subtype pres abs ITOL metadata

Make a CRISPR subtype presence-absence table for plotting with a tree in ITOL.

###Pres-abs table of all subtypes & taxa in CLdb

CLdb_subtypePA_ITOL.pl -d CLdb.sqlite

###Subtype count table of all subtypes & taxa in CLdb (not-binary)

CLdb_subtypePA_ITOL.pl -d CLdb.sqlite -a

###Subtype count table of loci containing CAS operons

CLdb_subtypePA_ITOL.pl -d CLdb.sqlite -q "AND operon_status!='absent'"

###Subtype count table of loci containing intact CAS operons (no broken or shuffled)

CLdb_subtypePA_ITOL.pl -d CLdb.sqlite -q "AND operon_status='intact'"

###User provided colors

CLdb_subtypePA_ITOL.pl -d CLdb.sqlite -c "#FF0000 #FF6600 #FFFF00"

###Pres-abs table of specific subtypes & taxa_names

CLdb_subtypePA_ITOL.pl -d CLdb.sqlite -sub I-A I-B I-C -taxon_name Ecoli Senterica Awoodii