def read_gene_list(args):
list_gene = []
global DICT_STRAND
DICT_STRAND = {}
for l in bb.fun_open_file(args.gene_position):
if l.split()[3] in list_gene:
bb.fun_print_error("there is repetitive names in gene position file, please remove the repeat name")
list_gene.append(l.split()[3])
DICT_STRAND[l.split()[3]] = l.split()[5]
return list_gene
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 find_ortho_pi(dict_cover):
os.system("sort -k1,1 -k2,2n {0}/{1}_{2}.bed > {0}/t && mv {0}/t {0}/{1}_{2}.bed && sort -k1,1 -k2,2n {3}/{2}/{2}.piRNA.ns.bed > {0}/t && mv {0}/t {3}/{2}/{2}.piRNA.ns.bed".format(PATH_OUT, SPECIES1, SPECIES2, PATH_PI))
command = "bedtools intersect -sorted -wo -s -a {0}/{1}_{2}.bed -b {3}/{2}/{2}.piRNA.ns.bed > {0}/{1}_{2}.ortho".format(PATH_OUT, SPECIES1, SPECIES2, PATH_PI)
if os.system(command) != 0:
bb.fun_print_error("intersectBed Error")
out = []
file_in = bb.fun_open_file("{0}/{1}_{2}.ortho".format(PATH_OUT, SPECIES1, SPECIES2))
for l in file_in:
line = l.strip().split()
LIST_OUT.append([line[3], 4, line[9],
line[4], dict_cover[line[3]][0], dict_cover[line[3]][1],
line[6], line[7], line[8], line[11]])
out.append(line[3])
return out
def check_args(args):
if not os.path.exists(args.align):
bb.fun_print_error("wrong input pathway: %s, please re-define the right pathway for align file"%args.align)
if not os.path.exists(args.gene_position):
bb.fun_print_error("wrong input pathway: %s, please re-define the right pathway for gene position file"%args.gene_position)
if args.format not in ["sam", "bam", "bed"]:
bb.fun_print_error("wrong format, the program only support sam, bam or bed")
DICT_CHROM2 = read_chrom("/data/tongji2/Annotation/ChromSize/%s.chrom.size"%DICT_SP[SPECIES2])
LIST_OUT = []
global PATH_QUERY_BED, PATH_QUERY_NS_BED
PATH_QUERY_BED = "0"
PATH_QUERY_NS_BED = "0"
if len(sys.argv) > 5:
PATH_QUERY_NS_BED = sys.argv[5]
PATH_QUERY_BED = sys.argv[6]
else:
PATH_QUERY_NS_BED = "{0}/{1}/{1}.piRNA.ns.bed".format(PATH_PI, SPECIES1)
PATH_QUERY_BED = "{0}/{1}/{1}.piRNA.bed".format(PATH_PI, SPECIES1)
global PATH_CHAIN
PATH_CHAIN = sys.argv[4].split(",")
def read_chrom(path):
out = {}
file_in = bb.fun_open_file(path)
for l in file_in:
line = l.strip().split()
out[line[0]] = int(line[1])
return out
# --------process--------
if __name__ == '__main__':
try:
main()
except KeyboardInterrupt:
bb.fun_print_error("user interrupted, abort!")
sys.exit(0)
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, "+"])