def test_parse_first_database(self):
"""Parse first db should build best_hits correctly"""
out_total_queries, out_best_hits = parse_first_database(self.db1, [0.80], [50])
self.assertEquals(out_total_queries, 2)
self.assertEquals(
out_best_hits,
{
"HABJ36W02EXF44": [
{
"a": {
"evalue": 0.0,
"subject_id": "NZ_ABEH01000018_641736102",
"bit_score": 1005.0,
"percentage_id": 99.42,
"alg_length": 519,
},
"b": {"subject_id": None, "bit_score": -1},
}
],
"HABJ36W02DLDSY": [
{
"a": {
"evalue": 0.0,
"subject_id": "NZ_ABEH01000005_641736102",
"bit_score": 959.0,
"percentage_id": 99.22,
"alg_length": 512,
},
"b": {"subject_id": None, "bit_score": -1},
}
],
},
)
def test_parse_first_database(self):
"""Parse first db should build best_hits correctly"""
out_total_queries, out_best_hits = parse_first_database(self.db1,
[.80], [50])
self.assertEquals(out_total_queries, 4)
self.assertEquals(
out_best_hits,
{'HABJ36W02EXF44': [
{'a': {'evalue': 0.0,
'subject_id': 'NZ_ABEH01000018_641736102',
'bit_score': 1005.0, 'percentage_id': 99.42,
'alg_length': 519},
'b': {'subject_id': None, 'bit_score': -1}}],
'BLANK-TEST-NOT-IN-SECOND': [
{'a': {'evalue': 4e-133,
'subject_id': 'NZ_ACZD01000120_647000262',
'bit_score': 482.0, 'percentage_id': 88.79,
'alg_length': 455},
'b': {'subject_id': None, 'bit_score': -1}}],
'HABJ36W02DLDSY': [
{'a': {'evalue': 0.0,
'subject_id': 'NZ_ABEH01000005_641736102',
'bit_score': 959.0, 'percentage_id': 99.22,
'alg_length': 512},
'b': {'subject_id': None, 'bit_score': -1}}]})
def test_parse_first_database(self):
"""Parse first db should build best_hits correctly"""
out_total_queries, out_best_hits = parse_first_database(self.db1,
[.80], [50])
self.assertEquals(out_total_queries, 4)
self.assertEquals(
out_best_hits,
{'HABJ36W02EXF44': [
{'a': {'evalue': 0.0,
'subject_id': 'NZ_ABEH01000018_641736102',
'bit_score': 1005.0, 'percentage_id': 99.42,
'alg_length': 519},
'b': {'subject_id': None, 'bit_score': -1}}],
'BLANK-TEST-NOT-IN-SECOND': [
{'a': {'evalue': 4e-133,
'subject_id': 'NZ_ACZD01000120_647000262',
'bit_score': 482.0, 'percentage_id': 88.79,
'alg_length': 455},
'b': {'subject_id': None, 'bit_score': -1}}],
'HABJ36W02DLDSY': [
{'a': {'evalue': 0.0,
'subject_id': 'NZ_ABEH01000005_641736102',
'bit_score': 959.0, 'percentage_id': 99.22,
'alg_length': 512},
'b': {'subject_id': None, 'bit_score': -1}}]})
def compare(interest_fp, other_fp, output_dir='blast-results-compare',
interest_pcts=None, interest_alg_lens=None, other_pcts=None,
other_alg_lens=None, hits_to_first=False, hits_to_second=False):
"""Compare two databases and write the outputs
Parameters
----------
interest_fp : str
BLAST results when searching against the database of interest.
other_fp : str
BLAST results when searching against the other database.
output_dir : str, optional
Name of the output file path.
interest_pcts : list, optional
Minimum percentage identity to be considered as a valid result in the
interest database search results. If None is passed, it defaults to
`[70]`.
interest_alg_lens : list, optional
Minimum alginment length to be considered a valid result in the
interest database search results. If None is passed, it defaults to
`[50]`.
other_pcts : list, optional
Minimum percentage identity to be considered as a valid result in the
other database search results. If None is passed, it defaults to
`[70]`.
other_lengths : list, optional
Minimum alginment length to be considered a valid result in the
other database search results. If None is passed, it defaults to
`[50]`.
hits_to_first : bool, optional defaults to False
Outputs the labels and counts of the sequences being hit in the first
database.
hits_to_second : bool, optional defaults to False
Outputs the labels and counts of the sequences being hit in the second
database.
