#interaction type in sif files is in abbreviated format - 'pp','up',''down' etc. This function retrieves the
#full format.
+#accepts abbreviated interaction type as argument
+#returns interaction type id from db
sub getInteractionTypeForSifFormat
{
+ # %interaction_types = map containing abbreviated and full forms of interaction_type as a key-value pair
($abbreviated_interaction_type) = @_;
while ( ($key, $value) = each %interaction_types )
{
}
$interaction_type ne "" || die "$abbreviated_interaction_type may not be present in the db";
+ #get interaction type id from the db
return getInteractionTypeId($interaction_type);
}
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", $entry);
+
# skip
next if(!defined($score));
next if($score =~ /D/);
$obj_id_r = getObjectIdFromAccession($obj_r);
}
- #check if the homology between the accessions is already recorded. If it is already, check the scores and
+ #check if the homology between the accessions is already recorded. If it is recorded already, check the scores and
#store the highest score. If the relation doesn't exist, insert into the homology table.
($homology_id,$origScore) = getHomologyIdAndScore($obj_id_l,$obj_id_r,$score);
if(isEmpty($homology_id) || $origScore < $score){
open(paralog_file, "$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", $entry);
+
# skip
next if(!defined($score));
next if($score =~ /D/);
print "reading seed interaction information from $fileName\n";
open(interactions_file, "$fileName") || die "Error: file '$fileName' can not be opened\n";
- print "Species id: ".$speciesIdForSif."\n";
+
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", $entry);
next if(isEmpty($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.
+ #check if the interaction is already recorded. Write to database only if it doesn't exist already.e
+ #an interaction is considered new under two conditions:
+ #a. interaction has not been recorded previously
+ #b. interaction is already recorded, but by a different curator - this is not something that we need right now
+ #but in the future, we may allow people other than the devs to upload the data themselves.
$interactionId = getInteractionId($accession_left_id,$interaction_type_id,$accession_right_id,$curator_id);
print "interaction id is: $interactionId\n";
if(isEmpty($interactionId)){
showUsage();
}
-
+#some initializations
$fileName = $ARGV[1];
$speciesIdForSif="";
$speciesIdForParalog="";
print "Usage: \n\tperl interactionPathsFromTsv <option> <fileName>\n";
print "options:\n\t";
print "1 - to import gene id data\n\t";
- print "2 - to import seed interaction data\n\t";
-
+ print "2 - to import seed interaction data\n\t";
}
#imports the tab separated file containing seed interaction
open(interactions_file, "$fileName") || die "Error: file '$fileName' can not be opened\n";
while(<interactions_file>){
my $entry = $_;
+
# strip off newline characters
chomp $entry;
$entry =~ s/\r//g;
$obj_id_right = getObjectIdFromAbbreviation($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 any of the above values are empty, print a 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";
next;
$evidence_code_id = getEvidenceCodeId($evidence_code);
$experiment_id = getExperimentId($experiment);
-
- $query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`mode_of_action_id`,
- `interactor_type_id_left`,`interactor_type_id_right`,`evidence_id`,`evidence_code_id`,`experiment_id`,`comments`,`curator_id`)
- VALUES ('$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')";
- executeDbQuery($query);
-
+ #get interaction_id to see if already exists
+ $interaction_id = getInteractionId($obj_id_left,$interaction_type_id,$obj_id_right,$curator_id)
+
+ #if not, insert data into to the database
+ if(isEmpty($interaction_id)){
+ $query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`mode_of_action_id`,
+ `interactor_type_id_left`,`interactor_type_id_right`,`evidence_id`,`evidence_code_id`,`experiment_id`,`comments`,`curator_id`)
+ VALUES ('$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')";
+ executeDbQuery($query);
+ }
}
}
print "New species $species_name added to the db\n";
}
- #gets synonym_id if exists already. else, inserts synonym and returns the id.
+ #gets synonym_id. The function returns the 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.
$userName = "";
$dbh = setUpDBConnection();
switch($optionId){
+ #import gene information - accession id, synonym etc
case "1"
{
importGeneInformation();
}
+ #import interaction data
case "2"
{
$curatorId = getCuratorId(getCuratorProperties());
projects / old-jaiswallab-svn / .git / commitdiff