Package Bio :: Package expressions :: Module fasta
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Module fasta

source code

Functions [hide private]
 
make_2id(s, dbname, primary_name, secondary_name) source code
 
make_1id(s, dbname, name) source code
Variables [hide private]
  ids = []
  gnl_id = Str("gnl|")+ Std.dbxref_dbname(UntilSep(sep= "| "))+ ...
  ncbi_word = Std.dbxref(reduce(operator.or_, ids))
  ncbi_term = ncbi_word+ Rep(Str("|")+ ncbi_word)
  generic_term = Std.dbxref(Std.dbxref_dbid(UntilSep(sep= " "), ...
  id_term = ncbi_term | generic_term
  comment_lines = Rep(Str("#")+ ToEol())
  title = Str(">")+ Std.description_line(id_term+ UntilEol())+ A...
  seqline = AssertNot(Str(">"))+ Std.sequence(UntilEol())+ AnyEol()
  seqline_nonewline = AssertNot(Str(">"))+ Std.sequence(Word())
  sequence = Std.sequence_block(Rep(seqline | seqline_nonewline))
  record = Std.record(comment_lines+ title+ sequence+ Rep(AnyEol...
  format = HeaderFooter("dataset", {"format": "fasta"}, comment_...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

gnl_id

Value:
Str("gnl|")+ Std.dbxref_dbname(UntilSep(sep= "| "))+ Str("|")+ Std.dbx\
ref_dbid(UntilSep(sep= "| "))

generic_term

Value:
Std.dbxref(Std.dbxref_dbid(UntilSep(sep= " "), {"dbname": "local"}))

title

Value:
Str(">")+ Std.description_line(id_term+ UntilEol())+ AnyEol()

record

Value:
Std.record(comment_lines+ title+ sequence+ Rep(AnyEol()))

format

Value:
HeaderFooter("dataset", {"format": "fasta"}, comment_lines, RecordRead\
er.Until, (">",), record, RecordReader.StartsWith, (">",), comment_lin\
es, RecordReader.Everything, ())

__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'>,
  4): 1}