diff fastq_name_affixer.py @ 3:e320ef2d105a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_name_affixer.py	Thu Sep 05 09:04:56 2019 -0400
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+import sys
+
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option("-f", "--fastq", dest="fastq", help="fastq file")
+parser.add_option("-p", "--prefix", dest="prefix", help="prefix to be added to names")
+parser.add_option("-s", "--suffix", dest="suffix", help="suffix to be added",default='')
+parser.add_option("-n", "--nspace", dest="nspace", help="number of spaces to ignore",default='0')
+options, args = parser.parse_args()
+nspace=int(options.nspace)
+
+f=open(options.fastq,"r")
+j=0
+for oneline in f:
+    if oneline=="":
+        continue
+    j+=1
+    if j==5:
+        j=1
+    if not oneline:
+        break
+   
+    if (oneline[0]=="@" and j==1) or (oneline[0]=="+" and len(oneline)>2 and j==3):
+        header=" ".join(oneline.split()[:1+nspace])
+        header_out=header[0]+options.prefix+header[1:]+options.suffix+"\n"
+        sys.stdout.write(header_out)
+    else:
+        sys.stdout.write(oneline)
+