[BioPython] Re: error parsing human genbank
Jay Hesselberth
jhessel@mail.utexas.edu
20 Jul 2002 12:50:21 -0500
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If you apply this patch to the alpha-4 version, it fixes your first
problem. It's a problem with 'linear' vs. 'circular' types in the LOCUS
line. But the parser barfs later on in the hs_chr9 gbk file :). I'll
look into that ...
Jay
--
________________________________________________
Jay Hesselberth jhessel@mail.utexas.edu
University of Texas (512) 471-6445
2500 Speedway / A4800
Austin, TX 78712
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*** genbank_format.py.orig Sat Jul 20 12:39:19 2002
--- genbank_format.py Sat Jul 20 12:44:45 2002
***************
*** 83,91 ****
residue_types =3D map(Martel.Str, valid_residue_types)
=20
residue_type =3D Martel.Group("residue_type",
Martel.Opt(Martel.Alt(*residue_prefixes)) +
Martel.Opt(Martel.Alt(*residue_types)) +
Martel.Opt(Martel.Opt(blank_space) +=20
! Martel.Str("circular")))
=20
date =3D Martel.Group("date",
--- 83,94 ----
residue_types =3D map(Martel.Str, valid_residue_types)
=20
+ valid_nucleic_acid_types =3D ["linear", "circular"]
+ nucleic_acid_types =3D map(Martel.Str, valid_nucleic_acid_types)
+=20
residue_type =3D Martel.Group("residue_type",
Martel.Opt(Martel.Alt(*residue_prefixes)) +
Martel.Opt(Martel.Alt(*residue_types)) +
Martel.Opt(Martel.Opt(blank_space) +=20
! Martel.Alt(*nucleic_acid_types)))
=20
date =3D Martel.Group("date",
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