Mercurial > repos > devteam > cummerbund

annotate cummeRbund_options.py @ 5:78fcfc04fcfe draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3
author devteam
date Thu, 23 Feb 2017 20:24:03 -0500
parents ac2ebc60ef5d
children c3b54a4b7741
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
ac2ebc60ef5d Uploaded corrected dynamic options
devteam
parents: 1
diff changeset
1 import sqlite3
0
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
3 def get_genes( database_path ):
2
ac2ebc60ef5d Uploaded corrected dynamic options
devteam
parents: 1
diff changeset
4 conn = sqlite3.connect( database_path )
ac2ebc60ef5d Uploaded corrected dynamic options
devteam
parents: 1
diff changeset
5 gene_ids = conn.execute( 'SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name' )
0
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
6 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ]
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
7
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
8 def get_samples( database_path ):
2
ac2ebc60ef5d Uploaded corrected dynamic options
devteam
parents: 1
diff changeset
9 conn = sqlite3.connect( database_path )
ac2ebc60ef5d Uploaded corrected dynamic options
devteam
parents: 1
diff changeset
10 samples = conn.execute( 'SELECT sample_name FROM samples ORDER BY sample_name' )
0
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
11 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ]