[Biopython-dev] [Bug 3009] Check the FASTA m10 alignment parser works with FASTA36

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3009





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2010-04-23 07:16 EST -------
There seems to be a bug in FASTA 36.1.2 m10 output where the pg_optcut line
lacks its leading semi-colon:

The following example command lines should illustrate the problem, using the
following input fasta files from the NCBI, both are relatively small with
three and 180 sequences each:

ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002127.faa
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Klebsiella_pneumoniae_MGH_78578/NC_009649.faa

$ ~/Downloads/Software/fasta-36.2.1/bin/fasta36 -Q -H -E 1 -m 10
NC_002127.faa NC_009649.faa > stdout.txt
$ more stdout.txt
...
[cut]
...
; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Mar 2010
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_join: 42
 pg_optcut: 30
; mp_extrap: 60000 500
; mp_stats: (shuffled [500]) Expectation_n fit: rho(ln(x))=
5.1864+/-0.0116; mu= 5.3472+/- 0.598  mean_var=54.6263+/-12.288, 0's:
0 Z-trim: 0  B-trim: 0 in 0/33  Lambda= 0.173529
; mp_KS: -0.0000 (N=0) at  20
; mp_Algorithm: FASTA (3.7 Mar 2010) [optimized]
...
[cut]

This breaks the Bio.AlignIO parser. Manually editing the file to insert the
semi colons seems to fix things.

I have reported this issue on the FASTA mailing list today:
https://list.mail.virginia.edu/mailman/listinfo/fasta_list


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