20
|
1 #!/usr/binsenv python
|
|
2
|
|
3 from __future__ import print_function
|
|
4
|
|
5 import re
|
|
6 import sys
|
|
7
|
|
8
|
|
9 class LineFilter(object):
|
|
10 def __init__(self, source, filter_dict):
|
|
11 self.source = source
|
|
12 self.filter_dict = filter_dict
|
|
13 self.func = lambda i, l: l.rstrip('\r\n') if l else None
|
|
14 self.src_lines = []
|
|
15 self.src_line_cnt = 0
|
|
16 if not filter_dict:
|
|
17 return
|
|
18 if filter_dict['filter'] == 'regex':
|
|
19 rgx = re.compile(filter_dict['pattern'])
|
|
20 if filter_dict['action'] == 'exclude_match':
|
|
21 self.func = lambda i, l: l if not rgx.match(l) else None
|
|
22 elif filter_dict['action'] == 'include_match':
|
|
23 self.func = lambda i, l: l if rgx.match(l) else None
|
|
24 elif filter_dict['action'] == 'exclude_find':
|
|
25 self.func = lambda i, l: l if not rgx.search(l) else None
|
|
26 elif filter_dict['action'] == 'include_find':
|
|
27 self.func = lambda i, l: l if rgx.search(l) else None
|
|
28 elif filter_dict['filter'] == 'select_columns':
|
|
29 cols = [int(c) - 1 for c in filter_dict['columns']]
|
|
30 self.func = lambda i, l: self.select_columns(l, cols)
|
|
31 elif filter_dict['filter'] == 'replace':
|
|
32 p = filter_dict['pattern']
|
|
33 r = filter_dict['replace']
|
|
34 c = int(filter_dict['column']) - 1
|
|
35 self.func = lambda i, l: '\t'.join(
|
|
36 [x if j != c else re.sub(p, r, x) for j, x in enumerate(l.split('\t'))])
|
|
37 elif filter_dict['filter'] == 'prepend_line_num':
|
|
38 self.func = lambda i, l: '%d\t%s' % (i, l)
|
|
39 elif filter_dict['filter'] == 'append_line_num':
|
|
40 self.func = lambda i, l: '%s\t%d' % (l.rstrip('\r\n'), i)
|
|
41 elif filter_dict['filter'] == 'prepend_text':
|
|
42 s = filter_dict['column_text']
|
|
43 self.func = lambda i, l: '%s\t%s' % (s, l)
|
|
44 elif filter_dict['filter'] == 'append_text':
|
|
45 s = filter_dict['column_text']
|
|
46 self.func = lambda i, l: '%s\t%s' % (l.rstrip('\r\n'), s)
|
|
47 elif filter_dict['filter'] == 'skip':
|
|
48 cnt = filter_dict['count']
|
|
49 self.func = lambda i, l: l if i > cnt else None
|
|
50 elif filter_dict['filter'] == 'normalize':
|
|
51 cols = [int(c) - 1 for c in filter_dict['columns']]
|
|
52 sep = filter_dict['separator']
|
|
53 self.func = lambda i, l: self.normalize(l, cols, sep)
|
|
54
|
|
55 def __iter__(self):
|
|
56 return self
|
|
57
|
|
58 def __next__(self):
|
|
59 if not self.src_lines:
|
|
60 self.get_lines()
|
|
61 if self.src_lines:
|
|
62 return self.src_lines.pop(0)
|
|
63 raise StopIteration
|
|
64
|
22
|
65 next = __next__
|
|
66
|
20
|
67 def select_columns(self, line, cols):
|
|
68 fields = line.split('\t')
|
|
69 return '\t'.join([fields[x] for x in cols])
|
|
70
|
|
71 def normalize(self, line, split_cols, sep):
|
|
72 lines = []
|
|
73 fields = line.rstrip('\r\n').split('\t')
|
|
74 split_fields = dict()
|
|
75 cnt = 0
|
|
76 for c in split_cols:
|
|
77 if c < len(fields):
|
|
78 split_fields[c] = fields[c].split(sep)
|
|
79 cnt = max(cnt, len(split_fields[c]))
|
|
80 if cnt == 0:
|
|
81 lines.append('\t'.join(fields))
|
|
82 else:
|
|
83 for n in range(0, cnt):
|
|
84 flds = [x if c not in split_cols else split_fields[c][n]
|
|
85 if n < len(split_fields[c])
|
|
86 else '' for (c, x) in enumerate(fields)]
|
|
87 lines.append('\t'.join(flds))
|
|
88 return lines
|
|
89
|
|
90 def get_lines(self):
|
|
91 for i, next_line in enumerate(self.source):
|
|
92 self.src_line_cnt += 1
|
|
93 line = self.func(self.src_line_cnt, next_line)
|
|
94 if line:
|
|
95 if isinstance(line, list):
|
|
96 self.src_lines.extend(line)
|
|
97 else:
|
|
98 self.src_lines.append(line)
|
|
99 return
|
|
100
|
|
101
|
|
102 class TabularReader:
|
|
103 """
|
|
104 Tabular file iterator. Returns a list
|
|
105 """
|
|
106 def __init__(self, input_file, skip=0, comment_char=None, col_idx=None,
|
|
107 filters=None):
|
|
108 self.skip = skip
|
|
109 self.comment_char = comment_char
|
|
110 self.col_idx = col_idx
|
|
111 self.filters = filters
|
|
112 self.tsv_file = \
|
22
|
113 input_file if hasattr(input_file, 'readline') else open(input_file)
|
20
|
114 if skip and skip > 0:
|
|
115 for i in range(skip):
|
|
116 if not self.tsv_file.readline():
|
|
117 break
|
|
118 source = LineFilter(self.tsv_file, None)
|
|
119 if comment_char:
|
|
120 source = LineFilter(source,
|
|
121 {"filter": "regex", "pattern": comment_char,
|
|
122 "action": "exclude_match"})
|
|
123 if filters:
|
|
124 for f in filters:
|
|
125 source = LineFilter(source, f)
|
|
126 self.source = source
|
|
127
|
|
128 def __iter__(self):
|
|
129 return self
|
|
130
|
|
131 def __next__(self):
|
|
132 ''' Iteration '''
|
|
133 for i, line in enumerate(self.source):
|
|
134 fields = line.rstrip('\r\n').split('\t')
|
|
135 if self.col_idx:
|
|
136 fields = [fields[i] for i in self.col_idx]
|
|
137 return fields
|
|
138 raise StopIteration
|
|
139
|
22
|
140 next = __next__
|
|
141
|
20
|
142
|
|
143 def filter_file(input_file, output, skip=0, comment_char='#', filters=None):
|
|
144 data_lines = 0
|
|
145 try:
|
|
146 tr = TabularReader(input_file, skip=skip, comment_char=comment_char,
|
|
147 filters=filters)
|
|
148 for linenum, fields in enumerate(tr):
|
|
149 data_lines += 1
|
|
150 try:
|
|
151 output.write('%s\n' % '\t'.join(fields))
|
|
152 except Exception as e:
|
|
153 print('Failed at line: %d err: %s' % (linenum, e),
|
|
154 file=sys.stderr)
|
|
155 except Exception as e:
|
22
|
156 exit('Error: %s' % (e))
|