Package Bio :: Package expressions :: Module transfac
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Module transfac

source code

A Martel format to parse the output from transfac.

Formats: format Format for a whole file.

Functions [hide private]
 
SS(exp) source code
Variables [hide private]
  blank_line = Opt(Spaces())+ AnyEol()
  MATRIX_LINE = Str("Search for sites by WeightMatrix library:")...
  SEQUENCE_LINE = Str("Sequence file:")+ Spaces()+ UntilEol("seq...
  PROFILE_LINE = Str("Site selection profile:")+ Spaces()+ Until...
  TITLE_LINE = Str("Inspecting sequence ID")+ Spaces()+ UntilSep...
  DATA_LINE = SS(UntilSep("matrix_identifier", sep= " |"))+ Str(...
  SEQUENCES_LENGTH_LINE = Spaces()+ Str("Total sequences length=...
  FOUND_SITES_LINE = Spaces()+ Str("Total number of found sites=...
  SITE_FREQUENCY_LINE = Spaces()+ Str("Frequency of sites per nu...
  format = MATRIX_LINE+ SEQUENCE_LINE+ PROFILE_LINE+ blank_line+...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

MATRIX_LINE

Value:
Str("Search for sites by WeightMatrix library:")+ Spaces()+ UntilEol("\
matrix_file")+ AnyEol()

SEQUENCE_LINE

Value:
Str("Sequence file:")+ Spaces()+ UntilEol("sequence_file")+ AnyEol()

PROFILE_LINE

Value:
Str("Site selection profile:")+ Spaces()+ UntilSep("profile_file", sep\
= " ")+ Spaces()+ UntilEol("profile_description")+ AnyEol()

TITLE_LINE

Value:
Str("Inspecting sequence ID")+ Spaces()+ UntilSep("entryname", sep= " \
")+ Spaces()+ UntilSep("dataclass", sep= ";")+ Str(";")+ Spaces()+ Unt\
ilSep("molecule", sep= ";")+ Str(";")+ Spaces()+ UntilSep("division", \
sep= ";")+ Str(";")+ Spaces()+ UntilSep("sequencelength", sep= " ")+ S\
paces()+ Str("BP")+ UntilEol()+ AnyEol()

DATA_LINE

Value:
SS(UntilSep("matrix_identifier", sep= " |"))+ Str("|")+ SS(UntilSep("p\
osition", sep= " "))+ SS(Str("(")+ Group("strand", Any("+-"))+ Str(")"\
))+ Str("|")+ SS(Float("core_match"))+ Str("|")+ SS(Float("matrix_matc\
h"))+ Str("|")+ Opt(Spaces())+ UntilEol("sequence")+ AnyEol()

SEQUENCES_LENGTH_LINE

Value:
Spaces()+ Str("Total sequences length=")+ Integer("sequences_length")+\
 AnyEol()

FOUND_SITES_LINE

Value:
Spaces()+ Str("Total number of found sites=")+ Integer("found_sites")+\
 AnyEol()

SITE_FREQUENCY_LINE

Value:
Spaces()+ Str("Frequency of sites per nucleotide=")+ Float("sites_per_\
nucleotide")+ AnyEol()

format

Value:
MATRIX_LINE+ SEQUENCE_LINE+ PROFILE_LINE+ blank_line+ TITLE_LINE+ blan\
k_line+ Rep(DATA_LINE)+ blank_line+ SEQUENCES_LENGTH_LINE+ blank_line+\
 FOUND_SITES_LINE+ blank_line+ SITE_FREQUENCY_LINE

__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}