[Bioperl-l] creating a simplealign object from strings

luisa pugliese luisa.pugliese at safan-bioinformatics.it
Wed Oct 20 10:38:32 EDT 2004

Dear all,
    I am working with a huge protein alignment that comes from a web page
and I would like to import it into bioperl. In order to do this I created a
hash with seqnames as keys and sequences, including gaps, as values. Then I
used LocatableSeq in order to create sequence objects that can be then
imported into a simplealign object with the function add_seq.
Using LocatableSeq I got the following error:
MSG: Attempting to set the sequence to
SKEFLA--RHRVTS-----------------------------] which does not look healthy
STACK Bio::PrimarySeq::seq
STACK Bio::PrimarySeq::new
STACK Bio::LocatableSeq::new
STACK toplevel /home/luisa/perl/string2seq.pl:33
This is not the first sequence in the file and on a smaller set the script
Does anybody knows what should I do in order to avoid this problem?
Thanking you all,
best regards

Luisa Pugliese, Ph.D.
luisa.pugliese at safan-bioinformatics.it
Corso Tazzoli 215/13 -10137 Torino - ITALY
tel +39 011 3026230
fax +39 011 3165080
cell. +39 333 6130644

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