument("-v", action="store_true", dest="verbose", default=False)
-	parser.add_argument('--version', action='version', version='1.0')   
-	parser.add_argument("-i", dest="input",  default=sys.stdin, 
-						help="input file [stdin]")
-	parser.add_argument("-o", dest="output", default=sys.stdout, 
-						help="output file [stdout]")
-	parser.add_argument("-l", dest="minLen", default=0, type=int,
-						help="skip reads shorter than [%(default)s]" )
-	parser.add_argument("-q", dest="qualityTh", default=0, type=int,
-						help="read is clipped @ first base having PHRED quality lower than [%(default)s]" )
-	#parser.add_argument("-q", dest="quals", default="", help="output quals to file [%(default)s]")
-	parser.add_argument("--offset", dest="offset", default=33, type=int, 
-						help="quality encoding; PHRED+33 (Sanger) or PHRED+64 (Illumina/Solexa) [%(default)s]")
+    usage   = "%(prog)s [options] -v " 
+    parser  = argparse.ArgumentParser( usage=usage,description=desc,epilog=epilog )
+
+    parser.add_argument("-v", action="store_true", dest="verbose", default=False)
+    parser.add_argument('--version', action='version', version='1.0')   
+    parser.add_argument("-i", dest="input",  default=sys.stdin, 
+                                            help="input file [stdin]")
+    parser.add_argument("-o", dest="output", default=sys.stdout, 
+                                            help="output file [stdout]")
+    parser.add_argument("-l", dest="minLen", default=0, type=int,
+                                            help="skip reads shorter than [%(default)s]" )
+    parser.add_argument("-q", dest="qualityTh", default=0, type=int,
+                                            help="read is clipped @ first base having PHRED quality lower than [%(default)s]" )
+    #parser.add_argument("-q", dest="quals", default="", help="output quals to file [%(default)s]")
+    parser.add_argument("--offset", dest="offset", default=33, type=int, 
+                                            help="quality encoding; PHRED+33 (Sanger) or PHRED+64 (Illumina/Solexa) [%(default)s]")
 
-	o = parser.parse_args()
+    o = parser.parse_args()
 
-	#fastq2fasta( o.inFn,o.outFn,o.quals,o.phred,o.verbose )
-	fastq2fasta(o.input, o.output, o.minLen, o.qualityTh, o.offset, o.verbose)
+    #fastq2fasta( o.inFn,o.outFn,o.quals,o.phred,o.verbose )
+    fastq2fasta(o.input, o.output, o.minLen, o.qualityTh, o.offset, o.verbose)
 
 if __name__=='__main__': 
-	t0=datetime.now()
-  try:
-  	main()
-  except KeyboardInterrupt:
-    sys.stderr.write("\nCtrl-C pressed!      \n")
-  except IOError as e:
-    sys.stderr.write("I/O error({0}): {1}\n".format(e.errno, e.strerror))
-	dt=datetime.now()-t0
-	sys.stderr.write("#Time elapsed: %s\n" % dt)
+    t0=datetime.now()
+    try:
+        main()
+    except KeyboardInterrupt:
+        sys.stderr.write("\nCtrl-C pressed!      \n")
+    except IOError as e:
+        sys.stderr.write("I/O error({0}): {1}\n".format(e.errno, e.strerror))
+    dt=datetime.now()-t0
+    sys.stderr.write("#Time elapsed: %s\n" % dt)

sam2fastx.py

@@ -147,6 +147,11 @@ def main():
 
 if __name__=='__main__': 
     t0 = datetime.now()
-    main()
+    try:
+        main()
+    except KeyboardInterrupt:
+        sys.stderr.write("\nCtrl-C pressed!      \n")
+    except IOError as e:
+        sys.stderr.write("I/O error({0}): {1}\n".format(e.errno, e.strerror))
     dt = datetime.now()-t0
     sys.stderr.write( "#Time elapsed: %s\n" % dt )