[BioPython] FSSP

[Shaheen Ahmed]

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

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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.

-- 
Shaheen Ahmed
Department of Biochemistry
University of Zuerich
Winterthurerstrasse 190
8057 Zuerich (Switzerland)

tel: ++41 1 635 55 68
mailto:ahmed at bioc.unizh.ch