Package Bio :: Package GFF :: Module easy
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Module easy

source code

Bio.GFF.easy: some functions to ease the use of Biopython


Version: $Revision: 1.11 $

Classes [hide private]
  FeatureDict
JH: accessing feature.qualifiers as a list is stupid.
  Location
this is really best interfaced through LocationFromString fuzzy: < or > join: {0 = no join, 1 = join, 2 = order}
  LocationJoin
  LocationFromCoords
  LocationFromString
Functions [hide private]
 
_hashname(location) source code
 
open_file(filename) source code
 
fasta_single(filename=None, string=None) source code
 
fasta_multi(filename=None) source code
 
fasta_readrecords(filename=None) source code
 
fasta_write(filename, records) source code
 
genbank_single(filename) source code
 
record_subseq(record, location, *args, **keywds) source code
 
record_sequence(record)
returns the sequence of a record
source code
 
record_coords(record, start, end, strand=0, upper=0) source code
 
_test(*args, **keywds) source code
Variables [hide private]
  re_complement = re.compile(r"^complement\((.*)\)$")
  re_seqname = re.compile(r"^(?!join|order|complement)([^\:]+?):...
  re_join = re.compile(r"^(join|order)\((.*)\)$")
  re_dotdot = re.compile(r"^([><]*\d+)\.\.([><]*\d+)$")
  re_fuzzy = re.compile(r"^([><])(\d+)")
Function Details [hide private]

record_sequence(record)

source code 

returns the sequence of a record

can be Bio.SeqRecord.SeqRecord or Bio.GenBank.Record.Record


Variables Details [hide private]

re_seqname

Value:
re.compile(r"^(?!join|order|complement)([^\:]+?):(.*)$")