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parse_ssearch.py
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parse_ssearch.py
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#!/usr/bin/env python
"""parse_ssearch.py. From the default output of ssearch36, this script parses each alignment to a .tsv format that can then be used in the companion
script parse_mirna_targets.py
Developed and tested with python 3.9.0
NOTES:
It is not entirely clear which ssearch36 parameters are used by psRNATarget, but using the following ssearch command followed by the execution of parse_ssearch.py
and then followed by the execution of this script with default paramemeters managed to reproduced the output of psRNATarget.
ssearch36 -f -8 -g -3 -E 10000 -T 8 -b 200 -r +4/-3 -n -U -W 10 -N 20000 -i <input_mirna.fasta> <reference_genome.fasta> > <output_file>
If you provide an already rev-complemented fasta file, you can omit the -i argument.
Julien Tremblay - julien.tremblay@nrc-cnrc.gc.ca
"""
import argparse
import os
import sys
import re
import signal
signal.signal(signal.SIGPIPE, signal.SIG_DFL)
def parse_command_line_arguments():
parser = argparse.ArgumentParser(description='Convert SSEARCH36 default output to a .tsv format output')
parser.add_argument('-i', '--infile', required=False, help='Input file (i.e. output of ssearch36). This argument is optional as the output of ssearch36 can be piped directly to this script as well.', type=argparse.FileType('r'))
parser.add_argument('--rev', default=False, action=argparse.BooleanOptionalAction, help='Reverse')
parser.add_argument('--verbose', default=False, action=argparse.BooleanOptionalAction, help='Verbose output')
args = parser.parse_args()
return args
def main(arguments):
args = parse_command_line_arguments()
verbose = args.verbose
rev = args.rev
hash = {}
curr_query = "";
curr_target = "";
curr_aln = "";
curr_query_length = int;
counter_match_nucl_string = 0;
curr_start = int;
curr_end = int;
start = int;
end = int;
hsp = int;
q_end = int;
q_start = int;
query_str = str;
aln_str = str;
subject_str = str;
i = 0;
strand = str;
if args.infile:
infile = os.path.abspath(args.infile.name)
fhand = open(infile, 'r') if args.infile else sys.stdin
for line in fhand:
line = line.rstrip()
if line.startswith("#"):
continue
match = re.match(r"\s+\d+>>>(\S+) - (\d+) nt", line)
if match:
if verbose: print("\n---------------------------------------------", file=sys.stderr)
counter_match_nucl_string = 0
curr_start = 0
curr_end = 0
curr_query = match.group(1)
curr_query_length = match.group(2)
i = 0
if verbose: print("curr_query: "+curr_query, file=sys.stderr)
continue
match = re.match(r"^>>(\S+) .*\((\d+) nt\)$", line)
if match:
i+=1
curr_target = match.group(1)+"_"+str(i)
continue
#Smith-Waterman score: 279 89.5% identity (100.0% similar) in 19 nt overlap (2-20:52164-52182)
match = re.match(r"^Smith-Waterman.*\((\d+)-(\d+):(\d+)-(\d+)\)$", line)
if match:
diff_start = int(match.group(1)) - 1
diff_end = int(curr_query_length)
start = int(match.group(3)) - diff_start
end = int(match.group(4)) + diff_end
hsp = int(match.group(4)) - int(match.group(3))
if rev is True:
q_start = int(match.group(1))
q_end = int(match.group(2))
strand = "-"
else:
# If fwd, qstart is in reverse orientation.
q_start = int(match.group(2))
q_end = int(match.group(1))
strand = "+"
continue
match = re.match(r"^>--$", line) #same contig, but in another location
if match:
i+=1
continue
match = re.match(r"^\S+\s+([ACGTU-]*)\s*$", line)
if match and counter_match_nucl_string == 0:
# Found a query nucl alignment string.
curr_start = match.span(1)[0]
curr_end = match.span(1)[1]
curr_str = line[curr_start:curr_end]
if curr_query not in hash:
hash[curr_query] = {}
hash[curr_query][curr_target + "_" + str(i)] = 1
else:
hash[curr_query][curr_target + "_" + str(i)] = 1
query_str = curr_str
counter_match_nucl_string = 1
continue
match = re.match(r"^\s+[\.\:]", line)
if match:
if counter_match_nucl_string == 1:
# Found a match string.
#extract substring at previously found positions.
curr_str = line[curr_start:curr_end]
aln_str = curr_str
continue
match = re.match(r"^\S+\s+[ACGTBDHUYNVWRMKS-]*\s*$", line)
if match and counter_match_nucl_string == 1:
#extract substring at previously found positions.
curr_str = line[curr_start:curr_end]
# Found subject string of current match.
subject_str = curr_str
if curr_target + "_" + str(i) not in hash[curr_query]:
raise Exception("Problem at " + curr_query + "\n" + curr_target + "_"+str(i)+"\n" + line + "\n" + "line number " +str(sys._getframe().f_lineno) + " in the alignment file")
counter_match_nucl_string = 0
print(str(curr_query) + "\t" + str(curr_target) + "\t" + str(aln_str) + "\t" + str(query_str) + "\t" + str(subject_str) + "\t" + str(q_start) + "\t" + str(q_end) + "\t" + str(start) + "\t" + str(end) + "\t" + str(strand) + "\t" + str(hsp), file=sys.stdout)
continue
fhand.close()
if __name__ == '__main__':
sys.exit(main(sys.argv[1:]))