Commit 684e2da1e25d2135c86564ad6834c2b9433fb584
1 parent
da6670c0fe
Exists in
master
Fixed bug extracting the corret E-value for projected domains
Showing 1 changed file with 43 additions and 40 deletions Side-by-side Diff
getDomainTopology.pl
View file @
684e2da
| ... | ... | @@ -82,56 +82,56 @@ |
| 82 | 82 | #print Data::Dumper->Dump([$tcids ], [qw(*tcids )]); |
| 83 | 83 | #exit; |
| 84 | 84 | |
| 85 | - #========================================================================== | |
| 86 | - #Setup the thresholds for parsing the PFAM output | |
| 85 | + #========================================================================== | |
| 86 | + #Setup the thresholds for parsing the PFAM output | |
| 87 | 87 | |
| 88 | - my $obj = ""; | |
| 89 | - if ($domainAnalysisMode eq "cdd") { | |
| 90 | - $obj = new TCDB::Domain::CDDparser(); | |
| 91 | - $obj->cddFile($cddFile); | |
| 92 | - } | |
| 93 | - else { | |
| 94 | - $obj = new TCDB::Domain::PfamParser(); | |
| 95 | - $obj->pfamFile($pfamFile); | |
| 96 | - } | |
| 88 | + my $obj = ""; | |
| 89 | + if ($domainAnalysisMode eq "cdd") { | |
| 90 | + $obj = new TCDB::Domain::CDDparser(); | |
| 91 | + $obj->cddFile($cddFile); | |
| 92 | + } | |
| 93 | + else { | |
| 94 | + $obj = new TCDB::Domain::PfamParser(); | |
| 95 | + $obj->pfamFile($pfamFile); | |
| 96 | + } | |
| 97 | 97 | |
| 98 | - $obj->analysisLevel($analysisLevel); | |
| 99 | - $obj->domCovCutoff($domain_cov); | |
| 100 | - $obj->tcCovCutoff($prot_cov); | |
| 101 | - $obj->evalueCutoff($evalue); | |
| 102 | - $obj->minProtsDom($prop_prots_w_domain); | |
| 103 | - $obj->treatAsSuperfamily($treatAsSuperfamily); | |
| 98 | + $obj->analysisLevel($analysisLevel); | |
| 99 | + $obj->domCovCutoff($domain_cov); | |
| 100 | + $obj->tcCovCutoff($prot_cov); | |
| 101 | + $obj->evalueCutoff($evalue); | |
| 102 | + $obj->minProtsDom($prop_prots_w_domain); | |
| 103 | + $obj->treatAsSuperfamily($treatAsSuperfamily); | |
| 104 | 104 | |
| 105 | 105 | |
| 106 | - my %domFreq = (); | |
| 107 | - my %domCoords = (); | |
| 108 | - $obj->getDomainStatsForUserFamilies(\@fams, $tcids, \%domFreq, \%domCoords); | |
| 106 | + my %domFreq = (); | |
| 107 | + my %domCoords = (); | |
| 108 | + $obj->getDomainStatsForUserFamilies(\@fams, $tcids, \%domFreq, \%domCoords); | |
| 109 | 109 | |
| 110 | -# print Data::Dumper->Dump([ \%domFreq, \%domCoords ], [qw( *domFreq *domCoords )]); | |
| 111 | -# exit; | |
| 110 | +# print Data::Dumper->Dump([ \%domFreq, \%domCoords ], [qw( *domFreq *domCoords )]); | |
| 111 | +# exit; | |
| 112 | 112 | |
| 113 | 113 | |
| 114 | 114 | |
| 115 | 115 | |
| 116 | 116 | |
| 117 | - #========================================================================== | |
| 118 | - #Attempt to rescue the domains that were not recognized by PFAM in some | |
| 119 | - #Family members | |
| 117 | + #========================================================================== | |
