Mercurial > repos > iracooke > tpp_prophets
comparison protein_prophet_wrapper.sh @ 9:c04896f31ff7
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 |
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| 8:d19a95abf2e4 | 9:c04896f31ff7 |
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| 1 #!/usr/bin/env bash | |
| 2 # | |
| 3 | |
| 4 actual_output_path_string=$1;shift | |
| 5 original_input_file=$1;shift | |
| 6 | |
| 7 # Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input | |
| 8 # name because peptide prophet can't handle anything else | |
| 9 | |
| 10 wd=`pwd` | |
| 11 | |
| 12 actual_input_path_string=$wd/`basename $original_input_file`.pep.xml | |
| 13 | |
| 14 ln -s $original_input_file $actual_input_path_string | |
| 15 | |
| 16 rvm 1.9.3@protk-1.2.2 do protein_prophet.rb $actual_input_path_string $@ -o protein_prophet_results.prot.xml | |
| 17 | |
| 18 if [ -f protein_prophet_results.prot.xml ]; then | |
| 19 sed -i.bak s%$actual_input_path_string%$original_input_file.pep.xml%g protein_prophet_results.prot.xml | |
| 20 fi | |
| 21 |