#use constant SITE_ADJECTIVE => ($ENV{'DevelopmentSite'} ? 'Development': 'Live');
use constant SITE_ADJECTIVE => 'Development';
+
+############First various sub routines are defined.############
+############Following it the main subroutine code is at the botton of the file############
+
+
sub showUsage
{
print "\n\nUsage: \n\tperl interactionsPathsFromSif <option> [<fileName>]\n";
open(paralog_file, "$fileName") || die "Error: file '$fileName' can not be opened\n";
while(<paralog_file>){
my $entry = $_;
+
# strip off newline characters
+ chomp $entry;
$entry =~ s/\r//g;
$entry =~ s/\n//g;
# split the columns into 3 separate variables
my ($obj_l, $obj_r, $score) = split("\t", $entry);
- # skip if $ident is empty or Nan
+ # skip
next if(!defined($score));
next if($score =~ /D/);
next if($score eq "");
while(<paralog_file>){
my $entry = $_;
# strip off newline characters
+ chomp $entry;
$entry =~ s/\r//g;
$entry =~ s/\n//g;
# split the columns into 3 separate variables
my ($obj_l, $obj_r, $score) = split("\t", $entry);
- # skip if $ident is empty or Nan
+ # skip
next if(!defined($score));
next if($score =~ /D/);
next if($score eq "");
while(<interactions_file>){
my $entry = $_;
# strip off newline characters
+ chomp $entry;
$entry =~ s/\r//g;
$entry =~ s/\n//g;
# split the columns into separate variables
my ($accession_left,$interaction_type,$accession_right) = split("\t", $entry);
- # skip if any of the variables are empty
+
+ # skip if any of the variables are empty
next if(isEmpty($accession_left));
next if(isEmpty($interaction_type));
next if(isEmpty($accession_right));
- #get object_id for object in the first column
+ #get object_id for object in the first column
$accession_left_id = getObjectIdFromAccession($accession_left);
+
#get interaction_type_id for object in the first column
$interaction_type_id = getInteractionTypeForSifFormat($interaction_type);
+
#get object_id for object in the second column
- $accesion_right_id = getObjectIdFromAccession($accession_right);
-
- next if(isEmpty($accession_left_id) || isEmpty($accession_right_id) || isEmpty($interaction_type_id));
+ $accession_right_id = getObjectIdFromAccession($accession_right);
+ next if(isEmpty($accession_left_id) || isEmpty($accession_right_id) || isEmpty($interaction_type_id));
+
#check if the interaction is already recorded. Write to database only if it doesn't exist already.
$interactionId = getInteractionId($accession_left_id,$interaction_type_id,$accession_right_id,$curator_id);
+ print "interaction id is: $interactionId\n";
if(isEmpty($interactionId)){
$query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`curator_id`)
- VALUES('$accession_left_id','$accession_right_id','interaction_type_id','$curatorId')";
- executeDbQuery($query);
- print "$accession_left_id\t$interaction_type_id\t$accession_right_id\t$curator_id\n";
+ VALUES('$accession_left_id','$accession_right_id','$interaction_type_id','$curatorId')";
+ executeDbQuery($query);
}
}
- print "Seed interaction data import completed";
+ print "Seed interaction data import completed\n";
}
-
$optionId = $ARGV[0];
if($optionId ne "0" && $#ARGV != 1){
showUsage();
print "\tncbi id of the species\n";
$curatorId = getCuratorId(getCuratorProperties());
$speciesIdForSif = getSpeciesId(getSpeciesProperties(0));
- $speciesIdForSif ne "" || die "";
+ $speciesIdForSif ne "" || die "Species id was not found for ".getSpeciesProperties(0)."\n";
importSifData();
}
else
use DBI;
use Config::IniFiles;
use Switch;
+
+#functions common to both interactionPathsFromSif and interactionPathsFromTsv are in this perl script file
require "interactionPath.pl";
#use constant SITE_ADJECTIVE => ($ENV{'DevelopmentSite'} ? 'Development': 'Live');
use constant SITE_ADJECTIVE => 'Development';
+
+############First various sub routines are defined.############
+############Following it the main subroutine code is at the botton of the file############
+
+
sub showUsage(){
print "Usage: \n\tperl interactionPathsFromTsv <option> <fileName>\n";
print "options:\n\t";
while(<interactions_file>){
my $entry = $_;
# strip off newline characters
+ chomp $entry;
$entry =~ s/\r//g;
$entry =~ s/\n//g;
+
# split the columns into separate variables
my ($obj_abbr_left,$int_type_left,$mode_of_action,$obj_abbr_right,$int_type_right,$interaction_type,$evidence,$evidence_code,$experiment,$comments) = split("\t", $entry);
+
#we need all the 3 values before we can insert data into the interaction table.
