featurExtract is a Python package for bioinformatics, containing two command programs. The first, featurExtract, includes ten subroutines: create, gene, promoter, UTR, uORF, CDS, dORF, exon, intron and intergenic. The create subroutine is used to create a database, while the promoter subroutine is used to extract promoter sequences. The uORF subroutine extracts upstream open reading frames sequences, and the UTR subroutine extracts untranslated region sequences. The CDS subroutine extracts coding sequences and the intergenic subroutine extracts intergenic sequences between two genes. The second command program, genBankExtract, includes four subroutines: gene, CDS, rRNA and tRNA.
Two way offer to install featurExtract module.
pip install featurExtract
# other
git clone https://github.com/SitaoZ/featurExtract.git
cd featurExtract
python setup.py installpython >= 3.7.6 python
pandas >= 1.2.4 pandas
gffutils >= 0.10.1 gffutils
setuptools >= 49.2.0 setuptools
biopython >= 1.78 biopython
featurExtract is designed for GFF and GTF file
and GenBankExtract is suited for GenBank file.
# gff or gtf database
which featurExtract
featurExtract -h
featurExtract create -h
featurExtract promoter -h
featurExtract UTR -h
featurExtract uORF -h
featurExtract CDS -h
featurExtract dORF -h
featurExtract exon -h
featurExtract intron -h
featurExtract intergenic -h# GenBank database
which genBankExtract
genBankExtract -h
genBankExtract gene -h
genBankExtract CDS -h
genBankExtract rRNA -h
genBankExtract tRNA -h# step 1 create database
featurExtract create -f GFF -g ath.gff3 -o ath
# step 2 command
# promoter whole genome
featurExtract promoter -d ath.GFF -f ath.fa -l 200 -u 100 -o promoter.csv --output_format fasta
# promoter one gene to stdout
featurExtract promoter -d ath.GFF -f ath.fa -l 200 -u 100 -g AT1G01010 -p --output_format fasta
featurExtract UTR -d ath.GFF -f ath.fa -o UTR.csv -s GFF
featurExtract uORF -d ath.GFF -f ath.fa -o uORF.csv -s GFF
featurExtract CDS -d ath.GFF -f ath.fa -o CDS.csv -s GFF
featurExtract mRNA -d ath.GFF -f ath.fa -o mRNA.fasta -s GFF --output_format fasta
featurExtract exon -d ath.GFF -f ath.fa -t AT1G01010.1 -p -s GFF
featurExtract intron -d ath.GFF -f ath.fa -t AT1G01010.1 -p -s GFF# GenBank step 3
genBankExtract gene -g NC_000932.gb -f dna -p
genBankExtract CDS -g NC_000932.gb -f dna -p
genBankExtract rRNA -g NC_000932.gb -f dna -p
genBankExtract tRNA -g NC_000932.gb -f dna -p
