Package Bio :: Package config :: Module FormatRegistry

Module FormatRegistry

Implements a Registry to store Martel-type format expressions.

Classes: FormatRegistry Holds Biopython formats in a dictionary-like interface. FormatObject Describes a Biopython file format. FormatGroup Describes a group of Biopython file formats.

Classes

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FormatRegistry
This implements a dictionary-like interface to Biopython file formats.

FormatObject
This object stores Biopython file formats and provides methods to work on them.

FormatGroup
This object holds a group of FormatObjects.

Functions

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_parses_file(expression, infile, debug_level)

source code

_parses_string(expression, s, debug_level)

source code

_normalize_expression(expression_or_path)

source code

_load_expression(path)

source code

_load_object(path)

source code

_load_first_existing(basemodulename, possible_formats)

source code

Variables

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formats = formats, exporting 'blast', 'blastn', 'blastp', 'bla...

Variables Details

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formats

Value:

formats, exporting 'blast', 'blastn', 'blastp', 'blastx', 'embl', 'emb
l/65', 'empty', 'fasta', 'genbank', 'genbank-records', 'genbank-releas
e', 'ipi', 'ncbi-blastn', 'ncbi-blastp', 'ncbi-blastx', 'ncbi-tblastn'
, 'ncbi-tblastx', 'search', 'sequence', 'swissprot', 'swissprot/38', '
swissprot/40', 'tblastn', 'tblastx', 'wu-blastn', 'wu-blastp', 'wu-bla
stx'