add_sequences

import pandas as pd
from Bio import SeqIO

# add sequences to either promoters or non-promoters

input_gtf_path = 'path_to_your_file'
input_genome_path = 'path_to_your_fasta_file'


def add_seqs(input_genome_path, input_gtf_path):
    column_names = ['Seqid', 'Source', 'Type', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Suppl']
    df = pd.read_csv(input_gtf_path, sep='\t', header=None, names=column_names, dtype={'Start': int, 'End': int}, comment='#')
    df['Seq'] = ""

    genome_sequences = SeqIO.to_dict(SeqIO.parse(input_genome_path, "fasta"))

    for index, row in df.iterrows():
        seqid = row['Seqid']
        strand = row['Strand']
        start = row['Start'] - 1
        end = row['End']
        if strand == '+':
            seq = str(genome_sequences[seqid].seq[start:end])
        elif strand == '-':
            seq = str(genome_sequences[seqid].seq[start:end].reverse_complement())
        else:
            seq = ""
        df.at[index, 'Seq'] = seq

    df.to_csv(input_gtf_path + '+rev_seqs.gtf', sep='\t', header=False, index=False)
    print('File with sequences was saved to +seqs.gtf')
    return df

add_seqs(input_genome_path, input_gtf_path)