diff deinterlacer.py @ 3:e320ef2d105a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deinterlacer.py	Thu Sep 05 09:04:56 2019 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+'''very simple deinterlacer - fasta and fastq'''
+import sys
+import itertools
+
+
+def is_header(line, counter, fasta):
+    ''' return True is line is header '''
+    if fasta:
+        if line[0] == ">":
+            return True
+    else:
+        if counter == 4 and line[0] == "@":
+            return True
+    return False
+
+
+def main():
+    '''deinterlace fasta or fastq format'''
+    infile = sys.argv[1]
+    file_a = sys.argv[2]
+    file_b = sys.argv[3]
+    with open(infile) as f, open(file_a, 'w') as A, open(file_b, 'w') as B:
+        ABiter = itertools.cycle([A, B])
+        counter = 3  # four lines per record in fastq
+        pos = f.tell()
+        is_fasta = f.readline()[0] == ">"
+        f.seek(pos)
+        for line in f:
+            counter += 1
+            if is_header(line, counter, is_fasta):
+                fout = next(ABiter)
+                counter = 0
+            fout.write(line)
+
+
+if __name__ == "__main__":
+    main()