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Python library that parses GFF, Fasta files into python classes

Latest Version: 0.2.7

# bioinfo_tools

## Installation

pip install bioinfo_tools

## Parsers

*HEADS UP!* These parsers are still under development and usage is not consistent from one parser to another.

### Fasta parser

from bioinfo_tools.parsers.fasta import FastaParser

fasta_parser = FastaParser()

# by default, sequence IDs are separated by the firstly found '|' or ':'
for seqid, sequence in"/path/to/file.fasta"):
print(seqid, sequence)

# you may specify a specific separator for your sequence ID (e.g white space):
for seqid, sequence in"/path/to/file.fasta", id_separator=" "):
print(seqid, sequence)

### GFF parser

from bioinfo_tools.parsers.gff import Gff3

gff_parser = Gff3()
with open("/path/to/file.gff") as fh:
for gene in

import gzip
with"/path/to/file.gz", "rb") as fh:
for gene in

### OBO parser

from bioinfo_tools.parsers.obo import OboParser

obo_parser = OboParser()
with open("/path/to/file.obo") as fh:
go_terms =

for go_term in go_terms.values():

# you may also get the GO term parents via the parser
parents = obo_parser.get_parents(go_term)
File Type Py Version Uploaded on Size
bioinfo_tools- (md5) Source 2017-12-07 10KB