next if(isEmpty($obj_abbr_left));
next if(isEmpty($obj_abbr_right));
$obj_id_left = getObjectIdFromAbbreviation($obj_abbr_left);
$obj_id_right = getObjectIdFromAbbreviation($obj_abbr_right);
$interaction_type_id = getInteractionTypeId($interaction_type);
+
#if any of the above values are empty, it means they are empty. print that message and move to the next line
if(isEmpty($obj_id_left)){
print "$obj_abbr_left was not found in the db. Skipping this line\n";
print "$interaction_type was not found in the db. Skipping this line\n";
next;
}
+
+ #get various primary ids from the table.
$int_type_id_left = getInteractorTypeId($int_type_left);
$int_type_id_right = getInteractorTypeId($int_type_right);
$mode_of_action_id = getModeOfActionId($mode_of_action);
$evidence_code_id = getEvidenceCodeId($evidence_code);
$experiment_id = getExperimentId($experiment);
- print $obj_id_left."\t".$obj_id_right."\t".$int_type_id_left."\t".$int_type_id_right."\t".$interaction_type_id.
- "\t".$evidence_id."\t".$evidence_code_id."\t".$experiment_id.$curator_id."\n";
-
+
$query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`mode_of_action_id`,
`interactor_type_id_left`,`interactor_type_id_right`,`evidence_id`,`evidence_code_id`,`experiment_id`,`comments`,`curator_id`)
VALUES ('$obj_id_left','$obj_id_right','$interaction_type_id','$mode_of_action_id','$int_type_id_left','$int_type_id_right'
- ,'$evidence_id','$evidence_code_id','$experiment_id','$comments','$curator_id')";
-
+ ,'$evidence_id','$evidence_code_id','$experiment_id','$comments','$curator_id')";
executeDbQuery($query);
}
open(gene_file, "$fileName") || die "Error: file '$fileName' can not be opened\n";
while(<gene_file>){
my $entry = $_;
+
# strip off newline characters
+ chomp $entry;
$entry =~ s/\r//g;
$entry =~ s/\n//g;
my ($accession, $is_gene,$is_metabolite,$symbol,$full_name,$synonym,$species_name,$ncbi_id) = split("\t", $entry);
+
#skip the line if accession value is empty
next if(isEmpty($accession));
+
$object_type=1;
if($is_metabolite eq "yes"){
$object_type=2;
}
+ #get species id, if the species is not present already, insert it
$species_id = getSpeciesId($species_name,$ncbi_id);
- #if the species is not present already, insert it
if(isEmpty($species_id)){
if(!isEmpty($ncbi_id)){
$query = "INSERT INTO Species(`species`,`NCBI_taxonomy_id`) VALUES ('$species_name','$ncbi_id')";
}
executeDbQuery($query);
$species_id = getSpeciesId($species_name,$ncbi_id);
+ print "New species $species_name added to the db\n";
}
#gets synonym_id if exists already. else, inserts synonym and returns the id.
$synonym_id = getSynonymId($synonym);
+ #construct the query and insert object information to the table.
$query = "INSERT INTO Object(`object_accession`,`species_id`,`object_full_name`,`object_abbreviation`,`object_type_id`) VALUES('$accession','$species_id','$full_name','$symbol','$object_type') ON DUPLICATE KEY UPDATE object_accession='$accession' ";
if(!isEmpty($full_name)){
$query = $query." , object_full_name='$full_name'";
projects / old-jaiswallab-svn / .git / commitdiff