annotate filters.py @ 15:90f657745fea draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
author iuc
date Thu, 27 Jun 2024 17:23:47 +0000
parents 4d5aae46f850
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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1 #!/usr/binsenv python
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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3 from __future__ import print_function
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4
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5 import re
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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6 import sys
13
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7 from itertools import chain
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8
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10 class LineFilter(object):
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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11 def __init__(self, source, filter_dict):
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12 self.source = source
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13 self.filter_dict = filter_dict
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14 self.func = lambda i, line: line.rstrip('\r\n') if line else None
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15 self.src_lines = []
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16 self.src_line_cnt = 0
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17
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18 def xint(x):
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19 if isinstance(x, int):
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20 return x
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21 try:
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22 return int(x)
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23 except Exception:
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24 return x if x else None
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25
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26 if not filter_dict:
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27 return
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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28 if filter_dict['filter'] == 'regex':
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29 rgx = re.compile(filter_dict['pattern'])
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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30 if filter_dict['action'] == 'exclude_match':
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31 self.func = lambda i, line: line if not rgx.match(line) else None
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32 elif filter_dict['action'] == 'include_match':
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33 self.func = lambda i, line: line if rgx.match(line) else None
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34 elif filter_dict['action'] == 'exclude_find':
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35 self.func = lambda i, line: line if not rgx.search(line) else None
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36 elif filter_dict['action'] == 'include_find':
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37 self.func = lambda i, line: line if rgx.search(line) else None
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38 elif filter_dict['filter'] == 'select_columns':
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39 cols = [int(c) - 1 for c in filter_dict['columns']]
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40 self.func = lambda i, line: self.select_columns(line, cols)
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41 elif filter_dict['filter'] == 'select_column_slices':
4d5aae46f850 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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42 cols = [x if isinstance(x, int) else [y if y is not None else None for y in [xint(k) for k in x.split(':')]] for x in [xint(c) for c in filter_dict['columns']]]
4d5aae46f850 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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43 if all([isinstance(x, int) for x in cols]):
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44 self.func = lambda i, line: self.select_columns(line, cols)
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45 else:
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46 cols = [slice(x[0], x[1], x[2] if len(x) > 2 else None) if isinstance(x, list) else x for x in cols]
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47 self.func = lambda i, line: self.select_slices(line, cols)
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48 elif filter_dict['filter'] == 'replace':
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49 p = filter_dict['pattern']
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50 r = filter_dict['replace']
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51 c = int(filter_dict['column']) - 1
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52 if 'add' not in filter_dict\
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53 or filter_dict['add'] not in ['prepend',
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54 'append',
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55 'before',
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56 'after']:
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57 self.func = lambda i, line: '\t'.join(
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58 [x if j != c else re.sub(p, r, x)
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59 for j, x in enumerate(line.split('\t'))])
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60 else:
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61 a = 0 if filter_dict['add'] == 'prepend'\
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62 else min(0, c - 1) if filter_dict['add'] == 'before'\
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63 else c + 1 if filter_dict['add'] == 'after'\
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64 else None
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65 self.func = lambda i, line: self.replace_add(line, p, r, c, a)
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66 elif filter_dict['filter'] == 'prepend_line_num':
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67 self.func = lambda i, line: '%d\t%s' % (i, line)
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68 elif filter_dict['filter'] == 'append_line_num':
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69 self.func = lambda i, line: '%s\t%d' % (line.rstrip('\r\n'), i)
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70 elif filter_dict['filter'] == 'prepend_text':
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71 s = filter_dict['column_text']
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72 self.func = lambda i, line: '%s\t%s' % (s, line)
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73 elif filter_dict['filter'] == 'append_text':
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74 s = filter_dict['column_text']
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75 self.func = lambda i, line: '%s\t%s' % (line.rstrip('\r\n'), s)
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76 elif filter_dict['filter'] == 'skip':
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77 cnt = filter_dict['count']
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78 self.func = lambda i, line: line if i > cnt else None
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79 elif filter_dict['filter'] == 'normalize':
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80 cols = [int(c) - 1 for c in filter_dict['columns']]
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81 sep = filter_dict['separator']
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82 self.func = lambda i, line: self.normalize(line, cols, sep)
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83
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84 def __iter__(self):
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85 return self
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parents:
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86
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
diff changeset
87 def __next__(self):
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iuc
parents:
diff changeset
88 if not self.src_lines:
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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89 self.get_lines()
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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90 if self.src_lines:
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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91 return self.src_lines.pop(0)
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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92 raise StopIteration
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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93
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iuc
parents:
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94 next = __next__
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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95
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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96 def select_columns(self, line, cols):
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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97 fields = line.split('\t')
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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98 return '\t'.join([fields[x] for x in cols])
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99
13
4d5aae46f850 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
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100 def select_slices(self, line, cols):
4d5aae46f850 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
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101 fields = line.split('\t')
