forked from boscoh/peptagram
-
Notifications
You must be signed in to change notification settings - Fork 0
/
do_reorder_peptagram.py
182 lines (141 loc) · 5.2 KB
/
do_reorder_peptagram.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
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
import os
import json
import webbrowser
import logging
import peptagram.proteins
from peptagram import parse
import Tkinter as tk
import tkFileDialog
import tkform
def load_data_jsonp(data_jsonp):
with open(data_jsonp) as f:
txt = f.read()
i_bracket = txt.find('(')
if i_bracket > 0:
txt = txt[i_bracket+1:]
i_bracket = txt.rfind(')')
if i_bracket > 0:
txt = txt[:i_bracket]
return json.loads(txt)
class ResortPeptagramForm(tkform.Form):
"""
Application window for Tkinter.
"""
def __init__(self, width=700, height=800, parent=None):
tkform.Form.__init__(self, parent, width, height)
self.title('Peptagram Rearranger')
self.push_text("Reorder Peptagram", 30)
self.push_line()
self.push_spacer()
self.push_text("REQUIRED INPUT DATA", 16)
self.push_text(u"Load existing peptagram directories; drag \u2630 to reorder; edit labels for peptagram")
self.push_peptagram_loader(
'in_peptagram', load_dir_text='+ peptagram directory')
self.push_spacer()
self.push_line()
self.push_spacer()
self.push_text("REORDERED-COMBINED PEPTAGRAM PARAMETERS", 16)
self.push_labeled_param(
'title', 'peptagram title', 'Reordered Peptagram')
self.push_labeled_param(
'out_dir', 'output directory', 'peptagram-reordered', load_dir_text='select')
self.push_spacer()
self.push_line()
self.push_spacer()
self.push_text("OPTIONAL FILTERS", 16)
self.push_labeled_param(
'exclude_seqids', 'Text file of excluded seqids',
load_file_text='select')
self.push_labeled_param(
'include_seqids', 'Text file of included seqids',
load_file_text='select')
self.push_text("Include matches:")
self.push_radio_param(
'match_filter',
['All peptides',
'Tryptic peptides',
'Semi-tryptic peptides',
'Modified peptides'])
self.push_spacer()
self.push_line()
self.push_spacer()
self.push_text("RESULTS", 16)
self.push_submit()
self.push_output()
def make_source_label(self, i_data, i_source):
return "Peptagram%d-Source%d" % (i_data+1, i_source+1)
def extract_indices_from_source_label(self, source_label):
s = source_label.replace('Peptagram', '').replace('Source', '')
a, b = map(int, s.split('-'))
return a-1, b-1
def push_peptagram_loader(self, param_id, load_dir_text):
self.file_list_loader = tkform.ReorderableList(self.interior)
self.datas = []
def load_peptagram():
pep_dir = tkFileDialog.askdirectory(title=load_dir_text)
try:
self.print_output('Loading peptagram in ' + pep_dir + '...')
data = load_data_jsonp(os.path.join(pep_dir, 'data.jsonp'))
except:
self.print_exception()
self.datas.append(data)
i_data = len(self.datas) - 1
for i_source, label in enumerate(data['source_labels']):
source_label = self.make_source_label(i_data, i_source)
self.file_list_loader.add_entry_label(source_label, label)
load_pep_button = tk.Button(self.interior, text=load_dir_text, command=load_peptagram)
self.push_row(load_pep_button)
self.push_row(self.file_list_loader)
self.mouse_widgets.append(self.file_list_loader)
self.param_entries[param_id] = self.file_list_loader
def run(self, params):
self.print_output("Building new peptagram...\n")
seqids = []
proteins = {}
for data in self.datas:
for seqid, protein in data['proteins'].iteritems():
if seqid not in proteins:
new_protein = peptagram.proteins.new_protein(seqid)
new_protein['sources'] = []
for key in ['sequence', 'description']:
new_protein[key] = protein[key]
new_protein['attr'] = protein['attr']
seqids.append(seqid)
proteins[seqid] = new_protein
new_sources = []
labels = []
for source_label, label in params['in_peptagram']:
i_data, i_source = self.extract_indices_from_source_label(source_label)
new_sources.append((i_data, i_source))
labels.append(label)
for seqid in seqids:
protein = proteins[seqid]
for i_data, i_source in new_sources:
old_data = self.datas[i_data]
if seqid in old_data['proteins']:
old_protein = old_data['proteins'][seqid]
old_source = old_protein['sources'][i_source]
protein['sources'].append(old_source)
else:
protein['sources'].append({'matches':[]})
peptagram.proteins.filter_proteins(proteins, params)
data = {
'title': params['title'],
'proteins': proteins,
'source_labels': labels,
'color_names': ['1.5', '1', '0.66'],
'mask_labels': [],
}
out_dir = os.path.abspath(params['out_dir'])
peptagram.proteins.make_graphical_comparison_visualisation(
data, out_dir)
self.print_output(
'Successfully built peptagram webpage (%s):\n' % \
parse.size_str(out_dir))
html = os.path.join(out_dir, 'index.html')
cmd_fn = lambda: webbrowser.open('file://' + html)
self.print_output(html, cmd_fn)
logging.basicConfig(level=logging.WARNING)
ResortPeptagramForm(800, -150).mainloop()