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 = "2.500";
- final static private String PRG_DATE = "170323";
- 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;
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
private static final boolean CALC_SIMILARITY_SCORES = false;
+ private static final String SEPARATOR_FOR_DA = "--";
@SuppressWarnings( "unchecked")
public static void main( final String args[] ) {
ForesterUtil
.programMessage( PRG_NAME,
"Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file );
- //
- if ( true ) { //TODO
- try {
- MinimalDomainomeCalculator.calcOme( false,
- intrees[ 0 ],
- protein_lists_per_species,
- "---",
- 1000,
- out_dir.toString() + "/" + output_file );
- }
- catch ( IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
+ final int LEVEL = 0;
+ try {
+ MinimalDomainomeCalculator.calc( false,
+ intrees[ 0 ],
+ LEVEL,
+ protein_lists_per_species,
+ SEPARATOR_FOR_DA,
+ -1,
+ out_dir.toString() + "/" + output_file,
+ true );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
- if ( true ) { //TODO
- try {
- MinimalDomainomeCalculator.calcOme( true,
- intrees[ 0 ],
- protein_lists_per_species,
- "---",
- 1000,
- out_dir.toString() + "/" + output_file );
- }
- catch ( IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
+ try {
+ MinimalDomainomeCalculator.calc( true,
+ intrees[ 0 ],
+ LEVEL,
+ protein_lists_per_species,
+ SEPARATOR_FOR_DA,
+ -1,
+ out_dir.toString() + "/" + output_file,
+ true );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
if ( da_analysis ) {
SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
"Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" );
ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" );
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 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();
}
}