pommevilla / MetaFunPrimer

Lines 136 to 139 in ccfe124

    
           for perc_ident in $(seq 0.8 0.01 1);  
        
           do 
        
           	echo "cd-hit -i ../$input_file -o $perc_ident.fa -c $perc_ident -n 5 -T 0 > /dev/null"  
        
           done > command.cluster.sh

mfpcluster currently only runs CD-HIT in fast mode. Add an optional argument to mfpcluster to allow the user to choose between accurate and fast mode.

This is done via the -g argument to CD-HIT. This parameter defaults to 0, which is fast mode, but will run in accurate mode if set to 1.

Tasks:

Add new arguments -m and --mode to mfpcluster that mirrors the -g parameter of CD-HIT.
Change the call to CD-HIT to include this parameter.

Depending on how slow CD-HIT runs in accurate mode, the highlighted lines may need to be modified to create and submit a job script instead of just running on the command line.

	for perc_ident in $(seq 0.8 0.01 1);
	do
	echo "cd-hit -i ../$input_file -o $perc_ident.fa -c $perc_ident -n 5 -T 0 > /dev/null"
	done > command.cluster.sh

mfpcluster: Allow user to toggle between accurate and fast mode in CD-HIT