Raises
------
click.BadParameter
If the `interest_pcts` and the `other_pcts` lists are of different
length.
If the `interest_alg_lens` and the `other_alg_lens` lists are of
different length.
"""
if interest_pcts is None:
interest_pcts = [70]
if interest_alg_lens is None:
interest_alg_lens = [50]
db_a = open(interest_fp, 'U')
db_b = open(other_fp, 'U')
# try to create the output directory, if it exists, just continue
create_dir(output_dir, False)
# run some validations on the input parameters
if other_pcts:
if len(interest_pcts) != len(other_pcts):
raise BadParameter("The percentage values for both databases "
"should be the same length: %s - %s" %
(interest_pcts, other_pcts))
else:
other_pcts = interest_pcts
if other_alg_lens:
if len(interest_alg_lens) != len(other_alg_lens):
raise BadParameter("The alignment length values for both databases"
" should be the length : %s - %s" %
(interest_alg_lens, other_alg_lens))
else:
other_alg_lens = interest_alg_lens
# process databases
total_queries, best_hits = parse_first_database(db_a, interest_pcts,
interest_alg_lens)
parse_second_database(db_b, best_hits, other_pcts,
other_alg_lens)
# parse results
results = process_results(interest_pcts, interest_alg_lens,
other_pcts, other_alg_lens, best_hits)
# Collating output and writing full results
for i, item in enumerate(results):
filename = join(output_dir, "summary_" + item['filename'] + ".txt")
with open(filename, 'w') as fd:
fd.write('\n'.join(item['summary']))
if i == 0:
combined_results = []
combined_results.append(['filename'])
combined_results.append(['interest db (%s)' %
basename(interest_fp)])
combined_results.append(['other db (%s)' % basename(other_fp)])
combined_results.append(['only interest'])
combined_results.append(['both dbs'])
combined_results.append(['no hits in interest db'])
no_hits = total_queries - item['db_interest'] - item['db_other'] - \
item['perfect_interest'] - item['equal']
combined_results[0].append(item['filename'])
combined_results[1].append(str(item['db_interest']))
combined_results[2].append(str(item['db_other']))
combined_results[3].append(str(item['perfect_interest']))
combined_results[4].append(str(item['equal']))
combined_results[5].append(str(no_hits))
# tiny helper function to save hits files
def save_hits(data, name):
s_hits = sorted(data, key=itemgetter(1), reverse=True)
filename = join(output_dir, name)
with open(filename, 'w') as fd:
fd.write('\n'.join(['%s\t%d' % (k, v)
for k, v in s_hits if v != 0]))
if hits_to_first:
save_hits(item['db_seqs_counts']['a'].items(),
"hits_to_first_db_%s.txt" % item['filename'])
if hits_to_second:
save_hits(item['db_seqs_counts']['b'].items(),
"hits_to_second_db_%s.txt" % item['filename'])
# saving collated results
with open(join(output_dir, "compile_output.txt"), 'w') as compiled_output:
compiled_output.write('\n'.join(['\t'.join(item)
for item in combined_results]))
fn = join(output_dir, "compile_output_no_nohits.txt")
with open(fn, 'w') as fd:
fd.write('\n'.join(['\t'.join(item)
for item in combined_results[:-1]]))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# turn a comma-separated list of numbers into a 1-D list of integers
list_of_ints = lambda string: map(int, string.split(","))
input_path_interest = opts.input_path_interest
input_path_other = opts.input_path_other
percentage_ids = list_of_ints(opts.percentage_ids)
alignment_lengths = list_of_ints(opts.alignment_lengths)
hits_to_1st = opts.hits_to_1st
hits_to_2nd = opts.hits_to_2nd
percentage_ids_other = opts.percentage_ids_other
alignment_lengths_other = opts.alignment_lengths_other
output_dir = opts.output_dir
db_a = open(input_path_interest, "U")
