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)
Bases:
SequenceIterator
Parser for IntelliGenetics files.
- modes = 't'
- __init__(source)
Iterate over IntelliGenetics records (as SeqRecord objects).
source - file-like object opened in text mode, or a path to a file
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 stream: ... for record in IgIterator(stream): ... print(f"{record.id} length {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
- __next__()
Iterate over the records in the IntelliGenetics file.
- __abstractmethods__ = frozenset({})
- __parameters__ = ()