-
Notifications
You must be signed in to change notification settings - Fork 0
/
ReadGTFutrdb.py
186 lines (174 loc) · 5.69 KB
/
ReadGTFutrdb.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
#!/usr/bin/env python2.7
import sys,os
try:
infile=sys.argv[1] #'gene.gtf' #'gencode.v33lift37.annotation.gtf'
except:
sys.exit('<gtf file>')
org=infile.split('.')[1]
tmpfile = infile.replace('.gtf','.tmp')
outfile = tmpfile.replace('.tmp','.annotations')
#edifile='listEditingSites.txt'
def getL(last):
d={}
last=last.replace('"','')
last=last.rstrip(';')
for i in last.split(';'):
if i.lstrip()=='': continue
ll=(i.lstrip()).split()
d[ll[0].replace('bio','')]=ll[1]
return d
def makeCluster(allcoord):
cluster=[]
remaining=[]
c1=allcoord[0][0]
c2=allcoord[0][1]
for i in range(len(allcoord)):
if allcoord[i]!=(c1,c2):
if c1<=allcoord[i][0]<=c2:
cluster.append(allcoord[i])
if allcoord[i][1]>c2:
c2=allcoord[i][1]
else:
remaining.append(allcoord[i])
else:
cluster.append((c1,c2))
return (c1,c2),remaining
def Clusters(interval):
coords=[]
interval.sort()
while len(interval)!=0:
coord,interval=makeCluster(interval)
coords.append(coord)
return coords
d={}
dg={}
dex={}
f=open(infile)
for i in f:
if i.startswith('#'): continue
l=(i.strip()).split('\t')
print l
if l[2] not in ['exon','CDS']: continue
last=getL(l[-1])
if (last['gene_id'].count('.') == 1 and last['gene_id'].split('.')[-1].isdigit()):
gene=last['gene_id'].split('.')[0]
else:
gene=last['gene_id']
if (last['transcript_id'].count('.') == 1 and last['transcript_id'].split('.')[-1].isdigit()):
tr=last['transcript_id'].split('.')[0]
else:
tr=last['transcript_id']
try: gname=last['gene_name']
except: gname=gene
try: gtype=last['gene_type']
except: gtype='unknown'
try: ttype=last['transcript_type']
except: ttype='unknown'
dg[gene]=(gname,gtype)
if d.has_key(gene):
if d[gene].has_key(tr):
d[gene][tr].append((int(l[3]),int(l[4]),l[2]))
else:
d[gene][tr]=[(int(l[3]),int(l[4]),l[2])]
d[gene]['info'][2][tr]=ttype
else:
d[gene]={}
d[gene]['info']=[l[0],l[6],{tr:ttype}]
d[gene][tr]=[(int(l[3]),int(l[4]),l[2])]
if dex.has_key(gene):
if l[2]=='exon': dex[gene].append((int(l[3]),int(l[4])))
else:
if l[2]=='exon': dex[gene]=[(int(l[3]),int(l[4]))]
f.close()
lg=[]
with open(tmpfile, 'w') as g:
header = ['geneid', 'symbol', 'gtype', 'trid', 'ttype', 'startg', 'endg', 'start', 'end', 'strand', 'chr', 'feat', 'org']
g.write('{}\n'.format('\t'.join(header)))
for i in d:
#print i,dg[i]
allex=dex[i]
allex.sort()
gcoord=(allex[0][0],allex[-1][1])
strand=d[i]['info'][1]
chr=d[i]['info'][0]
for j in d[i].keys():
if j=='info': continue
trt=d[i]['info'][2][j]
cds=[x for x in d[i][j] if x[2]=='CDS']
cds.sort()
if len(cds)>0: cdsc=(cds[0][0],cds[-1][1])
else: cdsc=()
str_tr=[]
if len(cdsc)>0:
# gene ha cds
up,md,dw=[],[],[]
