-
Notifications
You must be signed in to change notification settings - Fork 0
/
reformat-headers.py
250 lines (195 loc) · 5.16 KB
/
reformat-headers.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
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
#!/usr/bin/env python3
from collections import defaultdict
import re
import os
import textwrap
import argparse
import sys
def SUM(ls):
count = 0
for i in ls:
count += float(i)
return count
def deExt(string):
ls = string.split(".")
ls2 = ls[0:len(ls) - 1]
outstring = "".join(ls2)
return outstring
def unique(ls, ls2):
unqlist = []
for i in ls:
if i not in unqlist and i in ls2:
unqlist.append(i)
return len(unqlist)
def derep(ls):
outLS = []
for i in ls:
if i not in outLS:
outLS.append(i)
return outLS
def cluster(data, maxgap):
'''Arrange data into groups where successive elements
differ by no more than *maxgap*
#->>> cluster([1, 6, 9, 100, 102, 105, 109, 134, 139], maxgap=10)
[[1, 6, 9], [100, 102, 105, 109], [134, 139]]
#->>> cluster([1, 6, 9, 99, 100, 102, 105, 134, 139, 141], maxgap=10)
[[1, 6, 9], [99, 100, 102, 105], [134, 139, 141]]
'''
# data = sorted(data)
data.sort(key=int)
groups = [[data[0]]]
for x in data[1:]:
if abs(x - groups[-1][-1]) <= maxgap:
groups[-1].append(x)
else:
groups.append([x])
return groups
def lastItem(ls):
x = ''
for i in ls:
x = i
return x
def RemoveDuplicates(ls):
empLS = []
for i in ls:
if i not in empLS:
empLS.append(i)
else:
pass
return empLS
def allButTheLast(iterable, delim):
x = ''
length = len(iterable.split(delim))
for i in range(0, length - 1):
x += iterable.split(delim)[i]
x += delim
return x[0:len(x) - 1]
def secondToLastItem(ls):
x = ''
for i in ls[0:len(ls) - 1]:
x = i
return x
def pull(item, one, two):
ls = []
counter = 0
for i in item:
if counter == 0:
if i != one:
pass
else:
counter += 1
ls.append(i)
else:
if i != two:
ls.append(i)
else:
ls.append(i)
counter = 0
outstr = "".join(ls)
return outstr
def stabilityCounter(int):
if len(str(int)) == 1:
string = (str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 2:
string = (str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 3:
string = (str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 4:
string = (str(0) + str(int))
return (string)
def replace(stringOrlist, list, item):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
emptyList.append(item)
outString = "".join(emptyList)
return outString
def remove(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
outString = "".join(emptyList)
return outString
def remove2(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
# outString = "".join(emptyList)
return emptyList
def removeLS(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
return emptyList
def fasta(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[header] = seq
header = i[1:]
header = header.split(" # ")[0]
seq = ''
else:
header = i[1:]
header = header.split(" # ")[0]
seq = ''
else:
seq += i
Dict[header] = seq
return Dict
def filter(list, items):
outLS = []
for i in list:
if i not in items:
outLS.append(i)
return outLS
def delim(line):
ls = []
string = ''
for i in line:
if i != " ":
string += i
else:
ls.append(string)
string = ''
ls = filter(ls, [""])
return ls
parser = argparse.ArgumentParser(
prog="LithoGenie.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
*******************************************************
Developed by Arkadiy Garber and Gustavo Ramírez;
University of Southern California, Earth Sciences
Please send comments and inquiries to arkadiyg@usc.edu
*******************************************************
'''))
parser.add_argument('-i', type=str, help="input fasta")
parser.add_argument('-o', type=str, help="output fasta")
args = parser.parse_args()
out = open(args.o, "w")
file = open(args.i)
for i in file:
if not re.match(r'>', i):
out.write(i.rstrip() + "\n")
else:
out.write(remove(i.rstrip(), ["|", "/", " ", ",", "&", "$", "!"]) + "\n")
out.close()