[Biopython-dev] Martel-0.5

Andrew Dalke dalke at acm.org
Mon Jan 8 02:57:45 EST 2001

New version of Martel at

Biggest change is support for a lot more formats.
The current list is:

 GenBank - incomplete support for release 119 (does not parse
                 some records; need to resynch with Brad's work)
 MDL_10_1996 - MDL's .mol format, as described in documentation
                    dated 10/1996 and tested against WDI and ACD
                    (thanks Daylight!)

 PDB_2_1  - tested against 1PLM and will fail against most PDB files.
 PIR_3_0  - tested against all of PIR
 blastall_2_0_10 - tested against the non-master-slave 'blastall 2.0.10
                   records from biopython.Bio.Tests.Blast (thanks Jeff!)
 blocks_12  - tested against Blocks 12.0 format
 blocksplus - tested against Blocks+ 15Nov00 format
 embl65   - tested against hum7 from EMBL Release 65, December 2000
 enzyme26  - ENZYME nomenclature database, release 26 of May 2000
 primers  - PCR primers from EBI; database date is from 1997
 prodoc16  - the format version is 16, tested against Prosite release 39
 prosite16  - the format version is 16, tested against Prosite release 39
 swissprot38 - tested against all of SWISS-PROT 38.  Pretty complete.
 taxonomy  - NCBI's taxonomy database, dated 05-NOV-1998
 trembl14  - tested against hum and mam of TrEMBL release 14, June 2000

They still need builders to create biopython data structures.

- Changes between 0.5 and 0.4

Bug fix where HeaderFooter and ParseRecords weren't copying their
subexpressions when making a .copy()

Added SignedInteger and Float definitions.

Fixed some problems with the error reporting. (Status message,
location offset, rewrote HeaderFooterParser.)

Replaced \n with \R in the various format definitions.

Added a lot of formats, although most are incomplete in that
additional fields could be parsed.

Fixed swissprot parsing so non-existant fields don't generate empty


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