Bio.SeqIO.IgIO module

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

This module is for reading and writing IntelliGenetics format files as SeqRecord objects. This file format appears to be the same as the MASE multiple sequence alignment format.

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

class Bio.SeqIO.IgIO.IgIterator(source, alphabet=SingleLetterAlphabet())

Bases: Bio.SeqIO.Interfaces.SequenceIterator

Parser for IntelliGenetics files.

__init__(self, source, alphabet=SingleLetterAlphabet())

Iterate over IntelliGenetics records (as SeqRecord objects).

source - file-like object opened in text mode, or a path to a 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’.

Examples

>>> 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

parse(self, handle)

Start parsing the file, and return a SeqRecord generator.

iterate(self, handle)

Iterate over the records in the IntelliGenetics file.