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: