Package Bio :: Package expressions :: Package swissprot :: Module speclist
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Module speclist

source code

Parser for the SPECLIST.TXT file in SWISS-PROT.

You probably want to use the variables 'record' (for a single record) and 'format' (for a set of records).

Functions [hide private]
 
SkipLinesToNoEOL(expr) source code
Variables [hide private]
  DESCRIPTION = Str("Description:")+ Spaces()+ UntilEol("descrip...
  NAME = Str("Name:")+ Spaces()+ UntilEol("name")+ AnyEol()
  RELEASE = Str("Release:")+ Spaces()+ UntilEol("release")+ AnyE...
  TOTAL_CODES = Str("Total number of organism identification cod...
  TABLE_HEADER = Group("table_header", Str("Code")+ Spaces()+ St...
  _dash_line = Rep1(Str("-"))+ AnyEol()
  COPYRIGHT = Group("copyright", _dash_line+ Str("SWISS-PROT is ...
  _code_line = Group("code", Re(r"[A-Z0-9]{1,5}"))+ Spaces()+ Gr...
  _common_line = Spaces()+ Str("C=")+ Group("common_name", Until...
  _synonym_line = Spaces()+ Str("S=")+ Group("synonym", UntilEol...
  record = Group("record", _code_line+ Rep(_common_line)+ Rep(_s...
  format = Group("format", SkipLinesToNoEOL(DESCRIPTION)+ NAME+ ...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

DESCRIPTION

Value:
Str("Description:")+ Spaces()+ UntilEol("description")+ AnyEol()

RELEASE

Value:
Str("Release:")+ Spaces()+ UntilEol("release")+ AnyEol()

TOTAL_CODES

Value:
Str("Total number of organism identification codes currently defined:"\
)+ Spaces()+ Integer("num_organism_codes")+ Str(".")+ AnyEol()

TABLE_HEADER

Value:
Group("table_header", Str("Code")+ Spaces()+ Str("Taxon")+ Spaces()+ S\
tr("N=Official name")+ ToEol()+ Spaces()+ Str("Node")+ Spaces()+ Str("\
C=Common name")+ ToEol()+ Spaces()+ Str("S=Synonym")+ ToEol()+ Rep1(An\
y(" _"))+ AnyEol())

COPYRIGHT

Value:
Group("copyright", _dash_line+ Str("SWISS-PROT is copyright.")+ ToEol(\
)+ SkipLinesToNoEOL(_dash_line)+ Rep(AnyEol()))

_code_line

Value:
Group("code", Re(r"[A-Z0-9]{1,5}"))+ Spaces()+ Group("kingdom", Any("A\
BEV"))+ Spaces()+ Group("taxon_node", Digits())+ Str(":")+ Spaces()+ S\
tr("N=")+ Group("official_name", UntilEol())+ AnyEol()

_common_line

Value:
Spaces()+ Str("C=")+ Group("common_name", UntilEol())+ AnyEol()

_synonym_line

Value:
Spaces()+ Str("S=")+ Group("synonym", UntilEol())+ AnyEol()

record

Value:
Group("record", _code_line+ Rep(_common_line)+ Rep(_synonym_line))

format

Value:
Group("format", SkipLinesToNoEOL(DESCRIPTION)+ NAME+ RELEASE+ SkipLine\
sToNoEOL(TOTAL_CODES)+ SkipLinesToNoEOL(TABLE_HEADER)+ Rep1(record)+ A\
nyEol()+ COPYRIGHT)

__warningregistry__

Value:
{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
  <type 'exceptions.DeprecationWarning'>,
  9): 1}