dar19/pyGTF

Parse GTF/GFF, Fasta/Fastq file, convert gene annotation format and extract sequence

1. use pyGTF.py as script to Convert of Gene annotation format

Usage: python pyGTF.py --input --infmt --output --outfmt

• gtf2bed

  

• refseq_gff2genePred

  

• genePred2gtf

  

2. use pyGTF.py as script to Extract Feature sequence

   Usage: python pyGTF --input --infmt --Genome --Feature --Sequence

   • Extract coding sequence

     

   • Extract untranslated region sequence

     

3. use pyGTF.py as module

   • GTF_Reader

     

   • safe mode of GTF_Reader

     

   • Fasta_Reader