bjventers / repmatch_stats

Compute some basic statistics on the output of repmatch script

Replicate-match Statistics

Introduction

The scripts in this repository can be used to perform some basic statistics on the replicate-match files. The replicate-match files are the output file obtained by running rep-match python script on the peak-pair file.

The basic operations include counting a) peak-pairs in replicates and increasing window quantile scan of peak-pairs in replicates.

Requirements

• The script only requires Perl (5 or higher) to run.

THE SCRIPT WILL BREAK IF:

• The files have excel ^M character in it. For sanity check, open your file in terminal, to see if you can see ^M character in your file. In case, you find ^M character in your file, use the following command to remove it:

  $ perl -p -e 's/^M/\n/g;' <file_with_excel_char> > <new_file>
  

• If you change the name of the files "key.txt" and "orphan.txt", that are present in the folder produced by the repmatch script.

Installing and Running the scripts

Unpack the source code archive. The folder contains the following:

-  repmatch_stats.pl: Script for basic statistics.
-  README.rst: Readme file
-  Sample data: which includes (three peak-pair files: S_Reb1-rep2_s5e10F1_stdev.gff, S_Reb1-rep3_s5e10F1stdev.gff, S_Reb1-rep4_s5e10F1stdev.gff and a folder (repmatch_output_closest_d50r2u37l17) containing the output of repmatch script, that contains the primary files "key.txt" and "orphan.txt" used by the script.

If you get more information on option then type this:

$ perl  repmatch_stats.pl -h
$ Options: -k <path1>     path to the folder with key.txt and orphan.txt file.
$          -i <path2>     path to the folder with S_*.gff files.
$          -h             help

Do a test run of the script by typing:

$ perl repmatch_stats.pl -k  /usr/local/folder -i /folder1/peakpairs

The folder should now contain a "repmatch_stats.txt" file. This means that script runs fine on your system.

Output

All output files will be produced in the folder that contain "key.txt" and "orphan.txt" files. Following output files will be generated:

• "repmatch_stats.txt" containing the summary for each input file. The summary includes the following information:

  - Filename
  - number of Peak-pair
  - number of peak-pair in relicates.
  - top_1pt_peak-pairs_in_replicates.
  - top_5pt_peak-pairs_in_replicates.
  - top_10pt_peak-pairs_in_replicates.
  - top_25pt_peak-pairs_in_replicates.
  - top_50pt_peak-pairs_in_replicates.
  - top_75pt_peak-pairs_in_replicates.
  - top_100pt_peak-pairs_in_replicates.