Bioinformatics Tool: bioFile

Introduction

Retrieve data from various file formats used in RNA-Seq data analysis. The tool currently support:

• GTF file: genomic annotations
• GFF file: genomic annoations

quick installation

pip install biofile

Development

git clone git@github.com:Tiezhengyuan/bio_file.git
cd bio_file
source venv/bin/activate

Run unit testing:

pytest tests/unittests

Quick tour

Process GFF:

Retrieve annotations by features from <gff_file>. Multiple json files would be stored in <out_dir>

from biofile import GFF
g = GFF(gff_file, out_dir)
g.split_by_features()

Given an attribute, retrieve annotations from <gff_file>. and save dataframe in <out_dir>. Here, search all mRNA according to transcript_id. All related annotations are included. The output is transcript_id_mRNA.txt.

from biofile import GFF
g = GFF(gff_file, out_dir)
g.parse_attributes('transcript_id', 'mRNA')

Process GTF:

Retrieve annotations by features from <gtf_file>. Multiple json files would be stored in <out_dir>

from biofile import GTF
g = GTF(gtf_file, out_dir)
g.split_by_features()

Given an attribute, retrieve annotations from <gtf_file>. and save dataframe in <out_dir>. Here, search all mRNA according to transcript_id. All related annotations are included. The output is transcript_id_mRNA.txt.

from biofile import GTF
g = GTF(gtf_file, out_dir)
g.parse_attributes('transcript_id', 'mRNA')