Package Bio :: Package expressions :: Module blocks
[hide private]
[frames] | no frames]

Module blocks

source code

Variables [hide private]
  header = Rep(AssertNot(Str("ID "))+ ToEol())
  ID = Str("ID ")+ Std.dbid(ToSep(sep= ";"), {"type": "primary...
  AC = Str("AC ")+ Std.dbid(ToSep(sep= ";"), {"type": "accessi...
  DE = Str("DE ")+ ToEol("description")
  BL = Str("BL ")+ ToSep("protomat_id", ";")+ Str(" width=")+...
  identifier = Std.dbxref_dbid(UntilSep(sep= "|."), {"dbname": "...
  segment = AssertNot(Re(r".. "))+ identifier+ Re(r" *\( *")+ In...
  segment_block = Rep1(segment | AnyEol())
  end = Str("//")+ AnyEol()
  record = Group("record", ID+ AC+ DE+ BL+ segment_block+ end)
  format_expression = header+ Rep1(record)
  format = HeaderFooter("dataset", {"format": "blocks/12"}, head...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

ID

Value:
Str("ID   ")+ Std.dbid(ToSep(sep= ";"), {"type": "primary"})+ Str(" BL\
OCK")+ AnyEol()

AC

Value:
Str("AC   ")+ Std.dbid(ToSep(sep= ";"), {"type": "accession"})+ Str(" \
distance from previous block=(")+ Integer("dist1")+ Str(",")+ Integer(\
"dist2")+ Str(")")+ AnyEol()

BL

Value:
Str("BL   ")+ ToSep("protomat_id", ";")+ Str("  width=")+ Digits("widt\
h")+ Str("; seqs=")+ Digits("numseqs")+ Str("; 99.5%=")+ Digits("proto\
mat_count")+ Str("; strength=")+ Digits("strength")+ AnyEol()

identifier

Value:
Std.dbxref_dbid(UntilSep(sep= "|."), {"dbname": "swissprot", "type": "\
primary"})+ Str("|")+ Std.dbxref_dbid(UntilSep(sep= " "), {"dbname": "\
swissprot", "type": "accession"}) | Std.dbxref_dbid(UntilSep(sep= " ")\
)

segment

Value:
AssertNot(Re(r".. "))+ identifier+ Re(r" *\( *")+ Integer("position")+\
 Re(r"\) *")+ Word("matching_sequence")+ Spaces()+ Digits("weight")+ A\
nyEol()

format

Value:
HeaderFooter("dataset", {"format": "blocks/12"}, header, RecordReader.\
Until, ("ID ",), record, RecordReader.EndsWith, ("//\n",), None, None,\
 None)

__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}