def __init__(self, subject, query, blastn_opt="", miranda_opt=""):
"""
General initialization function for import and command line
"""
print("\nInitialize TargetPredict")
# Verify files readability
assert is_readable_file(subject), "{} is not readable".format(subject)
assert is_readable_file(query), "{} is not readable".format(query)
# Create a temporary folder for working files
self.temp_dir = mkdtemp()
# Extract gzip in temporary files if needed
self.original_subject = subject
self.orignal_query = query
self.subject = gunzip (subject, self.temp_dir) if is_gziped(subject) else subject
self.query = gunzip (query, self.temp_dir) if is_gziped(query) else query
self.blastn_opt = blastn_opt
self.miranda_opt = miranda_opt
# Define additional self variables
self.basename = "{}_{}".format(file_basename(subject), file_basename(query))
def __call__(self):
"""
"""
##### BLAST prediction #####
print ("\nFinding hits with BLASTN")
blast_hits =[]
# Create blastn database
print (" Create a blast database")
db_path = "{}/{}".format(self.temp_dir, file_basename(self.subject))
makeblastdb_cmd = "makeblastdb -dbtype nucl -input_type fasta -in {} -out {}".format(self.subject, db_path)
print ("\t"+makeblastdb_cmd)
makeblastdb_out = self._yield_cmd(makeblastdb_cmd)
with open (file_basename(self.subject)+"_makeblastdb.log", "w") as fout:
for line in makeblastdb_out:
fout.write(line)
# Perform blast
print (" Run blastn")
blastn_cmd = "blastn {} -num_threads {} -outfmt \"6 std qseq\" -dust no -query {} -db {}".format(self.blastn_opt, cpu_count(), self.query, db_path)
print ("\t"+blastn_cmd)
blastn_out = self._yield_cmd(blastn_cmd)
for line in blastn_out:
hit_split = line.strip().split()
assert len(hit_split) == 13, "Invalid blast line: {}".format(line)
blast_hits.append(BlastHit(*hit_split))
# Suppress hits on positive strand, keep best hit per subject only and sort by score
print (" Process hits")
blast_hits = [hit for hit in blast_hits if hit.strand == "-"]
blast_hit_dict = {}
for hit in blast_hits:
if hit.s_id in blast_hit_dict:
if hit.score > blast_hit_dict[hit.s_id].score:
blast_hit_dict[hit.s_id]=hit
else:
blast_hit_dict[hit.s_id]=hit
blast_hits = blast_hit_dict.values()
blast_hits.sort (key=lambda x: x.score, reverse=True)
# Write a complete blast report
print (" Write a blast report")
self._write_report (blast_hits, "{}_raw_blast_results.csv".format(self.basename))
##### MIRANDA prediction#####
print ("\nFinding hits with MIRANDA")
miranda_hits =[]
# Run miranda and parse output
print (" Run miranda")
miranda_cmd = "miranda {} {} -quiet {}".format(self.query, self.subject, self.miranda_opt)
print ("\t"+miranda_cmd)
miranda_output = self._yield_cmd(miranda_cmd)
for line in miranda_output:
if line[0] == ">" and line[1] != ">":
hit_split = line[1:].strip().split()
assert len(hit_split) == 11, "Invalid miranda line: {}".format(line)
miranda_hits.append (MirandaHit(*hit_split))
# Keep best hit per subject only and sort hits by score
print (" Process hits")
miranda_hit_dict = {}
for hit in miranda_hits:
if hit.s_id in miranda_hit_dict:
if hit.score > miranda_hit_dict[hit.s_id].score:
miranda_hit_dict[hit.s_id]=hit
else:
miranda_hit_dict[hit.s_id]=hit
miranda_hits = miranda_hit_dict.values()
miranda_hits.sort (key=lambda x: x.score, reverse=True)
# Write a complete miranda report
print (" Write a Miranda report")
self._write_report (miranda_hits, "{}_raw_miranda_results.csv".format(self.basename))
# Write a report
report_out = self.basename+".report.txt"
print ("\nGenerate a summary report")
with open (report_out, "w") as fout:
fout.write ("Program {}\tDate {}\n".format(self.VERSION,str(datetime.today())))
fout.write ("\n### OPTIONS ###\n")
fout.write ("Subject fasta file\t{}\n".format(self.original_subject))
fout.write ("Query fasta file\t{}\n".format(self.orignal_query))
fout.write ("Makeblastdb command\t{}\n".format(makeblastdb_cmd))
fout.write ("Blastn command\t{}\n".format(blastn_cmd))
fout.write ("Miranda command\t{}\n".format(miranda_cmd))
fout.write ("\n### COUNTS ###\n")
fout.write ("Blast Hits found\t{}\n".format(len(blast_hits)))
fout.write ("Miranda Hits found\t{}\n".format(len(miranda_hits)))
