[Bioperl-l] Bio:SeqIO fasta

[Stephen Baird]

Hi,
  I was using Bio:SeqIO in a CGI script taking in some data that's
supposed to be in fasta format from a text area. I noticed that if there
was no definition line (ie. one that starts with a >) it would take the
first line of sequence and put that as the defline. 
  I tried "the simplest ever reformatter" to recheck it and also noticed
that putting raw in as the format makes the IO.pm module fail. 

I was going to use Bio::SeqIO to help clean up user's sequence data pasted
in the wrong format. Should I just clean up the input using perl
or is there something in Bioperl that will test the sequence's
format....sort of like Don Gilbert's 'readseq'?

Thanks for all the hard work,

|--------------------------------------------------------------------|
| Stephen Baird                        sbaird@mgcheo.med.uottawa.ca  |
| Molecular Genetics                       tel: 613-738-3925         |
| Children's Hospital of Eastern Ontario   fax: 613-738-4833         |
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| K1H 8L1                                                            |
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