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# CONFIG FILE:  QUICKMINE.config
# FUNCTION:    List of commands to be run by QUICKMINE_script
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# To do additional analyses, just add a new line to the @cmd array
# Each command should take the form of an 'extension name' and an
# exact command line command to run a UNIX application.

# ["extension", "full command (with output file name LAST!")]

# Note: Can be used to run GCG applications, just convert each file to
# gcg format first (.seq files)


# Other UNIX applications that this could be used with:
# SSEARCH
# FASTA
# CLUSTALW
# etc...



@cmd = (
        #  $ext         $cmd
        # RULE: the outfile must be the last word in the command and
        # there must be a space before the output file name

        # this calls the program blastn against $contig for each $file
        #["SELF_blastn",         "blastall -p blastn -d $blast_database -i $file -o $file" ],

        # tblastx against a large db will take >30 seconds and should be sent through the queue
        ["pro_tblastx",         "blastall -p tblastx -d pro -i $file -o $file" ],

        # run the EMBOSS prog compseq2 to look at dinucleotide composition
        ["compseq2",            "compseq -sequence $file -word 2 -outfile $file"],
        );