[Bioperl-l] perl one-liner with Bio::SeqIO
Alper Yilmaz
alperyilmaz at gmail.com
Thu Jul 22 00:09:38 EDT 2010
Hi,
I was using Bio::SeqIO with perl one-liner and I noticed an oddity.
Can someone suggest a correction or workaround?
Let test.fa be;
>1
AGTC
>2
CTGA
Then, commandline below prints the expected output:
$ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while
($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' <
test.fa
output:
1 AGTC
2 CTGA
However, if use the command in a pipe, then the output has an issue
with primary_id of initial sequence.
$ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh
=>\*STDIN); while ($myseq=$seq->next_seq){ print
$myseq->id,"\t",$myseq->seq,"\n"}'
output:
AGTC
2 CTGA
What is the workaround to make Bio::SeqIO work correctly in a
one-liner with pipes?
thanks,
Alper Yilmaz
Post-doctoral Researcher
Plant Biotechnology Center
The Ohio State University
1060 Carmack Rd
Columbus, OH 43210
(614)688-4954
PS: Normally, the example is demonstrating useless use of cat, for the
sake giving an example, it can be "command1 | command2 | command3 |
perl -MBioSeqIO -e'...' " instead..
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