NAME

       tradis_gene_insert_sites - bio-tradis: take in plot file(s) and an embl file and produce a
       tab delimited file

SYNOPSIS

       tradis_gene_insert_sites

DESCRIPTION

       Take in a plot file(s) and an embl file and produce a tab delimited file with insert  site
       details to use as input to an R script to t est for essentiality.

       -o|output_suffix
              <suffix to add to output files (optional, default = tradis_gene_insert_sites.csv)>

       -trim5 <trim insertion sites from 5' end of gene (optional, default = 0)>

       -trim3 <trim insertion sites from 3' end of gene (optional, default = 0)>

       -j|joined_output
              <output a single file with all info. default = one file per input file>

       -h|help
              display this message

EXAMPLES

              tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz

              tradis_gene_insert_sites my_annotation.embl my_insert_site_plot

       # multiple plot files
              tradis_gene_insert_sites my_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz

       #    specify    an    output    suffix    this    will    result    in    a   file   named
       my_insert_site_plot1.my_output.csv
              tradis_gene_insert_sites -o my_output.csv my_annotation.embl my_insert_site_plot1

       # Trim insertion sites from start or end of gene
              tradis_gene_insert_sites    my_annotation.embl    -trim5     0.1     -trim3     0.1
              my_annotation.embl my_insert_site_plot.gz

       The trim parameter is the fraction of the gene length trimmed.

       # place all info into a single file
              tradis_gene_insert_sites   -o   output_suffix.csv  -j  my_annotation.embl  plot1.gz
              plot2.gz plot3.gz

       Resulting file: joined_output.output_suffix.csv

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.