def test_positive_region3_short_seq(): "test Rev 9b " Genome_seq_record = Genome_sequence["pathogens_Gpal_scaffold_3"] intergenic_region = get_len_upstream(Genome_seq_record.seq, 8, "+") # this has already been reverse complemented, so we want the # seq at the "end" of the ROI. assert_equal(intergenic_region, "ATGNNAT")
def test_negative_region3(): "test Rev intergenic_region 3 " Genome_seq_record = Genome_sequence["pathogens_Gpal_scaffold_2"] intergenic_region = get_len_upstream(Genome_seq_record.seq, 3, "-") # this has already been reverse complemented, so we want the # seq at the "end" of the ROI. assert_equal(intergenic_region, "NNN")
def test_positive_region3_short_seq(): "test Rev 9d " Genome_seq_record = Genome_sequence["pathogens_Gpal_scaffold_3"] intergenic_region = get_len_upstream(Genome_seq_record.seq, 14, "+") assert_equal(intergenic_region, "ATGNNATG")
def test_intergenic_region3(): "test intergenic_region 3 " Genome_seq_record = Genome_sequence["pathogens_Gpal_scaffold_1"] intergenic_region = get_len_upstream(Genome_seq_record.seq, 3, "+") assert_equal(intergenic_region, "GAG")
Genome_seq_record = Genome_sequence[scaff] else: warn = "could not find scaff: %s going to skip" % (scaff) logger.warning(warn) length_of_contig = len(Genome_seq_record.seq) # slice up the scaffold. # reverse complement for negative # this function gets the entire intergenic regions, regardless of # the desired length. intergenic_region, final_start, \ final_stop = slice_up_scaff(Genome_seq_record.seq, final_start, final_stop, direction) # this function then get the desired upstream chunk upstream_ROI = get_len_upstream(intergenic_region, upstream, direction) if description.upper() == "YES": info = "Scaff: %s | start-stop: %s:%s %s coding direction" % ( scaff, final_start, final_stop, direction) if len(upstream_ROI) >= min_len: write_out_to_file(outfile, gene, upstream, upstream_ROI, info) else: logger.warn write_out_gff(gff_outfile, scaff, final_start, final_stop, direction, gene, upstream) logger.info("gff made, this contains all intergenic regions") outfile.close() gff_outfile.close() user_defined_genic = int(user_defined_genic) if user_defined_genic != 0: