Mercurial > repos > yhoogstrate > fastq_replace_dots_for_n

annotate FASTQ_replace_dots_for_N.py @ 0:f2939b8fb2e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yhoogstrate
date Thu, 19 Dec 2013 10:53:31 -0500
parents
children f7c90e81c05d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
1 #!/usr/bin/env python
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
2
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
3 import sys
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
4 from Bio import Seq, SeqRecord, SeqIO
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
5
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
6 if(sys.argv[0] == ''):
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
7 input_stream = sys.stdin
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
8 else:
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
9 input_stream = fh.open(sys.argv[0],"r")
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
10
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
11 for record in SeqIO.parse(input_stream,"fastq-sanger"):
f2939b8fb2e1 Uploaded
yhoogstrate
parents:
diff changeset
12 SeqIO.write(SeqRecord.SeqRecord(seq=Seq.Seq(str(record.seq).replace(".","N")),letter_annotations=record.letter_annotations,id=record.id,name=record.name,description=record.description),sys.stdout,"fastq-sanger")