def main():
if len(sys.argv) < 2:
bb.fun_print_help("species_query", "species_target", "path_out", "chain_files(eg: rn5ToRn6,rn6ToMm10)","[query.ns.bed]",
"[query.bed]")
global_para()
if not os.path.exists(PATH_OUT):
bb.fun_print("create out path......", "red", "black", 1)
os.mkdir(PATH_OUT)
dict_pi = get_pi()
psl_map()
dict_exon_intron = read_exon_intron()
write_exon_intron_length(dict_exon_intron)
dict_cover = calculate_coverage(dict_exon_intron)
list_ortho = find_ortho_pi(dict_cover)
dict_synteny = get_synteny(dict_pi, list_ortho)
run_lastz(dict_synteny, dict_pi, dict_cover)
for i in dict_pi:
if i not in list_ortho and i not in dict_synteny:
LIST_OUT.append([i, 0, "none", "0", "0", "0", "chrNA", 1, 1, "+"])
file_out = bb.fun_open_file("{0}/{1}_{2}.conserve.tab".format(PATH_OUT, SPECIES1, SPECIES2), "w")
for i in LIST_OUT:
file_out.write(i[0])
for j in range(1, len(i)):
file_out.write("\t" + str(i[j]))
file_out.write("\n")
file_out.close()
os.system("rm {0}/temp*".format(PATH_OUT))
def run_lastz(dict_synteny, dict_pi, dict_cover):
for pi in dict_synteny:
bb.fun_print("start check conservation for " + pi, "green", "black", 1)
LIST_OUT.append([pi, 3, "none",
dict_synteny[pi][1][4], dict_cover[pi][0], dict_cover[pi][1],
dict_synteny[pi][1][0], dict_synteny[pi][1][1], dict_synteny[pi][1][2],
dict_synteny[pi][1][3]])
def psl_map():
TEMP_PSL_IN = PATH_QUERY_NS_BED
for chains in PATH_CHAIN:
TEMP_CHROM_SIZE = chains.split("To")[0] + ".chrom.size"
command = "BB_PslMap {0} {1} {2} {3}/temp_pslmap_out 0.1".format(TEMP_PSL_IN, TEMP_CHROM_SIZE, chains, PATH_OUT)
if os.system(command) != 0:
bb.fun_print(PATH_CHAIN)
bb.fun_print_error("BB_PslMap Error, please check chain files")
os.system("cp {0}/temp_pslmap_out.psl {0}/temp_pslmap_in.psl".format(PATH_OUT))
TEMP_PSL_IN = "{0}/temp_pslmap_in.psl".format(PATH_OUT)
os.system("cp {0}/temp_pslmap_out.psl {0}/{1}_{2}.psl && cp {0}/temp_pslmap_out.bed {0}/{1}_{2}.bed".format(PATH_OUT, SPECIES1, SPECIES2))
def main():
args = get_args()
args.align = prepare_align_file(args)
list_gene = read_gene_list(args)
dict_matrix = {}
for gn in list_gene:
dict_matrix[gn] = []
cmd = ["bedtools", "coverage", "-d", "-a", args.gene_position, "-b", args.align]
bb.fun_print("run bedtools coverage", "green", "black", 1)
ret = subprocess.Popen(cmd, stdout=subprocess.PIPE)
factor = 0
for l in bb.fun_open_file(args.align):
factor += 1
print "unique mapped reads number: %s"%factor
c = 0
r = 0
name = "0"
bb.fun_print("make matrix", "green", "black", 1)
tt = 0
for l in ret.stdout:
tt += 1
if tt % 1000000 == 0:
bb.fun_print("%s million lines processed......"%(tt/1000000))
line = l.strip().split()
if line[3] != name and name != "0" and r != 0:
dict_matrix[name].append(str(float(c)/args.resolution*1000000/factor))
r = 0
c = 0
name = line[3]
r += 1
c += int(line[7])
if r == args.resolution:
dict_matrix[name].append(str(float(c)/args.resolution*1000000/factor))
r = 0
c = 0
file_matrix = bb.fun_open_file(args.output, "w")
for gn in list_gene:
file_matrix.write(gn)
if DICT_STRAND[gn] == "+":
for dp in dict_matrix[gn]:
file_matrix.write("\t" + dp)
file_matrix.write("\n")
else:
for dp in dict_matrix[gn][::-1]:
file_matrix.write("\t" + dp)
file_matrix.write("\n")
file_matrix.close()
if args.format in ["sam", "bam"]:
subprocess.check_call("rm %s_temp*"%args.align)
def run_lastz(dict_synteny, dict_pi, dict_cover):
for pi in dict_synteny:
bb.fun_print("start check conservation for " + pi, "green", "black", 1)
bb.fun_quick_write(
"%s\t%s\t%s\t%s\t0\t%s\n" %
(dict_synteny[pi][0][0], dict_synteny[pi][0][1],
dict_synteny[pi][0][2], pi, dict_synteny[pi][0][3]),
"%s/temp1.bed" % PATH_OUT)
