[Bioperl-l] reading an alignment

[luisa pugliese]

Dear all,
   again me... now there is something that should be really trivial, but I
am not able to do.
I created an alignment with bioperl, then when I try to read it back, if I
use the syntax:
 $profile1 = 'test1.msf'
I am able to work on it with clustalw but I am not able to loop over it with
foreach my $sel_seq ($profile1->each_seq){
}
on the other side, I am not able to read it with the syntax:
my $in = Bio::AlignIO->new(-format => 'msf',
      -file   => 'test1.msf');
my $aln = $in ->next_aln();
because I get the following error message:

------------------- WARNING ---------------------
MSG: seq doesn't validate, mismatch is 1
---------------------------------------------------

------------- EXCEPTION  -------------
MSG: Attempting to set the sequence to
[/1-650-------------------ANQTL-GG-DFFL-LGIFS-----QISHPGR/1-650L---CL---LIF-
-SIF--L--MAVSWNIT-----LI----L----LIHI/1-650-----DSS-----LH-----TP-MY-----F--
FI-NQ-LSLIDLTYISV/1-650----TVPKMLVNQL-----AK-----DKTI--SVL-----GC-GTQMY--/1-
650--F----Y----L-----QL---GG---AE-C-----CL-----LAAMAY/1-650--D-R--YV-----AIC
H---PLR--YS-----V----LM---S---HR-/1-650---V-----CL-LL-----ASG-----CWFVGSVDGF
MLT--PIAMSF--/1-650---PF-----CRSHEIQHFFCEVPAVLKLS-CSDTSLYKIF-----MY--/1-650L
CCV--IMLLIPVTVISVSYYY-IILTIHKMNS--------VEGR-----/1-650KK----AFT-----T---C-S
SHITVV-SLFYG---------------AA/1-650IYNYMLP-----SSYQTPEKDMMSSFFYTIL---T---PV-
----L--NP/1-650----IIYS-----FRNK---D-----VTR----AL-----K-----K--M/1-650LSV--
---------------------------------------------] 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 Bio::AlignIO::msf::next_aln
/home/luisa/bioperl_new/bioperl-1.4/Bio/AlignIO/msf.pm:133
STACK toplevel /home/luisa/bioperl_course/work_on_clustalw.pl:71
------------------------------------
many thanks if somebody can open my eyes on what is going on!
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