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.