Mercurial > repos > iracooke > tpp_prophets

annotate protein_prophet_wrapper.sh @ 9:c04896f31ff7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added bash wrapper scripts and protxml to table
author Ira Cooke <iracooke@gmail.com>
date Mon, 10 Jun 2013 04:58:03 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
1 #!/usr/bin/env bash
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
2 #
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
3
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
4 actual_output_path_string=$1;shift
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
5 original_input_file=$1;shift
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
6
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
7 # Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
8 # name because peptide prophet can't handle anything else
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
9
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
10 wd=`pwd`
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
11
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
12 actual_input_path_string=$wd/`basename $original_input_file`.pep.xml
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
13
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
14 ln -s $original_input_file $actual_input_path_string
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
15
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
16 rvm 1.9.3@protk-1.2.2 do protein_prophet.rb $actual_input_path_string $@ -o protein_prophet_results.prot.xml
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
17
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
18 if [ -f protein_prophet_results.prot.xml ]; then
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
19 sed -i.bak s%$actual_input_path_string%$original_input_file.pep.xml%g protein_prophet_results.prot.xml
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
20 fi
c04896f31ff7 Added bash wrapper scripts and protxml to table
Ira Cooke <iracooke@gmail.com>
parents:
diff changeset
21