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Bio::expressions::genbank Namespace Reference


Detailed Description

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


Functions

def define_block

Variables

tuple accession
tuple accession_block
tuple authors_block = define_block(" AUTHORS", "authors_block", "authors")
tuple big_indent_space = Martel.Str(" " * FEATURE_KEY_INDENT)
tuple blank_space = Martel.Spaces()
tuple comment_block = define_block("COMMENT", "comment_block", "comment")
tuple consrtm_block = define_block(" CONSRTM", "consrtm_block", "consrtm")
tuple data_file_division
tuple date
tuple db_source_block = define_block("DBSOURCE", "db_source_block", "db_source")
tuple definition_block
tuple divisions = map(Martel.Str, valid_divisions)
tuple feature_key
int FEATURE_KEY_INDENT = 5
tuple feature_key_line
int FEATURE_QUALIFIER_INDENT = 21
tuple features_line
tuple gi
int INDENT = 12
tuple journal_block = define_block(" JOURNAL", "journal_block", "journal")
tuple keywords_block = define_block("KEYWORDS", "keywords_block", "keywords")
tuple location
tuple locus
tuple locus_line
tuple medline_line
tuple nid
tuple nid_line
tuple organism
tuple organism_block
tuple pid
tuple pid_line
tuple primary
tuple primary_line
tuple primary_ref_line
tuple pubmed_line
tuple qualifier_space = Martel.Str(" " * FEATURE_QUALIFIER_INDENT)
tuple quote = Martel.Str('"')quoted_chars = Std.feature_qualifier_description(Martel.Re(r'([^"\R]|"")
tuple reference
tuple reference_bases
tuple reference_line
tuple reference_num
tuple remark_block = define_block(" REMARK", "remark_block", "remark")
tuple residue_prefixes = map(Martel.Str, valid_residue_prefixes)
tuple residue_type
tuple residue_types = map(Martel.Str, valid_residue_types)
tuple segment
tuple segment_line
tuple size
tuple small_indent_space = Martel.Str(" " * 2)
tuple source_block = define_block("SOURCE", "source_block", "source")
tuple taxonomy
tuple title_block = define_block(" TITLE", "title_block", "title")
list valid_divisions
list valid_residue_prefixes = ["ss-", "ds-", "ms-"]
list valid_residue_types
tuple version
tuple version_line


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