def acr_homolog(FAA_FILE, GFF_FILE, FNA_FILE, MIN_PROTEINS_IN_LOCUS,
AA_THRESHOLD, DISTANCE_THRESHOLD, DIAMOND_ACRHOMOLOG_FILE,
OUTPUT_DIR, isProdigalUsed):
ORGANISM_SUBJECT = Organism(
[GFF_FILE, FAA_FILE],
FNA_FILE,
isProdigalUsed,
bufferSize=30720,
twoFileParse=True) # creates Organism object used to parse gff file
GCF = ORGANISM_SUBJECT.GCF # obtaions GCF ID that corresponds to subject
acr_hit_record = dict()
record_dict = SeqIO.to_dict(SeqIO.parse(FAA_FILE, 'fasta'))
HOMOLOGY_FINAL_RESULT_FILE = OUTPUT_DIR + GCF + '_homology_based.out'
candidate_loci = second_and_third_filter(
first_filter(ORGANISM_SUBJECT, MIN_PROTEINS_IN_LOCUS), GCF,
AA_THRESHOLD, DISTANCE_THRESHOLD, MIN_PROTEINS_IN_LOCUS)
WP_Maps_Protein = {
protein.id: protein
for _, proteinList in ORGANISM_SUBJECT.get_ncid_contents().items()
for protein in proteinList
}
Protein_Maps_Loci = {
protein.id: loci
for loci in candidate_loci for protein in loci
}
with open(DIAMOND_ACRHOMOLOG_FILE, 'r', 512) as handle:
for line in handle:
cols = line.rstrip().split('\t')
acr, wp, pident, evalue = cols[0], cols[1], cols[2], float(
cols[10])
if isProdigalUsed:
protein_info_list = record_dict[wp].description.split('#')
protein_start = protein_info_list[1].strip()
protein_end = protein_info_list[2].strip()
protein = 'Protein({0}-{1})'.format(protein_start, protein_end)
nc_id = wp[0:wp.rfind('_')]
_id = '-'.join([nc_id, protein])
if _id in acr_hit_record:
if evalue < acr_hit_record[_id]['evalue']:
acr_hit_record[_id] = {
'record': record_dict[wp],
'evalue': evalue,
'nc_id': nc_id,
'protein_id': protein,
'pident': pident,
'acr': acr
}
else:
acr_hit_record[_id] = {
'record': record_dict[wp],
'evalue': evalue,
'nc_id': nc_id,
'protein_id': protein,
'pident': pident,
'acr': acr
}
else:
if wp in acr_hit_record:
if evalue < acr_hit_record[wp]['evalue']:
acr_hit_record[wp] = {
'record': record_dict[wp],
'evalue': evalue,
'protein_id': wp,
'pident': pident,
'acr': acr
}
else:
acr_hit_record[wp] = {
'record': record_dict[wp],
'evalue': evalue,
'protein_id': wp,
'pident': pident,
'acr': acr
}
output = '#GCF\tNC ID\tStart\tEnd\tStrand\tProtein ID\taa Length\tGenome_Loci|start|end\tAcr_Hit|pident\tSequence\n'
used_wp = set()
if len(acr_hit_record) > 0:
for wp in acr_hit_record:
if wp in Protein_Maps_Loci:
if wp not in used_wp:
startList = []
endList = []
loci_list = []
for loci_protein in Protein_Maps_Loci[wp]:
loci_list.append(str(loci_protein.wp))
startList.append(loci_protein.start)
endList.append(loci_protein.end)
start = min(startList)
end = max(endList)
for loci_protein in Protein_Maps_Loci[wp]:
protein = loci_protein
output += "{}\t{}\t{}\t{}\t{}\t{}\t{}\t".format(
GCF, protein.nc, protein.start, protein.end,
protein.strand, protein.wp,
str(int(((protein.end - protein.start + 1) / 3))))
output += "{}|{}|{}\t".format('-'.join(loci_list),
start, end)
if loci_protein.id in acr_hit_record:
output += "{}|{}\t".format(
acr_hit_record[protein.id]['acr'],
acr_hit_record[protein.id]['pident'])
else:
output += "---\t"
output += "{}\n".format(protein.sequence)
used_wp.add(protein.id)
output += "\n"
else:
protein = WP_Maps_Protein[wp]
output += "{}\t{}\t{}\t{}\t{}\t{}\t{}\t".format(
GCF, protein.nc, protein.start, protein.end,
protein.strand, protein.wp,
str(int(((protein.end - protein.start + 1) / 3))))
output += "---\t{}|{}\t".format(acr_hit_record[wp]['acr'],
acr_hit_record[wp]['pident'])
output += "{}\n\n".format(protein.sequence)
# protein = WP_Maps_Protein[wp]
# output += "{}\t{}\t{}\t{}\t{}\t{}\t{}\t".format(GCF, protein.nc, protein.start, protein.end, protein.strand, protein.wp, str( int(((protein.end - protein.start + 1) / 3)) ) )
# if wp in Protein_Maps_Loci:
# startList = []; endList = []; loci_list = []
# for loci_protein in Protein_Maps_Loci[wp]:
# loci_list.append(str(loci_protein.wp))
# startList.append(loci_protein.start)
# endList.append(loci_protein.end)
# start = min(startList); end = max(endList)
# output += "{}|{}|{}\t{}|{}\t".format('-'.join(loci_list), start, end, acr_hit_record[wp]['acr'], acr_hit_record[wp]['pident'])
# else:
# output += "---\t---\t"
# output += "{}\n".format(protein.sequence)
with open(HOMOLOGY_FINAL_RESULT_FILE, 'w') as out_handle:
out_handle.write(output)
return acr_hit_record, HOMOLOGY_FINAL_RESULT_FILE
else:
return acr_hit_record, None