| 118 | + #Attempt to rescue the domains that were not recognized by PFAM in some | |
| 119 | + #Family members | |
| 120 | 120 | |
| 121 | 121 | |
| 122 | - my $rescueObj = new TCDB::Domain::Characterize(); | |
| 123 | - $rescueObj->rootDir($rootDir); | |
| 124 | - $rescueObj->tcdbFaa($tcdbSeqsFile); | |
| 125 | - $rescueObj->domCoords(\%domCoords); | |
| 126 | - $rescueObj->domFreq(\%domFreq); | |
| 127 | - $rescueObj->tcids($tcids); | |
| 128 | - $rescueObj->searchWith($prog); | |
| 129 | - $rescueObj->blastdb($blastdb); | |
| 130 | - $rescueObj->evalue($evalue); | |
| 131 | - $rescueObj->treatAsSuperfamily($treatAsSuperfamily); | |
| 122 | + my $rescueObj = new TCDB::Domain::Characterize(); | |
| 123 | + $rescueObj->rootDir($rootDir); | |
| 124 | + $rescueObj->tcdbFaa($tcdbSeqsFile); | |
| 125 | + $rescueObj->domCoords(\%domCoords); | |
| 126 | + $rescueObj->domFreq(\%domFreq); | |
| 127 | + $rescueObj->tcids($tcids); | |
| 128 | + $rescueObj->searchWith($prog); | |
| 129 | + $rescueObj->blastdb($blastdb); | |
| 130 | + $rescueObj->evalue($evalue); | |
| 131 | + $rescueObj->treatAsSuperfamily($treatAsSuperfamily); | |
| 132 | 132 | |
| 133 | 133 | |
| 134 | - $rescueObj->rescueDomains(\@fams); | |
| 134 | + $rescueObj->rescueDomains(\@fams); | |
| 135 | 135 | |
| 136 | 136 | } |
| 137 | 137 | else { |
| 138 | 138 | |
| ... | ... | @@ -166,11 +166,11 @@ |
| 166 | 166 | $obj->minProtsDom($prop_prots_w_domain); |
| 167 | 167 | |
| 168 | 168 | |
| 169 | - my %domFreq = (); | |
| 170 | - my %domCoords = (); | |
| 169 | + my %domFreq = (); | |
| 170 | + my %domCoords = (); | |
| 171 | 171 | $obj->getDomainStatsForUserFamilies([], $tcids, \%domFreq, \%domCoords); |
| 172 | 172 | |
| 173 | -# print Data::Dumper->Dump([ \%domFreq, \%domCoords ], [qw( *domFreq *domCoords )]); | |
| 173 | +# print Data::Dumper->Dump([ \%domFreq, \%domCoords], [qw( *domFreq *domCoords)]); | |
| 174 | 174 | # exit; |
| 175 | 175 | |
| 176 | 176 | |
| ... | ... | @@ -206,7 +206,6 @@ |
| 206 | 206 | ########################################################################### |
| 207 | 207 | |
| 208 | 208 | |
| 209 | - | |
| 210 | 209 | sub read_command_line_arguments { |
| 211 | 210 | |
| 212 | 211 | #if no arguments are given print the help |
| ... | ... | @@ -268,6 +267,9 @@ |
| 268 | 267 | } |
| 269 | 268 | |
| 270 | 269 | |
| 270 | + | |
| 271 | + | |
| 272 | + | |
| 271 | 273 | #========================================================================== |
| 272 | 274 | #Setup the environment for projection of domains onto sequences that are |
| 273 | 275 | #not present in TCDB. |
| ... | ... | @@ -391,6 +393,7 @@ |
| 391 | 393 | #For all purposes update the TCDB sequence file to point to the new "customized" file. |
| 392 | 394 | $tcdbSeqsFile = $new_tcdbSeqsFile; |
| 393 | 395 | } |
| 396 | + | |
| 394 | 397 | |
| 395 | 398 | |
| 396 | 399 |