[BioPython] Re: error parsing human genbank

[Jay Hesselberth]

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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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