db_b = open(input_path_other, "U")
# try to create the output directory, if it exists, just continue
create_dir(output_dir, False)
# run some validations on the input parameters
if percentage_ids_other:
percentage_ids_other = list_of_ints(percentage_ids_other)
if len(percentage_ids) != len(percentage_ids_other):
option_parser.error(
"The percentage values for both databases "
"should be the same length: %s - %s" % (percentage_ids, percentage_ids_other)
)
else:
percentage_ids_other = percentage_ids
if alignment_lengths_other:
alignment_lengths_other = list_of_ints(alignment_lengths_other)
if len(alignment_lengths) != len(alignment_lengths_other):
option_parser.error(
"The alignment length values for both databases"
" should be the length : %s - %s" % (alignment_lengths, alignment_lengths_other)
)
else:
alignment_lengths_other = alignment_lengths
# Process databases
total_queries, best_hits = parse_first_database(db_a, percentage_ids, alignment_lengths)
parse_second_database(db_b, best_hits, percentage_ids_other, alignment_lengths_other)
# Parse results
results = process_results(
percentage_ids,
alignment_lengths,
percentage_ids_other,
alignment_lengths_other,
best_hits,
input_path_interest,
input_path_other,
)
# Collating output and writing full results
for i, item in enumerate(results):
filename = join(output_dir, "summary_" + item["filename"] + ".txt")
fd = open(filename, "w")
fd.write("\n".join(item["summary"]))
fd.close()
if i == 0:
combined_results = []
combined_results.append(["filename"])
combined_results.append(["interestdb (%s)" % input_path_interest])
combined_results.append(["other db (%s)" % input_path_other])
combined_results.append(["only interest"])
combined_results.append(["both dbs"])
combined_results.append(["no hits in interest db"])
no_hits = total_queries - item["db_interest"] - item["db_other"] - item["perfect_interest"] - item["equal"]
combined_results[0].append(item["filename"])
combined_results[1].append(str(item["db_interest"]))
combined_results[2].append(str(item["db_other"]))
combined_results[3].append(str(item["perfect_interest"]))
combined_results[4].append(str(item["equal"]))
combined_results[5].append(str(no_hits))
# Printing count of hits to the db
if hits_to_1st:
s_hits = sorted(item["db_seqs_counts"]["a"].items(), key=itemgetter(1), reverse=True)
filename = join(output_dir, "hits_to_1st_db_" + item["filename"] + ".txt")
fd = open(filename, "w")
fd.write("\n".join(["%s\t%d" % (k, v) for k, v in s_hits if v != 0]))
fd.close()
if hits_to_2nd:
s_hits = sorted(item["db_seqs_counts"]["b"].items(), key=itemgetter(1), reverse=True)
filename = join(output_dir, "hits_to_2nd_db_" + item["filename"] + ".txt")
fd = open(filename, "w")
fd.write("\n".join(["%s: %d" % (k, v) for k, v in s_hits if v != 0]))
fd.close()
# Printing collated results
compiled_output_fd = open(join(output_dir, "compile_output.txt"), "w")
compiled_output_fd.write("\n".join(["\t".join(item) for item in combined_results]))
compiled_output_fd.close()
compiled_output_no_hits_fd = open(join(output_dir, "compile_output_no_nohits.txt"), "w")
compiled_output_no_hits_fd.write("\n".join(["\t".join(item) for item in combined_results[:-1]]))
compiled_output_no_hits_fd.close()
def compare(interest_fp,
other_fp,
output_dir='blast-results-compare',
interest_pcts=None,
interest_alg_lens=None,
other_pcts=None,
other_alg_lens=None,
hits_to_first=False,
hits_to_second=False):
"""Compare two databases and write the outputs
Parameters
----------
interest_fp : str
BLAST results when searching against the database of interest.
other_fp : str
BLAST results when searching against the other database.
