bioinfo_tools 0.1.3

Python library that parses GFF, Fasta files into python classes

===================
bioinfo_tools 0.1.3
===================

# Installation

```bash
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

```python
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 fasta_parser.read("/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 fasta_parser.read("/path/to/file.fasta", id_separator=" "):
print(seqid, sequence)
```

## GFF parser

```python
from bioinfo_tools.parsers.gff import Gff3

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

## OBO parser

```python
from bioinfo_tools.parsers.obo import OboParser

obo_parser = OboParser()
go_terms = obo_parser.read("http://geneontology.org/ontology/go-basic.obo")

for go_term in go_terms.values():
print(go_term)

# you may also get the GO term parents via the parser
parents = obo_parser.get_parents(go_term)
```