gffSlicer.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pandas as pd
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
import csv

def gffSlicer(annotation, id, start, end, move, output):
    """Extract fasta files from annotations
    """
    df_gff = pd.read_csv(annotation, index_col=False, sep='\t', header=None)
    df_gff.columns = ['seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame', 'attribute']
    if start and end:
        if start != None and end != None:
            df_extract = df_gff[(df_gff.seqname == id) & (df_gff.start >= start) & (df_gff.end <= end)]
        if start != None and end is None:
            df_extract = df_gff[(df_gff.seqname == id) & (df_gff.start >= start)]
        if start is None and end != None:
            df_extract = df_gff[(df_gff.seqname == id) & (df_gff.end <= end)]
        if start is None and end is None:
            df_extract = df_gff[(df_gff.seqname == id)]
        if move:
            df_extract['start'] -=  start
            df_extract['end'] -=  start
    else:
        #only by id
        df_extract = df_gff[(df_gff.seqname == id)]
    if output is None:
        print df_extract.to_string(output, index=False, header=False)
    else:
        df_extract.to_csv(output,sep='\t', encoding='utf-8',index=False,header=False,quoting=csv.QUOTE_NONE)

if __name__ == "__main__":
    import argparse
    parser = argparse.ArgumentParser()#pylint: disable=invalid-name
    parser.add_argument("-a", "--annotation", help="Annotation file (.gff3 format)", required=True)
    parser.add_argument("-o", "--output", help="Output file (.fasta)", default=None)
    parser.add_argument("-m", "--move_position", help="Start and end position will be moved -start",default=False)
    parser.add_argument("-i", "--sequence_id", help="Sequence name id (empty for sinlge seq files)")
    parser.add_argument("-s", "--start", help="Start position (empty for start of seq)", type=int)
    parser.add_argument("-e", "--end", help="End position (empty for end of seq)", type=int)
    args = parser.parse_args()#pylint: disable=invalid-name
    gffSlicer(args.annotation, args.sequence_id, args.start, args.end, args.move_position, args.output)