4d5aae46f850 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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102 return '\t'.join(chain.from_iterable([y if isinstance(y, list) else [y] for y in [fields[x] for x in cols]]))
4d5aae46f850 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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103
9
69b08fc9557c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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104 def replace_add(self, line, pat, rep, col, pos):
69b08fc9557c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
iuc
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diff changeset
105 fields = line.rstrip('\r\n').split('\t')
11
6544e4b87a4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit d624cde6382bc326a5ae318482e16e643ef7d7d1"
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106 i = pos if pos is not None else len(fields)
9
69b08fc9557c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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107 val = ''
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iuc
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108 if col < len(fields) and re.search(pat, fields[col]):
69b08fc9557c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
iuc
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109 val = re.sub(pat, rep, fields[col]).replace('\t', ' ')
69b08fc9557c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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110 return '\t'.join(fields[:i] + [val] + fields[i:])
69b08fc9557c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
iuc
parents: 1
diff changeset
111
0
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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112 def normalize(self, line, split_cols, sep):
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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113 lines = []
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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114 fields = line.rstrip('\r\n').split('\t')
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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115 split_fields = dict()
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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116 cnt = 0
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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117 for c in split_cols:
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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118 if c < len(fields):
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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119 split_fields[c] = fields[c].split(sep)
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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120 cnt = max(cnt, len(split_fields[c]))
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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121 if cnt == 0:
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iuc
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122 lines.append('\t'.join(fields))
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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123 else:
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124 for n in range(0, cnt):
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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125 flds = [x if c not in split_cols else split_fields[c][n]
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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126 if n < len(split_fields[c])
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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127 else '' for (c, x) in enumerate(fields)]
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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128 lines.append('\t'.join(flds))
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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129 return lines
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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130
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131 def get_lines(self):
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132 for i, next_line in enumerate(self.source):
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133 self.src_line_cnt += 1
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iuc
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134 line = self.func(self.src_line_cnt, next_line)
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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135 if line:
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136 if isinstance(line, list):
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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137 self.src_lines.extend(line)
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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138 else:
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139 self.src_lines.append(line)
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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140 return
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141
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142
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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143 class TabularReader:
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144 """
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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145 Tabular file iterator. Returns a list
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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146 """
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147 def __init__(self, input_file, skip=0, comment_char=None, col_idx=None,
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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148 filters=None):
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149 self.skip = skip
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150 self.comment_char = comment_char
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151 self.col_idx = col_idx
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152 self.filters = filters
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153 self.tsv_file = \
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154 input_file if hasattr(input_file, 'readline') else open(input_file)
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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155 if skip and skip > 0:
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156 for i in range(skip):
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157 if not self.tsv_file.readline():
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parents:
diff changeset
158 break
6fbd9d25ceef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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159 source = LineFilter(self.tsv_file, None)
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160 if comment_char:
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161 source = LineFilter(source,
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162 {"filter": "regex", "pattern": comment_char,
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diff changeset
163 "action": "exclude_match"})
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164 if filters:
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165 for f in filters:
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iuc
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diff changeset
166 source = LineFilter(source, f)
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iuc
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167 self.source = source
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diff changeset
168
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diff changeset
169 def __iter__(self):
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170 return self
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171
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diff changeset
172 def __next__(self):
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diff changeset
173 ''' Iteration '''
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174 for i, line in enumerate(self.source):
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175 fields = line.rstrip('\r\n').split('\t')
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176 if self.col_idx:
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177 fields = [fields[i] for i in self.col_idx]
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178 return fields
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179 raise StopIteration
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180
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181 next = __next__
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182
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183
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184 def filter_file(input_file, output, skip=0, comment_char='#', filters=None):
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185 data_lines = 0
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186 try:
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187 tr = TabularReader(input_file, skip=skip, comment_char=comment_char,
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188 filters=filters)
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189 for linenum, fields in enumerate(tr):
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190 data_lines += 1
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191 try:
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192 output.write('%s\n' % '\t'.join(fields))
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193 except Exception as e:
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194 print('Failed at line: %d err: %s' % (linenum, e),
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195 file=sys.stderr)
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196 except Exception as e:
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197 exit('Error: %s' % (e))