[Bioperl-l] Removing seq from SimpleAlign

[James Wasmuth]

Good Afternoon all,

I'm want to remove certain sequences from a multi-sequence alignment 
(msf format, converted from fasta), which is stored as a SimpleAlign object.

I know I'm supposed to use remove_seq() and that the arguement is a 
LocatableSeq object.  I create this latter object correctly, it seems, 
awarding it '-id', '-start' & '-end' properties.  

However I get the following error; MSG: Could not find the sequence to 
remoce from the start-end list

(typo's not mine!  ;o) )

I've looked at the remove_seq code to see what may be wrong.

It meets the  "if (exists $self->{'_start_end_lists'}->{$id})" condition 
and the -start and -end properties are coords from the alignment file, 
so I'm clearly not understanding what this start-end list is.  

 From the alignment file the sequence I'm trying to remove is
Name: NBC00095_6-157/1-164        Len:    164  Check:  8761  Weight:  1.00

And the LocatableSeq object is
-id='NBC00095_6-157', -start='1', -end='164'


Any pointers?

Many Thanks
James

-- 

Nematode Bioinformatics
Blaxter Nematode Genomics Group
Institute of Cell, Animal and Population Biology
Ashworth Labs
University of Edinburgh
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UK

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