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.

tradis_gene_insert_sites 1.3.1                     March 2017                        TRADIS_GENE_INSERT_SITES(1)