final static private String INPUT_GENOMES_FILE_OPTION = "genomes";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
- final static private String PRG_VERSION = "2.501";
- final static private String PRG_DATE = "170327";
- final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String PRG_VERSION = "2.503";
+ final static private String PRG_DATE = "170518";
+ final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
ForesterUtil
.programMessage( PRG_NAME,
"Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file );
+ final int LEVEL = 0;
try {
MinimalDomainomeCalculator.calc( false,
intrees[ 0 ],
+ LEVEL,
protein_lists_per_species,
SEPARATOR_FOR_DA,
-1,
try {
MinimalDomainomeCalculator.calc( true,
intrees[ 0 ],
+ LEVEL,
protein_lists_per_species,
SEPARATOR_FOR_DA,
-1,
ForesterUtil.programMessage( PRG_NAME, surfacing.WWW );
ForesterUtil
.programMessage( PRG_NAME,
- "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs ../../genome_locations.txt]" );
+ "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
ForesterUtil.programMessage( PRG_NAME, "OK" );
System.out.println();
}
System.out
.println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" );
System.out.println();
+ System.out
+ .println( "Example 3: surfacing -species_tree=master_tree.xml -no_eo -ie=1e-6 -mrel=0.5 -mo=10 -dufs -genomes=genomes.txt -out_dir=a605 -o=a605" );
+ System.out.println();
+ System.out
+ .println( "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
+ System.out.println();
}
}