#!/usr/bin/env python import re import io def count_motifs(seq, motif): pieces = re.split(motif, seq) return len(pieces) - 1 fhandle = io.open("grape_promoters.txt", "rU") for line in fhandle: linestripped = line.strip() line_list = re.split(r"\s+", linestripped) gid = line_list[0] seq = line_list[1] num_motifs = count_motifs(seq, r"[AT]GATA[GA]") print(gid + "\t" + str(num_motifs)) fhandle.close()