Skip to main content

Process various file format for RNA-Seq data analysis

Project description

\n# 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')

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

biofile-0.1.0.tar.gz (12.8 kB view hashes)

Uploaded Source

Built Distribution

biofile-0.1.0-py3-none-any.whl (16.6 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page