Package Bio :: Package expressions :: Module genbank
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Module Bio.expressions.genbank

Martel based parser to read GenBank formatted files.

This is a huge regular regular expression for GenBank, built using the 'regular expressions on steroids' capabilities of Martel.

Documentation for GenBank format that I found:

o GenBank/EMBL feature tables are described at: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

o There are also descriptions of different GenBank lines at: http://www.ibc.wustl.edu/standards/gbrel.txt
Function Summary
  define_block(identifier, block_tag, block_data, std_block_tag, std_tag)
Define a Martel grouping which can parse a block of text.

Function Details

define_block(identifier, block_tag, block_data, std_block_tag=None, std_tag=None)

Define a Martel grouping which can parse a block of text.

Many of the GenBank lines we'll want to process are grouped into a block like:

IDENTIFIER Blah blah blah

Where blah blah blah can wrap for multiple lines. This function makes it easy to consistently define a definition for these blocks.

Arguments: o identifier - The identifier that begins the block (like DEFINITION). o block_tag - A callback tag for the entire block. o block_data - A callback tag for the data in the block (ie. the stuff you are interested in). o std_block_tag - A Bio.Std Martel tag used to register the entire block as having being a "standard" type of information. o std_tag - A Bio.Std Martel tag used to register just the information in the block as being "standard"

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