def save_scores(fimo_dir):
fimo_file = os.path.join(fimo_dir, 'fimo.txt')
fimo_sites = fimo_to_sites(fimo_file)
subset = fimo_sites.loc[:, [
'chrom', 'motifStartZeroBased', 'motifEndOneBased', 'strand'
]]
subset.loc[:, 'motifStartZeroBased'] = subset[
'motifStartZeroBased'] - flank_length
subset.loc[:,
'motifEndOneBased'] = subset['motifEndOneBased'] + flank_length
intervals = [tuple(x) for x in subset.to_records(index=False)]
scores_phastcons = phastcons_wig.query(intervals)
if len(fimo_sites.index):
scores_phastcons_mean = np.nanmean(scores_phastcons, axis=0)
np.savetxt(os.path.join(fimo_dir, 'phastcons.raw.txt'),
scores_phastcons,
fmt='%.4f')
np.savetxt(os.path.join(fimo_dir, 'phastcons.mean.txt'),
scores_phastcons_mean,
fmt='%.4f')
else:
touch(os.path.join(fimo_dir, 'phastcons.raw.txt'))
touch(os.path.join(fimo_dir, 'phastcons.mean.txt'))
def test_fimostd(self):
"""Test fimo to sites with
standard sequence names"""
fimo_file = 'tests/data/fimo.std.txt'
fimo_df = fimo_to_sites(os.path.abspath(fimo_file))
for _, row in fimo_df.iterrows():
record_id = row['sequence name']
fimo_sequence = row['matched sequence']
start = row['start']
end = row['stop'] # 1-based end
strand = row['strand']
assert start-1 == row['motifStartZeroBased']
assert end == row['motifEndOneBased']
def test_fimotosites(self):
"""Test fimo_to_sites"""
fimo_file = 'tests/data/expected_out/fimo_analysis/fimo.txt'
record_dict = SeqIO.to_dict(SeqIO.parse(open(self.meme_fasta), 'fasta'))
fimo_df = fimo_to_sites(os.path.abspath(fimo_file))
for _, row in fimo_df.iterrows():
record_id = row['sequence name']
fimo_sequence = row['matched sequence']
start = row['start']-1 # 0-based start
end = row['stop'] # 1-based end
strand = row['strand']
fasta_sequence = record_dict[record_id].seq
if strand == '+':
assert str(fasta_sequence)[start:end] == fimo_sequence
else:
assert str(fasta_sequence[start:end].reverse_complement()) == fimo_sequence
