Mercurial > repos > vipints > rdiff

annotate rDiff/examples/run_example.sh @ 2:233c30f91d66

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 07:15:44 -0400
parents 0f80a5141704
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
1 #/bin/bash
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
2 include ../bin/rdiff_config.sh
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
3
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
4 set -e
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
5
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
6 echo
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
7 echo ${PROG}: This program is part of the rDiff version $RDIFF_VERSION.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
8 echo
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
9 echo rDiff performs differential expression testing from RNA-Seq measurements.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
10 echo
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
11
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
12 if [ -z "$1" -o "$1" == '--help' ];
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
13 then
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
14 echo Usage: $0 poisson\|param\|nonparam
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
15 echo " or:" $0 --help
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
16 false
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
17 fi
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
18 if [ "$1" != 'poisson' -a "$1" != 'param' -a "$1" != 'nonparam' ];
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
19 then
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
20 echo invalid parameter: $1
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
21 false
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
22 fi
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
23
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
24
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
25
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
26 ../bin/rdiff -o results -d data/ -a example_condition_A_replicate_1.bam,example_condition_A_replicate_2.bam -b example_condition_B_replicate_1.bam,example_condition_B_replicate_2.bam -g data/genes_example.gff3 -m $1