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')
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