[Bioperl-l] Still a problem with sort_alphabetically

[AUnderwood@PHLS.org.uk]

Having read in alignment using AlignIO, I can process the alignment with no
problems. However as soon as I execute the command $aln->sort_aplhabetically
I get the following error message:


MSG: Got a sequence with no letters in - cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet
C:/Perl/site/lib/Bio/PrimarySeq.pm:822
STACK Bio::PrimarySeq::seq C:/Perl/site/lib/Bio/PrimarySeq.pm:286
STACK Bio::PrimarySeq::new C:/Perl/site/lib/Bio/PrimarySeq.pm:231
STACK Bio::LocatableSeq::new C:/Perl/site/lib/Bio/LocatableSeq.pm:102 

At first I thought this was due to gaps at the beginning of the alignment
but then I tried it with a flush alignment:

PileUp



   MSF: 1171  Type: N    Check:  6151   .. 

 Name: Shigellasonnei_strainSSP1 oo  Len: 1171  Check:  7039  Weight:  33.0
 Name: Shigellaboydii_strainSBP1 oo  Len: 1171  Check:  9320  Weight:  33.0
 Name: Shigellaflexneri_strainSFP1 oo  Len: 1171  Check:  9792  Weight:
33.0

//



Shigellasonnei_strainSSP1        CGATAACTCC TATAAAGTGT CCGGCGGTCT GCACGGCGTT
GGTGTTTCGG Shigellaboydii_strainSBP1        CGATAACTCC TATAAAGTGT CCGGCGGTCT GCACGGCGTT
GGTGTTTCGG Shigellaflexneri_strainSFP1      CGATAACTCC TATAAAGTGT CCGGCGGTCT GCACGGCGTT
GGTGTTTCGG 



Shigellasonnei_strainSSP1        TAGTAAACGC CCTGTCGCAA AAACTGGAGC TGGTTATCCA
GCGCGAGGGT Shigellaboydii_strainSBP1        TAGTAAACGC CCTGTCGCAA AAACTGGAGC TGGTTATCCA
GCGCGAGGGT Shigellaflexneri_strainSFP1      TAGTAAACGC CCTGTCGCAA AAACTGGAGC TGGTTATTCA
GCGCGAGGGT 

etc ....................................
However the same error message appeared, Changing the alignment format (e.g
to phylip didn't work either). Can anybody suggest what's going wrong here.

Many thanks,

Anthony


Dr Anthony Underwood
Bioinformatics Unit
Central Public Health Laboratory
61 Colindale Avenue
London
NW9 5HT
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: aunderwood@phls.org.uk