IDEAS repository DONE

bin/bed2inv.py

@@ -0,0 +1,89 @@
+#module load python/2.7
+import os
+import numpy as np
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+from scipy.stats import norm
+
+################################################################################################
+### read 2d array
+def read2d_array(filename,dtype_used):
+	import numpy as np
+	data=open(filename,'r')
+	data0=[]
+	for records in data:
+		tmp = [x.strip() for x in records.split(' ')]
+		data0.append(tmp)
+	data0 = np.array(data0,dtype=dtype_used)
+	data.close()
+	return data0
+
+################################################################################################
+### write 2d matrix
+def write2d_array(array,output):
+	r1=open(output,'w')
+	for records in array:
+		for i in range(0,len(records)-1):
+			r1.write(str(records[i])+'\t')
+		r1.write(str(records[len(records)-1])+'\n')
+	r1.close()
+
+################################################################################################
+### bed2inv
+def bed2inv(input_bed, output_inv):
+	data0 = read2d_array(input_bed, str)
+	data_chr_dict = {}
+	data_chr_vec = []
+	data_chr_inv = []
+
+	### loop bed
+	for bed_info in data0:
+		chrom = bed_info[0]
+		if not (chrom in data_chr_dict):
+			data_chr_dict[chrom] = 1
+			data_chr_vec.append(chrom)
+		else:
+			data_chr_dict[chrom] = data_chr_dict[chrom] + 1
+
+	### get inv file
+	start_num = 0
+	for chrom in data_chr_vec:
+		chrom_bin_num = data_chr_dict[chrom]
+		end_num = start_num+chrom_bin_num
+		inv_vec = [chrom, start_num, end_num]
+		data_chr_inv.append(inv_vec)
+		start_num = end_num
+
+	data_chr_inv = np.array(data_chr_inv)
+	write2d_array(data_chr_inv,output_inv)
+
+
+
+############################################################################
+#time python bed2inv.py -i input.bed -o output.inv
+
+import getopt
+import sys
+def main(argv):
+	try:
+		opts, args = getopt.getopt(argv,"hi:o:")
+	except getopt.GetoptError:
+		print 'time python bed2inv.py -i input.bed -o output.inv'
+		sys.exit(2)
+
+	for opt,arg in opts:
+		if opt=="-h":
+			print 'time python bed2inv.py -i input.bed -o output.inv'
+			sys.exit()
+		elif opt=="-i":
+			input_bed=str(arg.strip())
+		elif opt=="-o":
+			output_inv=str(arg.strip())
+
+	bed2inv(input_bed, output_inv)
+
+if __name__=="__main__":
+	main(sys.argv[1:])
+
+

data/hg19.genome

@@ -0,0 +1,93 @@
+chr1	249250621
+chr2	243199373
+chr3	198022430
+chr4	191154276
+chr5	180915260
+chr6	171115067
+chr7	159138663
+chrX	155270560
+chr8	146364022
+chr9	141213431
+chr10	135534747
+chr11	135006516
+chr12	133851895
+chr13	115169878
+chr14	107349540
+chr15	102531392
+chr16	90354753
+chr17	81195210
+chr18	78077248
+chr20	63025520
+chrY	59373566
+chr19	59128983
+chr22	51304566
+chr21	48129895
+chr6_ssto_hap7	4928567
+chr6_mcf_hap5	4833398
+chr6_cox_hap2	4795371
+chr6_mann_hap4	4683263
+chr6_apd_hap1	4622290
+chr6_qbl_hap6	4611984
+chr6_dbb_hap3	4610396
+chr17_ctg5_hap1	1680828
+chr4_ctg9_hap1	590426
+chr1_gl000192_random	547496
+chrUn_gl000225	211173
+chr4_gl000194_random	191469
+chr4_gl000193_random	189789
+chr9_gl000200_random	187035
+chrUn_gl000222	186861
+chrUn_gl000212	186858
+chr7_gl000195_random	182896
+chrUn_gl000223	180455
+chrUn_gl000224	179693
+chrUn_gl000219	179198
+chr17_gl000205_random	174588
+chrUn_gl000215	172545
+chrUn_gl000216	172294
+chrUn_gl000217	172149
+chr9_gl000199_random	169874
+chrUn_gl000211	166566
+chrUn_gl000213	164239
+chrUn_gl000220	161802
+chrUn_gl000218	161147
+chr19_gl000209_random	159169
+chrUn_gl000221	155397
+chrUn_gl000214	137718
+chrUn_gl000228	129120
+chrUn_gl000227	128374
+chr1_gl000191_random	106433
+chr19_gl000208_random	92689
+chr9_gl000198_random	90085
+chr17_gl000204_random	81310
+chrUn_gl000233	45941
+chrUn_gl000237	45867
+chrUn_gl000230	43691
+chrUn_gl000242	43523
+chrUn_gl000243	43341
+chrUn_gl000241	42152
+chrUn_gl000236	41934
+chrUn_gl000240	41933
+chr17_gl000206_random	41001
+chrUn_gl000232	40652
+chrUn_gl000234	40531
+chr11_gl000202_random	40103
+chrUn_gl000238	39939
+chrUn_gl000244	39929
+chrUn_gl000248	39786
+chr8_gl000196_random	38914
+chrUn_gl000249	38502
+chrUn_gl000246	38154
+chr17_gl000203_random	37498
+chr8_gl000197_random	37175
+chrUn_gl000245	36651
+chrUn_gl000247	36422
+chr9_gl000201_random	36148
+chrUn_gl000235	34474
+chrUn_gl000239	33824
+chr21_gl000210_random	27682
+chrUn_gl000231	27386
+chrUn_gl000229	19913
+chrM	16571
+chrUn_gl000226	15008
+chr18_gl000207_random	4262