Genome-stats/script.py at master · Barush/Genome-stats · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
import sys
import re

inputname = sys.argv[1]
f = open(inputname)

#load file
inputdata = f.readlines()
f.close()

#prepare gentypes
type1 = ["protein_coding", "IG_C_gene", "IG_D_gene", "IG_J_gene", "IG_V_gene", "TR_C_gene", "TR_D_gene", "TR_J_gene", "TR_V_gene"]
type2 = ["snRNA", "rRNA", "snoRNA", "miRNA", "misc_RNA"]
type3 = ["lincRNA", "non_coding", "processed_transcript", "antisense", "3prime_overlapping_ncrna", "sense_intronic", "sense_overlapping", "known_ncrna"]
type4 = ["unitary_pseudogene", "IG_C_pseudogene", "translated_processed_pseudogene", "polymorphic_pseudogene", "TR_J_pseudogene", "IG_J_pseudogene", "TR_V_pseudogene", "IG_V_pseudogene", "pseudogene", "unprocessed_pseudogene", "transcribed_unprocessed_pseudogene", "translated_unprocessed_pseudogene", "transcribed_processed_pseudogene", "processed_pseudogene", "transcribed_unitary_pseudogene"]

#prepare counts
count1 = [0,0,0,0,0,0,0,0,0]
count2 = [0,0,0,0,0]
count3 = [0,0,0,0,0,0,0,0]
count4 = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
count5 = [0,0]

#prepare lengths
len1 = [0,0,0,0,0,0,0,0,0]
len2 = [0,0,0,0,0]
len3 = [0,0,0,0,0,0,0,0]
len4 = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
len5 = [0,0]

#prepare ends
end1 = [0,0,0,0,0,0,0,0,0]
end2 = [0,0,0,0,0]
end3 = [0,0,0,0,0,0,0,0]
end4 = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
end5 = [0,0]

#parse file line by line
for i in range (0, len(inputdata)):
	if(not inputdata[i].startswith("#")):
		#parse line
		value = inputdata[i].split("\t")

		start = int(value[3])
		stop = int(value[4])

		params = value[len(value)-1].split(";")

		#find type of the record
		biotype = re.compile(".*biotype.*")
		t = 0
		while(not biotype.match(params[t])):
			t += 1
		gentype = params[t].split(" ")[2][1:-1]

		if(value[2] == "gene"):
			#determine where the type fits
			for g in range(0, len(type1)):
				if(gentype == type1[g]):
					count1[g] += 1
					if (start < end1[g]):
						start = end1[g]
					if (stop < end1[g]):
						stop = end1[g]
					len1[g]+= (stop - start)
					end1[g] = stop

			for g in range(0, len(type2)):
				if(gentype == type2[g]):
					count2[g] += 2
					if(start < end2[g]):
						start = end2[g]
					if(stop < end2[g]):
						stop = end2[g]
					len2[g] += (stop - start)
					end2[g] = stop

			for g in range(0, len(type3)):
				if(gentype == type3[g]):
					count3[g] += 3
					if(start < end3[g]):
						start = end3[g]
					if(stop < end3[g]):
						stop = end3[g]
					len3[g] += (stop - start)
					end3[g] = stop

			for g in range(0, len(type4)):
				if(gentype == type4[g]):
					count4[g] += 1
					if(start < end4[g]):
						start = end4[g]
					if(stop < end4[g]):
						stop = end4[g]
					len4[g]  += (stop - start)
					end4[g] = stop
		elif((value[2] == "CDS") or (value[2] == "transcript")):
			if(gentype == "protein_coding"):
				if(value[2] == "transcript"):
					count5[0] += 1
					if(start < end5[0]):
						start = end5[0]
					if(stop < end5[0]):
						stop = end5[0]
					len5[0] += (stop - start)
					end5[0] = stop
				elif(value[2] == "CDS"):
					count5[1] += 1
					if(start < end5[1]):
						start = end5[1]
					if(stop < end5[1]):
						stop = end5[1]
					len5[1] += (stop - start)
					end5[1] = stop


#print results
cnt_s1 = 0
len_s1 = 0
for i in range (0, len(type1)):
	print type1[i], count1[i], len1[i]
	cnt_s1 += count1[i]
	len_s1 += len1[i]
print "Summary", cnt_s1, len_s1, "\n"

cnt_s2 = 0
len_s2 = 0
for i in range (0, len(type2)):
	print type2[i], count2[i], len2[i]
	cnt_s2 += count2[i]
	len_s2 += len2[i]
print "Summary", cnt_s2, len_s2, "\n"

cnt_s3 = 0
len_s3 = 0
for i in range (0, len(type3)):
	print type3[i], count3[i], len3[i]
	cnt_s3 += count3[i]
	len_s3 += len3[i]
print "Summary", cnt_s3, len_s3, "\n"

cnt_s4 = 0
len_s4 = 0
for i in range (0, len(type4)):
	print type4[i], count4[i], len4[i]
	cnt_s4 += count4[i]
	len_s4 += len4[i]
print "Summary", cnt_s4, len_s4, "\n"

print "Coding transcripts", count5[0], len5[0]
print "CDS", count5[1], len5[1]