tsv : class for tsv files with named fields, especially for bioinfomatics use.
tsv now is part of BioUtil module. code here may out of date.
This module defines two class: tsvFile and tsvRecord, which serve as the superclass for derived tsv file types.
the subclasses of tsvFile should specify the Record attribute, which is typically a tsvRecord subclass. To define a subclass of tsvRecord, you at least to specifiy _fields, the attribute names for Record columns.
The tsvFile also support file with header lines. The tsvRecord also support self-defined behavior for each filed. See document for details
- define bed file
import tsv
class bedFile(tsv.tsvFile):
class Record(tsv.tsvRecord):
_fields = ("chr", "start", "end")
_fields_parser = {"start":int, "end": int}- Read file, invoke fields and write file
with bedFile.open("out.bed", 'w') as out:
for rec in bedFile.open("input.bed", 'r'):
if rec.end - rec.start <= 500:
out.write(rec)Python >= 2.6
Sein Tao
GNU GPL v2