Package Bio :: Package SeqIO :: Module IgIO
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Module IgIO

source code

Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format.

You are expected to use this module via the Bio.SeqIO functions.

Functions [hide private]
 
IgIterator(handle, alphabet=SingleLetterAlphabet())
Iterate over IntelliGenetics records (as SeqRecord objects).
source code
Variables [hide private]
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

IgIterator(handle, alphabet=SingleLetterAlphabet())

source code 

Iterate over IntelliGenetics records (as SeqRecord objects).

handle - input file alphabet - optional alphabet

The optional free format file header lines (which start with two semi-colons) are ignored.

The free format commentary lines at the start of each record (which start with a semi-colon) are recorded as a single string with embedded new line characters in the SeqRecord's annotations dictionary under the key 'comment'.

Example:

>>> with open("IntelliGenetics/TAT_mase_nuc.txt") as handle:
...     for record in IgIterator(handle):
...         print("%s length %i" % (record.id, len(record)))
...
A_U455 length 303
B_HXB2R length 306
C_UG268A length 267
D_ELI length 309
F_BZ163A length 309
O_ANT70 length 342
O_MVP5180 length 348
CPZGAB length 309
CPZANT length 309
A_ROD length 390
B_EHOA length 420
D_MM251 length 390
STM_STM length 387
VER_AGM3 length 354
GRI_AGM677 length 264
SAB_SAB1C length 219
SYK_SYK length 330