[Bioperl-l] Bio::SeqIO issue

[Kevin Brown]

SeqIO is just a base framework for reading/writing of files. If you want
it to read a fasta format, then you tell it create it the object.

$seqio = Bio::SeqIO->new(-format=>'fasta');

Will tell the program to use Bio::SeqIO::fasta for the object. Look at
the docs for the various formats that Bio::SeqIO supports.

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilgert, Uwe
Sent: Wednesday, August 05, 2009 1:27 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Bio::SeqIO issue

Is my impression correct that Bio::SeqIO just assumes that sequences are
being submitted in FASTA format? In our experience, implementing
Bio::SeqIO led to the first line of files being cut off, regardless of
whether the files were indeed fasta files or files that only contained
sequence. Which, in the latter, led to sequence submissions that had the
first line of nucleotides removed. Has anyone tried to write a fix for
this?

 

Thanks,

Uwe

 

 

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

Uwe Hilgert, Ph.D.

Dolan DNA Learning Center

Cold Spring Harbor Laboratory

 

V: (516) 367-5185

E: hilgert at cshl.edu <mailto:hilgert at cshl.edu> 

F: (516) 367-5182

W: http://www.dnalc.org

 


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