[Bioperl-l] creating a simplealign object from strings

[luisa pugliese]

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
[----------DPQMWDFDDLNFTG-MP-PADE-DYSPCMLET-ETLNKYVV---II---AYA--LVF--L--LSL
LGNSL-----VM----L----VILY-----SRV-----GR-----SV-TD-----V--YL-LN-LALADLLFAL--
---TLPIWAASKV-----NG------WIF--GTF-----LC-KVVSL----L----K----E-----VN---FY--
-SG-I-----LL-----LACISV--D-R--YL-----AIVH---ATR---T-----L----TQ---K---RH----
L-----VK-FV-----CLG-----CWGLSMNLSL-----PFFLFRQ----AY-----HPNNSSP--VCYEVLG---
--NDTAKWRMVL-----RI--LPHT--FGFIVPLFVMLFCYGF-TLRTLFKAHM-----------------GQ---
-KHR-----A---M-RVIFAVV-LIFLLC---WLP----YNLVLLADTLMRTQV7TCERRNNIGRALDATEILGFL
---H---SC-----L--NP----IIYA-----FIGQ---N-----FRH----GF-----L-----K--ILAMHGLV
SKEFLA--RHRVTS-----------------------------] which does not look healthy
STACK Bio::PrimarySeq::seq
/home/luisa/bioperl_new/bioperl-1.4/Bio/PrimarySeq.pm:268
STACK Bio::PrimarySeq::new
/home/luisa/bioperl_new/bioperl-1.4/Bio/PrimarySeq.pm:217
STACK Bio::LocatableSeq::new
/home/luisa/bioperl_new/bioperl-1.4/Bio/LocatableSeq.pm:100
STACK toplevel /home/luisa/perl/string2seq.pl:33
-------------------------------
This is not the first sequence in the file and on a smaller set the script
worked.
Does anybody knows what should I do in order to avoid this problem?
Thanking you all,
best regards
Luisa

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