Mercurial > repos > bgruening > column_arrange_by_header

annotate column_arrange.py @ 1:b97f0d9a31ff draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
author bgruening
date Fri, 16 Oct 2015 14:19:29 -0400
parents b84c81b7d762
children a69463bf1801
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
2 import pandas as pd
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
3 import argparse
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
4
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
5 parser = argparse.ArgumentParser()
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
6 parser.add_argument('-i', '--input', help='Tabular Input File Name')
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
7 parser.add_argument('-o','--output', help='Tabular Output File')
1
b97f0d9a31ff planemo upload commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
bgruening
parents: 0
diff changeset
8 parser.add_argument('-c', '--columns', nargs='+', help='Column Headers to Sort By')
0
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
9 args=parser.parse_args()
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
10
1
b97f0d9a31ff planemo upload commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
bgruening
parents: 0
diff changeset
11 cols = args.columns
b97f0d9a31ff planemo upload commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
bgruening
parents: 0
diff changeset
12 table = pd.read_csv(args.input, sep='\t')
0
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
13 blist = list(table.columns)
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
14 for token in cols:
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
15 blist.remove(token)
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
16 sorted_table = table[args.columns + blist]
b84c81b7d762 Uploaded
bgruening
parents:
diff changeset
17 # write without index, seperated by tabs
1
b97f0d9a31ff planemo upload commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
bgruening
parents: 0
diff changeset
18 sorted_table.to_csv(args.output, sep='\t', index=False)