prefs = {'evalue': 0.001, 'outfmt_pref': 6}
print "blasting,",
if blast_mode == 'n':
local_blastn_2file(infile, dbfile_path, outfile, prefs)
elif blast_mode == 'tx':
local_tblastx_2file(infile, dbfile_path, outfile, prefs)
elif blast_mode == 'tn':
local_tblastn_2file(infile, dbfile_path, outfile, prefs)
except Exception:
print "failed to blast"
break
else:
print "finding range,"
try:
# load blast results from file
rec_array = read_array(outfile, blast_dtypes)
except IOError:
print "failed to load blast results"
break
except Exception:
print "failed to load blast results (unknown error)"
break
else:
print rec_array[0]
# take first line (= best hit) only
try:
line = rec_array[0]
except IndexError:
print "empty blast results"
break
if line[8] < line[9]:
from sys import argv
from Bio.SeqRecord import SeqRecord
from libs.common import read_array, blast_dtypes, load_fasta, write_fasta, ensure_dir
data_dir = "data/" + argv[1] + "/"
main_in = data_dir + argv[2] + "_results.txt"
main_out = data_dir + argv[2] + "_ctxt.fas"
ctx_dir = data_dir + "context/"
capture_span = int(argv[3])
ensure_dir([ctx_dir])
records = []
rec_array = read_array(main_in, blast_dtypes)
descript = "Context of " + argv[2] + " (" + argv[3] + " bp either side)"
for line in rec_array:
query = line[0]
subject = line[1]
print subject
rev_flag = False
if line[8] < line[9]:
q_start, q_stop = line[8] - 1, line[9]
rev_flag = False
else:
prefs = {'evalue': 0.001, 'outfmt_pref': 6}
print "blasting,",
if blast_mode == 'n':
local_blastn_2file(infile, dbfile_path, outfile, prefs)
elif blast_mode == 'tx':
local_tblastx_2file(infile, dbfile_path, outfile, prefs)
elif blast_mode == 'tn':
local_tblastn_2file(infile, dbfile_path, outfile, prefs)
except Exception:
print "failed to blast"
break
else:
print "finding range,"
try:
# load blast results from file
rec_array = read_array(outfile, blast_dtypes)
except IOError:
print "failed to load blast results"
break
except Exception:
print "failed to load blast results (unknown error)"
break
else:
print rec_array[0]
# take first line (= best hit) only
try:
line = rec_array[0]
except IndexError:
print "empty blast results"
break
if line[8] < line[9]:
from libs.common import from_dir, read_array, blast_dtypes, load_fasta, write_fasta
data_dir = "data/" + argv[1] + "/"
blast_out_dir = "data/" + argv[1] + "/blast_out/"
idp = int(argv[2])
main_out = open(data_dir + "comp_results.txt", 'w')
records_dict = {}
# list files in blast results directory
filenames = from_dir(blast_out_dir, re.compile(r'.*\.txt.*'))
for filename in filenames:
counter = 0
# load text
rec_array = read_array(blast_out_dir + filename, blast_dtypes)
# parse lines
for line in rec_array:
# if idp is higher than spec'd:
if line[2] > idp:
query = line[0]
subject = line[1]
# write line to compiled results file
main_out.write("\t".join([str(item) for item in line]) + "\n")
outfile = data_dir + query + "_results.txt"
if not path.exists(outfile):
# create file
out_handle = open(outfile, 'w')
else:
counter += 1
out_handle = open(outfile, 'a')
from sys import argv
from Bio.SeqRecord import SeqRecord
from libs.common import read_array, blast_dtypes, load_fasta, write_fasta, ensure_dir
data_dir = "data/"+argv[1]+"/"
main_in = data_dir+argv[2]+"_results.txt"
main_out = data_dir+argv[2]+"_ctxt.fas"
ctx_dir = data_dir+"context/"
capture_span = int(argv[3])
ensure_dir([ctx_dir])
records = []
rec_array = read_array(main_in, blast_dtypes)
descript = "Context of "+argv[2]+" ("+argv[3]+" bp either side)"
for line in rec_array:
query = line[0]
subject = line[1]
print subject
rev_flag = False
if line[8] < line[9]:
q_start, q_stop = line[8]-1, line[9]
rev_flag = False
else:
else:
# tblastn against the reference DB
infile = data_dir + 'temp.fas'
outfile = data_dir + 'temp.txt'
write_fasta(infile,
SeqRecord(rec.seq.translate(), id='temp'))
prefs = {'evalue': 0.001, 'outfmt_pref': 6}
try:
local_tblastn_2file(infile, db_path, outfile, prefs)
except Exception:
print "failed to blast"
exit()
# parse output -- take only first hit
try:
hit = read_array(outfile, blast_dtypes)[0]
except IndexError:
print '-',
# add record to DB as new symbol
sym_cnt += 1
symbol = 'N' + str(sym_cnt)
rec.id = symbol
symbolDB[symbol] = [rec]
g_vector.append(symbol)
init_DB = True
else:
if hit[2] > threshold:
print '+',
# add record to DB as secondary match
symbol = hit[1]
rec.id = symbol + '_' + str(
from libs.common import from_dir, read_array, blast_dtypes, load_fasta, write_fasta
data_dir = "data/"+argv[1]+"/"
blast_out_dir = "data/"+argv[1]+"/blast_out/"
idp = int(argv[2])
main_out = open(data_dir+"comp_results.txt", 'w')
records_dict = {}
# list files in blast results directory
filenames = from_dir(blast_out_dir, re.compile(r'.*\.txt.*'))
for filename in filenames:
counter = 0
# load text
rec_array = read_array(blast_out_dir+filename, blast_dtypes)
# parse lines
for line in rec_array:
# if idp is higher than spec'd:
if line[2] > idp:
query = line[0]
subject = line[1]
# write line to compiled results file
main_out.write("\t".join([str(item) for item in line])+"\n")
outfile = data_dir+query+"_results.txt"
if not path.exists(outfile):
# create file
out_handle = open(outfile, 'w')
else:
counter +=1
out_handle = open(outfile, 'a')
else:
# tblastn against the reference DB
infile = data_dir+'temp.fas'
outfile = data_dir+'temp.txt'
write_fasta(infile, SeqRecord(rec.seq.translate(), id='temp'))
prefs = {'evalue': 0.001, 'outfmt_pref': 6}
try:
local_tblastn_2file(infile, db_path, outfile, prefs)
except Exception:
print "failed to blast"
exit()
# parse output -- take only first hit
try:
hit = read_array(outfile, blast_dtypes)[0]
except IndexError:
print '-',
# add record to DB as new symbol
sym_cnt +=1
symbol = 'N'+str(sym_cnt)
rec.id = symbol
symbolDB[symbol] = [rec]
g_vector.append(symbol)
init_DB = True
else:
if hit[2] > threshold:
print '+',
# add record to DB as secondary match
symbol = hit[1]
rec.id = symbol+'_'+str(len(symbolDB[symbol])+1)
