def simulate_reads(ref, chr, readlen, readcov, dupnum, duplen, sam, chr_len):
final_SAM_fns = [] # List containing all SAM files to be combined together. First contains regular read simulation SAM file, with regional duplication SAM files added later
chr_list = []
pattern = "Chr\d{1,}"
recomp = re.compile(pattern)
if chr == "All":
for chr_temp in chr_len:
match = recomp.match(chr_temp)
if match:
chr_list.append(chr_temp)
else:
chr_list = [entry for entry in chr.split(',')]
for chr in chr_list:
for i in range(0,len(chr_len[chr]),10000):
out_fn = str(sam[:-3]) + "_temp_" + str(chr) + "_" + str(i)
new_fasta = ">" + str(chr) + "\n" + chr_len[chr][i:i+10000]
temp_fasta = "regtemp_" + str(i) + ".fasta"
with open(temp_fasta, 'w') as outfile:
outfile.write(new_fasta)
params = ' '.join(["art_illumina.exe", "-i", str(temp_fasta), "-l", str(readlen), "-f", str(readcov), "-o", out_fn, "-sam", "-q"])
#Example usage: art_illumina.exe -i ../at9_chr3.fasta -l 34 -f 2 -o Output/RandomAtReads -sam
simulation = subprocess.Popen(params)
simulation.wait()
new_out_fn = out_fn + ".sam"
if i > 0:
reg_SAM = SAM.parse(new_out_fn, True)
for j in range(0,len(reg_SAM.sam_list)):
reg_SAM.sam_list[j][3] = str(int(reg_SAM.sam_list[j][3]) + i) # Changing SAM file read numbers
reg_SAM.output(new_out_fn)
os.remove(temp_fasta)
os.remove(out_fn + ".fq")
os.remove(out_fn + ".aln")
final_SAM_fns.append(new_out_fn) # Regular read profile files assigned here
prev_sel = []
for i in range(1,dupnum+1):
spos = 0
undupped_region = False
ok_regions = 0
while undupped_region == False:
chr = ''.join(sample(chr_list,1))
spos = randrange(0,len(chr_len[chr]))
epos = spos + duplen
if epos > len(chr_len[chr]): continue
for entry in prev_sel:
(c, start, end) = entry
if chr == c:
if not (int(spos) >= int(start) and int(spos) <= int(end)) or (int(epos) >= int(start) and int(epos) <= int(end)):
# Testing to make sure that newly selected duplicated region is not within a region already selected to be duplicated
ok_regions += 1
else:
break
else:
ok_regions += 1
if ok_regions == len(prev_sel):
undupped_region = True
prev_sel.append((chr,spos,epos))
new_fasta = ">" + str(chr) + "\n" + chr_len[chr][spos:epos]
temp_fasta = "duptemp_" + str(i) + ".fasta"
with open(temp_fasta, 'w') as outfile:
outfile.write(new_fasta)
params = ' '.join(["art_illumina.exe", "-i", str(temp_fasta), "-l", str(readlen), "-f", str(readcov), "-o", str(temp_fasta[:-6]), "-sam", "-q"])
simulation = subprocess.Popen(params)
simulation.wait()
dup_fn = temp_fasta[:-6] + ".sam"
dup_SAM = SAM.parse(dup_fn, True)
for i in range(0,len(dup_SAM.sam_list)):
dup_SAM.sam_list[i][3] = str(int(dup_SAM.sam_list[i][3]) + spos)
dup_SAM.output(dup_fn[:-4] + "_temp.sam")
os.remove(temp_fasta)
os.remove(temp_fasta[:-6] + ".fq")
os.remove(temp_fasta[:-6] + ".aln")
os.remove(dup_fn)
final_SAM_fns.append(dup_fn[:-4] + "_temp.sam")
final_SAM = SAM.parse(final_SAM_fns, True)
pattern2 = r"Chr\d{1}-(\d+)"
recomp2 = re.compile(pattern2)
max_read = final_SAM.sam_list[0][0]
match = recomp2.match(max_read)
max_num = int(match.group(1))
min_met = False
for i in range(0, len(final_SAM.sam_list)): # Ensure that read names from one SAM file do not coincide with read names from another SAM file
r_name = final_SAM.sam_list[i][0]
match = recomp2.match(r_name)
if match:
r_num = int(match.group(1))
if r_num == 1 and min_met == False:
min_met = True
continue
if min_met == True:
max_num += 1
line = final_SAM.sam_list[i]
line[0] = r_name[:5] + str(max_num)
final_SAM.sam_list[i] = line
final_SAM.header = sorted(final_SAM.header, key = lambda read: read[1][6:])
final_SAM.sam_list = sorted(final_SAM.sam_list, key = lambda read: int(read[0][5:]))
for i in range(0,len(final_SAM.header)): # Set chromosome length in header portion of SAM file to correct length (will be 10,000 in temporary simulation SAM files)
chr = final_SAM.header[i][1][3:]
final_SAM.header[i][2] = "LN:" + str(len(chr_len[chr]))
final_SAM.output(sam[:-3])
for file in final_SAM_fns:
os.remove(file)
params = ' '.join([str(pypath) + " FixARTSAMFile.py", "-i", sam[:-3], "-o", sam])
fixSAM = subprocess.Popen(params) # Replaces new CIGAR string format for matches, which uses = and X, to the old format M for both
fixSAM.wait()
print("Duplicated regions are located at:\n")
for entry in sorted(prev_sel, key = lambda entry:(entry[0], entry[1])):
(chr, spos, epos) = entry
print(str(chr), ":", str(spos),"-", str(epos), sep="")