bb.fun_quick_write(
"%s\t%s\t%s\t%s\t0\t%s\n" %
(dict_pi[pi][0], max(1, dict_pi[pi][1] - 10000),
min(DICT_CHROM1[dict_pi[pi][0]],
dict_pi[pi][2] + 10000), pi, dict_pi[pi][4]),
"%s/temp.shuffle1.bed" % PATH_OUT)
bb.fun_quick_write(
"%s\t%s\t%s\t%s\t0\t%s\n" %
(dict_synteny[pi][1][0], dict_synteny[pi][1][1],
dict_synteny[pi][1][2], pi, dict_synteny[pi][1][3]),
"%s/temp2.bed" % PATH_OUT)
command = "bedtools getfasta -fi /data/tongji2/Annotation/Fasta/{0}.fa \
-fo {1}/temp1.fa -bed {1}/temp1.bed -name -s".format(
DICT_SP[SPECIES1], PATH_OUT)
if os.system(command) != 0:
bb.fun_print_error("getfasta Error")
command = "bedtools getfasta -fi /data/tongji2/Annotation/Fasta/{0}.fa \
-fo {1}/temp.shuffle1.fa -bed {1}/temp.shuffle1.bed -name -s".format(
DICT_SP[SPECIES1], PATH_OUT)
if os.system(command) != 0:
bb.fun_print_error("getfasta Error")
command = "bedtools getfasta -fi /data/tongji2/Annotation/Fasta/{0}.fa \
-fo {1}/temp2.fa -bed {1}/temp2.bed -name -s".format(
DICT_SP[SPECIES2], PATH_OUT)
if os.system(command) != 0:
bb.fun_print_error("getfasta Error")
# shuffle
bb.fun_print("start shuffling......", "blue", "black", font=1)
shuffle_scores = [0]
for i in range(0):
command = "bedtools shuffle -i {0}/temp.shuffle1.bed -g /data/tongji2/Annotation/ChromSize/{1}.chrom.size > {0}/temp.shuffle2.bed".format(
PATH_OUT, DICT_SP[SPECIES2])
if os.system(command) != 0:
bb.fun_print_error("bedtools shuffle Error")
command = "bedtools getfasta -fi /data/tongji2/Annotation/Fasta/{0}.fa \
-fo {1}/temp.shuffle2.fa -bed {1}/temp.shuffle2.bed -name -s".format(
DICT_SP[SPECIES2], PATH_OUT)
if os.system(command) != 0:
bb.fun_print_error("getfasta Error")
command = "lastz {0}/temp.shuffle1.fa {0}/temp.shuffle2.fa --strand=plus --chain \
--output={0}/temp.shuffle.lastz --format=general:score".format(
PATH_OUT)
os.system(command)
file_shuffle = bb.fun_open_file(
"{0}/temp.shuffle.lastz".format(PATH_OUT))
lines = file_shuffle.readlines()
if len(lines) == 1:
shuffle_scores.append(0)
else:
for record in lines:
if record[0] != "#":
shuffle_scores.append(float(record.strip()))
shuffle_scores.sort()
cutoff = shuffle_scores[int(len(shuffle_scores) * 0.95)] #p-value=0.05
bb.fun_print("p 0.05 cutoff mapping score: " + str(cutoff),
"blue",
"black",
font=1)
# end shuffle
command = "lastz {0}/temp1.fa {0}/temp2.fa --strand=plus --chain \
--rdotplot={0}/temp.rplot --output={0}/temp.lastz \
--format=general:name1,start1,end1,name2,start2,end2,nmatch,identity,score".format(
PATH_OUT)
if os.path.getsize(
"{0}/temp1.fa".format(PATH_OUT)) and os.path.getsize(
"{0}/temp1.fa".format(PATH_OUT)):
if os.system(command) != 0:
bb.fun_print_error("lastz Error")
else:
LIST_OUT.append([pi, 1, "none", "0", "0", "0", "chrNA", 1, 1, "+"])
continue
os.system("sort -k2,2n {0}/temp.lastz > {0}/temp.sort.lastz".format(
PATH_OUT))
file_in = bb.fun_open_file("%s/temp.lastz" % PATH_OUT)
list_lastz = []
start = dict_synteny[pi][0][1]
end = dict_synteny[pi][0][2]
k = 0
for l in file_in:
if l[0] == "#":
continue
line = l.strip().split()
if float(line[-1]) > cutoff:
list_lastz.append([int(line[1]), int(line[2])])
if dict_synteny[pi][0][3] == "+":
pi_start = dict_pi[pi][1] - start
pi_end = dict_pi[pi][2] - start
else:
pi_start = end - dict_pi[pi][2]
pi_end = end - dict_pi[pi][1]
for i in list_lastz:
if pi_end < i[0] or pi_start > i[1]:
continue
else:
LIST_OUT.append([
pi, 3, "none", dict_synteny[pi][1][4], dict_cover[pi][0],
dict_cover[pi][1], dict_synteny[pi][1][0],
dict_synteny[pi][1][1], dict_synteny[pi][1][2],
dict_synteny[pi][1][3]
])
k = 1
break
if k == 0:
LIST_OUT.append([pi, 2, "none", "0", "0", "0", "chrNA", 1, 1, "+"])