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Problem with commands to run script

Hi! I have to files generated from ORF finding tool and Genemark and a script that is supposed to convert them to Artemis friendly formats. Here is the instructions, but I don't get it, what should I write in the command? 

    GenePrediction2Artemis.pl - conversion script for gene predictions.

=head1 PURPOSE

    GenePrediction2Artemis.pl converts the output file from getorf or GeneMark to a file that can be read in Artemis. Give input and output and either getorf or genemark.

=head1 USAGE

    GenePrediction2Artemis.pl -i|input gene_precition -o|output artemis_file [ -getorf -genemark ]

    -getorf for getorf output files

    -genemark for GeneMark output files
artemis perl
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written by Mimmi Ahlmén • Mimmi Ahlmén

1 answer 

$ perl GenePrediction2Artemis.pl -i gene_prediction_file -o outputfile

Then, at the end of the command, append -getorf if your input file is a result from (what I assume is) the getorf program. Similarly, if you used GeneMark for your prediction, give -genemark. I presume this is to tell the script what format to expect in the input file.

• 1 views • link
written by Joe Joe

Alright, and can I just type -o outputfile for the output then?

• 1 views • link
written by Mimmi Ahlmén • Mimmi Ahlmén

Yep. Well, replace outputfile with whatever you want the name of the output file to be.

I don't know if its a required option or not (it doesn't look like it), but if it isn’t , normally the results will be printed to screen.

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written by Joe Joe

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