-
Notifications
You must be signed in to change notification settings - Fork 0
/
gb_creator.py
187 lines (175 loc) · 5.72 KB
/
gb_creator.py
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
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
import xlsxwriter
import pandas as pd
import openpyxl
def gb_writer(gene_dict, genes, fs, fam):
name = "gene"+str(fam)
for g in genes:
tup = gene_dict[g]
if tup[0] == "chr1":
fs[0].write(" "+name)
if tup[3] == '+':
fs[0].write(" "+str(tup[1])+".."+str(tup[2])+"\n")
elif tup[3] == '-':
fs[0].write(" complement(" + str(tup[1]) + ".." + str(tup[2]) + ")\n")
fs[0].write(" /gene="+"\""+g+"\"\n")
elif tup[0] == "chr2":
fs[1].write(" " + name)
if tup[3] == '+':
fs[1].write(" " + str(tup[1]) + ".." + str(tup[2]) + "\n")
elif tup[3] == '-':
fs[1].write(" complement(" + str(tup[1]) + ".." + str(tup[2]) + ")\n")
fs[1].write(" /gene=" + "\"" + g + "\"\n")
elif tup[0] == "chr3":
fs[2].write(" " + name)
if tup[3] == '+':
fs[2].write(" " + str(tup[1]) + ".." + str(tup[2]) + "\n")
elif tup[3] == '-':
fs[2].write(" complement(" + str(tup[1]) + ".." + str(tup[2]) + ")\n")
fs[2].write(" /gene=" + "\"" + g + "\"\n")
elif tup[0] == "chr4":
fs[3].write(" " + name)
if tup[3] == '+':
fs[3].write(" " + str(tup[1]) + ".." + str(tup[2]) + "\n")
elif tup[3] == '-':
fs[3].write(" complement(" + str(tup[1]) + ".." + str(tup[2]) + ")\n")
fs[3].write(" /gene=" + "\"" + g + "\"\n")
elif tup[0] == "chr5":
fs[4].write(" " + name)
if tup[3] == '+':
fs[4].write(" " + str(tup[1]) + ".." + str(tup[2]) + "\n")
elif tup[3] == '-':
fs[4].write(" complement(" + str(tup[1]) + ".." + str(tup[2]) + ")\n")
fs[4].write(" /gene=" + "\"" + g + "\"\n")
entries = ["chr1", "chr2", "chr3", "chr4", "chr5"]
families = pd.read_excel("gene_family.xlsx", engine="openpyxl")
gene_list = pd.read_excel("gene_list.xlsx", engine="openpyxl")
#fam = "RAP domain"
fam = open("gene_family.txt", "r")
genes = []
while True:
line = fam.readline().strip()
if not line:
break
#if line[1:-1] == fam:
# genes = f.readline().strip().split(",")
# break
genes += fam.readline().strip().split(",")
fam.close()
gene_dict = {}
for ID in genes:
val = gene_list[gene_list["ID"] == ID]
tup = str(val.values[0])[1:-1].split()
ch = tup[1][1:-1]
start = int(tup[2])
end = int(tup[3])
sign = tup[4][1:-1]
if ch in entries:
gene_dict[ID] = (ch, start, end, sign)
dup = open("MGFs/duplicate.txt", "r")
dup_gene = []
while True:
line = dup.readline().strip()
if not line:
break
g = line.split("-")[0]
if g in gene_dict.keys():
dup_gene.append(g)
print(len(dup_gene))
fs = [open("temp/chr1.txt", "w"), open("temp/chr2.txt", "w"), open("temp/chr3.txt", "w"), open("temp/chr4.txt", "w"), open("temp/chr5.txt", "w")]
gb_writer(gene_dict, dup_gene, fs, 9)
"""
gpi = open("MGFs/gpi.txt", "r")
ap = open("MGFs/ap.txt", "r")
gpi_gene, ap_gene = [], []
while True:
line = gpi.readline().strip()
if not line:
break
g = line.split("-")[0]
if g in gene_dict.keys():
gpi_gene.append(g)
while True:
line = ap.readline().strip()
if not line:
break
g = line.split("-")[0]
if g in gene_dict.keys():
ap_gene.append(g)
print(len(gpi_gene), len(ap_gene))
ufam1 = open("MGFs/umgf1.txt", "r")
ufam2 = open("MGFs/umgf2.txt", "r")
ufam3 = open("MGFs/umgf3.txt", "r")
ofam1 = open("MGFs/OG6_101304.txt", "r")
ofam2 = open("MGFs/OG6_101515.txt", "r")
ofam3 = open("MGFs/OG6_103347.txt", "r")
gene1, gene2, gene3 = [], [], []
genes_1 = ufam1.readline().strip().split("\t")
print(len(genes_1))
#gene1 = [g.split("-")[0] for g in genes_1]
for g in genes_1:
n = g.split("-")[0]
if n in gene_dict.keys():
gene1.append(n)
ufam1.close()
genes_2 = ufam2.readline().strip().split("\t")
print(len(genes_2))
#gene2 = [g.split("-")[0] for g in genes_2]
for g in genes_2:
n = g.split("-")[0]
if n in gene_dict.keys():
gene2.append(n)
ufam2.close()
genes_3 = ufam3.readline().strip().split("\t")
print(len(genes_3))
#gene3 = [g.split("-")[0] for g in genes_3]
for g in genes_3:
n = g.split("-")[0]
if n in gene_dict.keys():
gene3.append(n)
ufam3.close()
gene4, gene5, gene6 = [], [], []
while True:
line = ofam1.readline().strip()
if not line:
break
g = line.split("-")[0]
if g in gene_dict.keys():
gene4.append(g)
while True:
line = ofam2.readline().strip()
if not line:
break
g = line.split("-")[0]
if g in gene_dict.keys():
gene5.append(g)
while True:
line = ofam3.readline().strip()
if not line:
break
g = line.split("-")[0]
if g in gene_dict.keys():
gene6.append(g)
ofam1.close()
ofam2.close()
ofam3.close()
print(len(gene1), len(gene2), len(gene3), len(gene4), len(gene5), len(gene6))
fs = [open("temp/chr1.txt", "w"), open("temp/chr2.txt", "w"), open("temp/chr3.txt", "w"), open("temp/chr4.txt", "w"), open("temp/chr5.txt", "w")]
# gene1
gb_writer(gene_dict, gene1, fs, 1)
# gene2
gb_writer(gene_dict, gene2, fs, 2)
# gene3
gb_writer(gene_dict, gene3, fs, 3)
# gene4
gb_writer(gene_dict, gene4, fs, 4)
# gene5
gb_writer(gene_dict, gene5, fs, 5)
# gene6
gb_writer(gene_dict, gene6, fs, 6)
# gene7
gb_writer(gene_dict, gpi_gene, fs, 7) # color: brown
# gene8
gb_writer(gene_dict, ap_gene, fs, 8) # color: light sky blue
"""
for f in fs:
f.close()