output_dir : str, optional
Name of the output file path.
interest_pcts : list, optional
Minimum percentage identity to be considered as a valid result in the
interest database search results. If None is passed, it defaults to
`[70]`.
interest_alg_lens : list, optional
Minimum alginment length to be considered a valid result in the
interest database search results. If None is passed, it defaults to
`[50]`.
other_pcts : list, optional
Minimum percentage identity to be considered as a valid result in the
other database search results. If None is passed, it defaults to
`[70]`.
other_lengths : list, optional
Minimum alginment length to be considered a valid result in the
other database search results. If None is passed, it defaults to
`[50]`.
hits_to_first : bool, optional defaults to False
Outputs the labels and counts of the sequences being hit in the first
database.
hits_to_second : bool, optional defaults to False
Outputs the labels and counts of the sequences being hit in the second
database.
Raises
------
click.BadParameter
If the `interest_pcts` and the `other_pcts` lists are of different
length.
If the `interest_alg_lens` and the `other_alg_lens` lists are of
different length.
"""
if interest_pcts is None:
interest_pcts = [70]
if interest_alg_lens is None:
interest_alg_lens = [50]
db_a = open(interest_fp, 'U')
db_b = open(other_fp, 'U')
# try to create the output directory, if it exists, just continue
create_dir(output_dir, False)
# run some validations on the input parameters
if other_pcts:
if len(interest_pcts) != len(other_pcts):
raise BadParameter("The percentage values for both databases "
"should be the same length: %s - %s" %
(interest_pcts, other_pcts))
else:
other_pcts = interest_pcts
if other_alg_lens:
if len(interest_alg_lens) != len(other_alg_lens):
raise BadParameter("The alignment length values for both databases"
" should be the length : %s - %s" %
(interest_alg_lens, other_alg_lens))
else:
other_alg_lens = interest_alg_lens
# process databases
total_queries, best_hits = parse_first_database(db_a, interest_pcts,
interest_alg_lens)
parse_second_database(db_b, best_hits, other_pcts, other_alg_lens)
# parse results
results = process_results(interest_pcts, interest_alg_lens, other_pcts,
other_alg_lens, best_hits)
# Collating output and writing full results
for i, item in enumerate(results):
filename = join(output_dir, "summary_" + item['filename'] + ".txt")
with open(filename, 'w') as fd:
fd.write('\n'.join(item['summary']))
if i == 0:
combined_results = []
combined_results.append(['filename'])
combined_results.append(
['interest db (%s)' % basename(interest_fp)])
combined_results.append(['other db (%s)' % basename(other_fp)])
combined_results.append(['only interest'])
combined_results.append(['both dbs'])
combined_results.append(['no hits in interest db'])
no_hits = total_queries - item['db_interest'] - item['db_other'] - \
item['perfect_interest'] - item['equal']
combined_results[0].append(item['filename'])
combined_results[1].append(str(item['db_interest']))
combined_results[2].append(str(item['db_other']))
combined_results[3].append(str(item['perfect_interest']))
combined_results[4].append(str(item['equal']))
combined_results[5].append(str(no_hits))
# tiny helper function to save hits files
def save_hits(data, name):
s_hits = sorted(data, key=itemgetter(1), reverse=True)
filename = join(output_dir, name)
with open(filename, 'w') as fd:
fd.write('\n'.join(
['%s\t%d' % (k, v) for k, v in s_hits if v != 0]))
if hits_to_first:
save_hits(item['db_seqs_counts']['a'].items(),
"hits_to_first_db_%s.txt" % item['filename'])
if hits_to_second:
save_hits(item['db_seqs_counts']['b'].items(),
"hits_to_second_db_%s.txt" % item['filename'])
# saving collated results
with open(join(output_dir, "compile_output.txt"), 'w') as compiled_output:
compiled_output.write('\n'.join(
['\t'.join(item) for item in combined_results]))
fn = join(output_dir, "compile_output_no_nohits.txt")
with open(fn, 'w') as fd:
fd.write('\n'.join(['\t'.join(item)
for item in combined_results[:-1]]))
