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README.md

README.md

VALIDATOR

Requirements

  • Python2.6+
  • cPickle
  • itertools
  • xlwt
  • pybindgen

Installation

git submodule update --init
cd code/fragment-singleton
python -c "from distutils.sysconfig import get_python_lib; print get_python_lib()"

Copy the output to the PYTHON_INCLUDE in Makefile

make
cp *.so ../.

Set environment variable LD_LIBRARY_PATH="."

USAGE - Piecemeal

All code is run from code/

Validator

  • Copy or move the folder containing your Mascot DAT files to the data folder
python validator.py <data folder name>
# eg. python validator.py "sample_data"

The program will take about five minutes to run for a 100mb DAT file.

The resulting files will be placed in "output_files/" in a folder named the same as your data folder. There are three data files produced:

  • information_file.txt contains some information about the variables used in the run
  • Val_1_pairs.csv contains the list of Validator 1 pairs
  • validator_3.xls contains the validator 3 data

CROSSREF

The inputs files to this script are:

  • Val_1_pairs.csv
  • A file exported from CPAS/Peptide prophet. Export with no filters and heavy area > 0 and light area > 0.
perl ValidatorCrossRef.pl <val_1_file> <CPAS file> <output_filename> Val1
# e.g. perl ValidatorCrossRef.pl ../output_files/sample_data/F004642_sec_12/Val_1_pairs.csv ../supporting_data/MS2Runs_E1sec12.txt ../output_files/sample_data/F004642_sec_12/E1sec12_crossref_pass.txt Val1

The resulting files will be placed in <output_filename> with the name you supplied above.

QUANT

The inputs files to this script are t-table and p-table files located in supporting_data. These have been supplied for you.

perl HanashQuantRevise.pl <name of cross ref file> all
# e.g. perl HanashQuantRevise.pl ../output_files/sample_data/F004642_sec_12/E1sec12_crossref_pass.txt all

The resulting files will be placed in your output folder - all.events and all.quant.

VALIDATOR PARSE

Requirements

Spreadsheet-ParseExcel at least version 0.59. This module has several pre-requisites of its own. These files are located in the folder code/perl_modules_required.

Usage
  • Create a file called ValidatorList in the supporting_files folder contains:
  • First Line: Path to excel output file from Validator. This path should be relative to the data folder.
  • Second line, list he name of the excel output file.
perl ValidatorParse.pl ../supporting_data/ValidatorList

Three files will be created:

  • AllMatch
  • HLRecover
  • MascotMatch

Usage - Toolchain

The software stack can also be run with all of the file parameters provided on the command line. To see the command line options run:

python validator_cli.py --help

By default validator_cli.py only Validator runs. If you include a CPAS/Peptide Prophet file as a parameter validator_cli.py will also run Crossref, Quant, and Validator Parse