[BioPython] FSSP

[Iddo Friedberg]

Nice catch Shaheen. FSSP.py had a problem with parsing negative PDB 
residue numbering. I committed changes to CVS. Please give about 30 
minutes for the change to migrate to the public CVS.

Best,

Iddo

Shaheen Ahmed wrote:
> Dear all,
> 
> I have problems when trying to generate a clustalw alignment of the fssp 
> database file -> 1ycc.fssp.
> 
> I use the following biopython script:
> 
> -------------------------------------------------------------------
> 
> #!/usr/bin/python
> 
> from Bio import FSSP
> from Bio.FSSP import FSSPTools
> from Bio import Align
> from Bio.Align import AlignInfo
> from Bio.Align.FormatConvert import FormatConverter
> from Bio import SubsMat
> from Bio.SubsMat import SeqMat
> from Bio import Alphabet
> from Bio.Alphabet import IUPAC
> from Bio import Clustalw
> from Bio.SeqRecord import SeqRecord
> 
> import sys
> import string
> 
> for arg in sys.argv[1:]:
> my_header, my_sum, my_align = FSSP.read_fssp(open(arg))
> 
> # To Filter From The Alignment Only Those Alignments With A Percent Id
> # Above 30%:
> 
> filtered_sum, filtered_alignment = FSSPTools.filter( 
> my_sum,my_align,'pID',30,100)
> filtered_ali = FSSPTools.mult_align(filtered_sum, filtered_alignment)
> converter = FormatConverter(filtered_ali)
> clustal_align = converter.to_clustal()
> print clustal_align
> 
> ----------------------------------------------------------------------
> 
> The alignment is not generated, but I get the following error messages:
> 
> ----------------------------------------------------------------------
> 
>   File "./fssp_example.py", line 30, in ?
>     filtered_ali = FSSPTools.mult_align(filtered_sum, filtered_alignment)
>   File "/usr/lib/python2.0/site-packages/Bio/FSSP/FSSPTools.py", line 
> 22, in mult_align
>     for j in align_dict.abs(1).pos_align_dict.keys():
>   File "/usr/lib/python2.0/site-packages/Bio/FSSP/__init__.py", line 
> 168, in abs
>     return self[self.abs_res_dict[num]]
> KeyError: 1
> 
> ----------------------------------------------------------------------
> 
> Does anybody have a clue what's going wrong? I'd be greatful for any 
> suggestions.
> 
> Best wishes,
> 
> Shaheen
> 
> P.S.: For most of the other fssp database files I tried, the above 
> script seems to work and a clustalw alignment is generated and printed.
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://bioinformatics.ljcrf.edu/~iddo