[BioPython] FSSP
Iddo Friedberg
idoerg at burnham.org
Wed Apr 30 10:16:40 EDT 2003
Hi,
I guess I'm in charge of this. Thanks for notifying. Watch this space.
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
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