stex=[]
for k in d[i][j]:
if k[2]!='exon': continue
if cdsc[0] > k[1] and cdsc[1] > k[1]: up.append(k)
if cdsc[1] < k[0] and cdsc[1] < k[1]: dw.append(k)
if cdsc[0]< k[0]< cdsc[1] and cdsc[0]< k[1]< cdsc[1]: md.append(k)
if k[0]<=cdsc[0]<=k[1]: stex.append(k)
if k[0]<=cdsc[1]<=k[1]: stex.append(k)
stex.sort()
if stex[0][0] == cdsc[0]:
md.append(stex[0])
elif stex[0][0] < cdsc[0] < stex[0][1]:
up.append((stex[0][0],cdsc[0]-1,''))
md.append((cdsc[0],stex[0][1],''))
elif stex[0][1] == cdsc[0]: up.append(stex[0])
if len(stex) > 1:
if stex[1][0] == cdsc[1]:
dw.append(stex[1])
elif stex[1][0] < cdsc[1] < stex[1][1]:
md.append((stex[1][0],cdsc[1],''))
dw.append((cdsc[1]+1,stex[1][1],''))
elif stex[1][1] == cdsc[1]:
md.append(stex[1])
if strand=='+':
for k in up: str_tr.append((k[0],k[1],'5UTR',strand,'red'))
for k in md: str_tr.append((k[0],k[1],'CDS',strand,'orange'))
for k in dw: str_tr.append((k[0],k[1],'3UTR',strand,'blue'))
elif strand=='-':
for k in dw: str_tr.append((k[0],k[1],'5UTR',strand,'red'))
for k in md: str_tr.append((k[0],k[1],'CDS',strand,'orange'))
for k in up: str_tr.append((k[0],k[1],'3UTR',strand,'blue'))
str_tr.sort()
for k in range(len(str_tr)-1):
c1=str_tr[k][1]+1
c2=str_tr[k+1][0]-1
if (c2-c1)+1 > 0:
str_tr.append((c1,c2,'Intron',strand,'black'))
str_tr.sort()
#print str_tr
for k in str_tr:
line=[i,dg[i][0],dg[i][1],j,trt,str(gcoord[0]),str(gcoord[1]),str(k[0]),str(k[1]),k[3],chr,k[2],org]
#line="{x: %i,x2: %i, y: 0, pointWidth: 20,color: '%s',name:'Gene: %s - %s<br>Transcript: %s - %s<br>Strand: %s<br>Feature: %s<br>%s'}" %(k[0],k[1],k[4],dg[i][0],dg[i][1],j,trt,k[3],k[2],chr)
#print dg[i][0]+'\t'+j+'\t'+line
#print '\t'.join(line)
g.write('{}\n'.format('\t'.join(line)))
else:
color='green'
feat='EXON'
exon=[x for x in d[i][j] if x[2]=='exon']
exon.sort()
intron=[(exon[x][1]+1,exon[x+1][0]-1) for x in range(len(exon)-1)]
for k in exon:
line=[i,dg[i][0],dg[i][1],j,trt,str(gcoord[0]),str(gcoord[1]),str(k[0]),str(k[1]),strand,chr,feat,org]
#print '\t'.join(line)
g.write('{}\n'.format('\t'.join(line)))
for k in intron:
line=[i,dg[i][0],dg[i][1],j,trt,str(gcoord[0]),str(gcoord[1]),str(k[0]),str(k[1]),strand,chr,'Intron',org]
#line="{x: %i,x2: %i, y: 0, pointWidth: 20,color: '%s',name:'Gene: %s - %s<br>Transcript: %s - %s<br>Strand: %s<br>Feature: %s<br>%s'}" %(k[0],k[1],color,dg[i][0],dg[i][1],j,trt,strand,feat,chr)
#print dg[i][0]+'\t'+j+'\t'+line
#print '\t'.join(line)
g.write('{}\n'.format('\t'.join(line)))
cmd = '''awk '!visited[$0]++' {} > {}'''.format(tmpfile, outfile)
print 'Removing duplicates...'
os.system(cmd)
print 'Removing temporary files'
cmd1 = '''rm -rf {}'''.format(tmpfile)
os.system(cmd1)
print 'Gzipping annotations file'
cmd2 = '''gzip {}'''.format(outfile)
os.system(cmd2)