Mercurial > repos > immport-devteam > rearrange_columns

annotate editColumnHeadings.py @ 1:ce206587d42f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
author azomics
date Thu, 16 Jul 2020 07:22:06 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
1 #!/usr/bin/env python
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
2
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
3 ######################################################################
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
4 # Copyright (c) 2016 Northrop Grumman.
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
5 # All rights reserved.
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
6 ######################################################################
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
7 #
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
8 # Cristel Thomas - May 2018
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
9 # Version 2 -- with Pandas!
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
10 #
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
11
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
12 import sys
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
13
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
14 from argparse import ArgumentParser
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
15 import pandas as pd
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
16
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
17
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
18 def is_integer(s):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
19 try:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
20 int(s)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
21 return True
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
22 except ValueError:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
23 return False
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
24
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
25
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
26 def rearrange_file(input_file, output_file, new_cols, new_order, flag_text):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
27 df = pd.read_table(input_file)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
28 original_columns = [x for x in df.columns]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
29 if new_cols:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
30 edited_cols = []
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
31 if len(new_cols) > len(df.columns):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
32 sys.exit(6)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
33 for i in range(0, len(df.columns)):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
34 if df.columns[i] in new_cols:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
35 edited_cols.append(new_cols[df.columns[i]])
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
36 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
37 edited_cols.append(df.columns[i])
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
38 df.columns = edited_cols
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
39
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
40 if new_order:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
41 if len(new_order) > len(df.columns):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
42 sys.exit(6)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
43 subset = []
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
44 if flag_text:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
45 existing_cols = list(df.columns)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
46 unknown_elements = list(set(new_order) - set(existing_cols))
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
47 if len(unknown_elements):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
48 print("%s of the provided columns for reorder is/are not in the input file." % len(unknown_elements), file=sys.stderr)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
49 print("Existing columns:", file=sys.stderr)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
50 for col in existing_cols:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
51 print(col, file=sys.stderr)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
52 print("Provided columns for new order which are not in the original list:", file=sys.stderr)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
53 for col in unknown_elements:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
54 print(col, file=sys.stderr)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
55 sys.exit(9)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
56 subset = new_order
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
57 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
58 subset = [df.columns[x] for x in new_order]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
59 df = df[subset]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
60
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
61 df.to_csv(output_file, sep="\t", index=False)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
62 if new_cols:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
63 for c in new_cols:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
64 if c not in original_columns:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
65 sys.exit(10)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
66
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
67 if __name__ == "__main__":
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
68 parser = ArgumentParser(
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
69 prog="editColumnHeadings",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
70 description="Cut, rearrange and rename columns in a tab-separated file.")
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
71
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
72 parser.add_argument(
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
73 '-i',
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
74 dest="input_file",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
75 required=True,
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
76 help="File location for the text file.")
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
77
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
78 parser.add_argument(
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
79 '-r',
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
80 dest="columns",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
81 action="append",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
82 help="Columns to replace.")
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
83
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
84 parser.add_argument(
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
85 '-w',
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
86 dest="replace_with",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
87 action="append",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
88 help="new column headers.")
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
89
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
90 parser.add_argument(
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
91 '-n',
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
92 dest="new_order",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
93 help="New column order if re-ordering or subsetting.")
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
94
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
95 parser.add_argument(
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
96 '-o',
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
97 dest="output_file",
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
98 required=True,
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
99 help="Name of the output file.")
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
100
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
101 args = parser.parse_args()
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
102
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
103
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
104 new_order = []
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
105 new_cols = {}
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
106 # flag = False
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
107 # exit_codes = [3,4,7,8,9,10,2]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
108 defaults = ["i.e.:TLR 6, TLR6PE", "i.e.:TLR6", "i.e.:1,2,5 or CD3,CD4,CCR3", "default", "Default", ""]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
109 flag_text = False
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
110
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
111 if args.new_order:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
112 if args.new_order not in defaults:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
113 nwor = [x.strip() for x in args.new_order.strip().split(",")]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
114 check_integer = [is_integer(x) for x in nwor]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
115 if sum(check_integer) != len(check_integer):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
116 flag_text = True
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
117 new_order = [str(x) if flag_text else int(x)-1 for x in nwor]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
118 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
119 sys.exit(8)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
120
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
121 if args.columns:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
122 if args.replace_with:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
123 cols_to_change = [c.strip().split(",") if c not in defaults else None for c in args.columns]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
124 replacements = [r.strip() if r not in defaults else None for r in args.replace_with]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
125 check_col = sum([True if x is not None else False for x in cols_to_change])
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
126 check_rep = sum([True if x is not None else False for x in replacements])
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
127 if check_col != check_rep:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
128 sys.exit(7)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
129 for i in range(0, check_col):
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
130 if cols_to_change[i]:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
131 if replacements[i]:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
132 for c in cols_to_change[i]:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
133 new_cols[c.strip()] = replacements[i]
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
134 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
135 sys.exit(4)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
136 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
137 sys.exit(3)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
138 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
139 sys.exit(7)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
140 else:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
141 if args.replace_with:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
142 sys.exit(7)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
143
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
144 if not new_order and not new_cols:
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
145 sys.exit(2)
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
146
ce206587d42f "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/rearrange_columns commit 3289c1f97444f45f946ff92d47c490c9d58f3d94"
azomics
parents:
diff changeset
147 rearrange_file(args.input_file, args.output_file, new_cols, new_order, flag_text)