bictools - Python

bictools overview

For this tutorial you need a working installation of python with all packages listed at the previous page. If you are on Windows "Anaconda" is a very easy way to get a working python installation. On Linux and Windows packages can usually be installed via pip or setup tools.

Installing bictools

To install bictools (not yet part of PyPi, sorry!) you have to download the dist package from the bictools project homepage. Installation is as easy as:

pip install bictools-0.1dev.tar.gz

What can you do with bictools

There are two parts of bictools: First, a very small API to access and deal with BICEPS identifications. Second, a few command line scripts that get installed automatically. We will only focus on the scripts and how to use them. Each script has a short command line interface with short help messages and examples. The scripts that are available are:

1) bictools-bic_CSV

A small script that converts BICEPS result files into proper table-like result files. This is handy if you want to process the data in Excel / R / python.

Usage:
bictools-bic_CSV --infile input.txt --outfile output.csv

2) bictools-bic_DB ######

Command line tool to create customized databases from biceps results. The input requires the biceps search results, the target databases and a desired output directory. The biceps search results can either be a directory or a single file.

Main script with many important parameters (e.g. FDR, mass filter, maximum number of mutations). It is also possible to use the decoy free estimation of false positives via CurveFDP. This requires a working installation of R. Moreover, the "bic_cutoff.R" file needs to be downloaded from the project homepage and passed as an argument. However, FDR estimation within BICEPS is not necessary but has an influence on the results.

Usage:
bictools-bic_DB --in_bic Biceps.Results.HCT_all.txt
--in_db HS_reviewed_19092014.fasta
--out_dir /home/results

3) bictools-bic_evaluate

A script to evaluate and filter search identifications on a customized variant database. The input files are OpenMS result files (can be created via KNIME), processed biceps files (output from bictools-bic_DB), a fasta database as used in the initial biceps call.

Usage:
bictools-bic_evaluate --in_oms /home/bick/test/TextExporterOutput/ --in_bic /home/bick/test/
--in_db /home/bick/test/db.fasta

Script location

On linux the scripts are usually installed to the python path that is probably already in your path variable. On Windows you should find the scripts in the python/Lib/site-packages/bictools folder. Note, the package is not tested under Windows / OSX.