From 0f87a83202601a265797067dd06e097cd5702e5a Mon Sep 17 00:00:00 2001 From: athreyab Date: Thu, 26 Jan 2012 01:50:36 +0000 Subject: [PATCH] addressed a few review comments from Justin svn path=/; revision=279 --- .../interactions/interactionPathsFromSif.pl | 20 +++++++++---------- .../interactions/interactionPathsFromTsv.pl | 19 ++++++++---------- 2 files changed, 18 insertions(+), 21 deletions(-) diff --git a/Personnel/athreyab/interactions/interactionPathsFromSif.pl b/Personnel/athreyab/interactions/interactionPathsFromSif.pl index 3a32d0a..da35aac 100644 --- a/Personnel/athreyab/interactions/interactionPathsFromSif.pl +++ b/Personnel/athreyab/interactions/interactionPathsFromSif.pl @@ -1,10 +1,10 @@ #!/usr/bin/perl -w #use strict; - +use Switch; use DBI; use Config::IniFiles; -use Switch; + require "interactionPath.pl"; @@ -40,7 +40,7 @@ sub getInteractionTypeForSifFormat { if($key eq $abbreviated_interaction_type){ $interaction_type = $value; - break; + last; } } $interaction_type ne "" || die "$abbreviated_interaction_type may not be present in the db"; @@ -191,8 +191,7 @@ sub importSifData #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"; + $interactionId = getInteractionId($accession_left_id,$interaction_type_id,$accession_right_id,$curatorId); if(isEmpty($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')"; @@ -215,14 +214,14 @@ $speciesId1ForOrtholog=""; $speciesId2ForOrtholog=""; $curatorId = ""; %interaction_types=(pp=>"protein-protein binding",up=>"up regulation",down=>"down regulation"); -$dbh = setUpDBConnection(); + switch($optionId){ #add a new species to our database. case "0" { - $speciesId = addNewSpecies(getSpeciesProperties(1)); + addNewSpecies(getSpeciesProperties(1)); } #import ortholog information case "1" @@ -231,12 +230,13 @@ switch($optionId){ print "Species - 1. Species to which gene ids in the first column belong to"; $speciesId1ForOrtholog = getSpeciesId(getSpeciesProperties(0)); - $speciesId1ForOrtholog ne "" || die "species not found in our tables.\n"; - + #$speciesId1ForOrtholog ne "" || die "species not found in our tables.\n"; + !isEmpty($speciesId1ForOrtholog) || die ""; print "\nSpecies - 2. Species to which gene ids in the second column belong to"; $speciesId2ForOrtholog = getSpeciesId(getSpeciesProperties(0)); - $speciesId2ForOrtholog ne "" || die "species not found in our tables.\n"; + !isEmpty($speciesId2ForOrtholog) || die ""; + $speciesId1ForOrtholog ne $speciesId2ForOrtholog || die "species have to be different\n"; print "$speciesId1ForOrtholog"."\t"."$speciesId2ForOrtholog"."\n"; importOrthologData(); } diff --git a/Personnel/athreyab/interactions/interactionPathsFromTsv.pl b/Personnel/athreyab/interactions/interactionPathsFromTsv.pl index 99ea7a5..bf0b174 100644 --- a/Personnel/athreyab/interactions/interactionPathsFromTsv.pl +++ b/Personnel/athreyab/interactions/interactionPathsFromTsv.pl @@ -40,10 +40,8 @@ sub importSeedInteractionData(){ # split the columns into separate variables my ($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($obj_abbr_right)); - next if(isEmpty($interaction_type)); + #skip + next if(isEmpty($obj_abbr_left)); #get ids(primary keys) from other tables $obj_id_left = getObjectIdFromAbbreviation($obj_abbr_left); @@ -73,8 +71,8 @@ sub importSeedInteractionData(){ $experiment_id = getExperimentId($experiment); #get interaction_id to see if already exists - $interaction_id = getInteractionId($obj_id_left,$interaction_type_id,$obj_id_right,$curator_id) - + $interaction_id = getInteractionId($obj_id_left,$interaction_type_id,$obj_id_right,$curator_id); + print "interaction_id:$interaction_id\n"; #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`, @@ -95,7 +93,7 @@ sub importGeneInformation(){ # strip off newline characters chomp $entry; $entry =~ s/\r//g; - $entry =~ s/\n//g; + $entry =~ s/\n//g; my ($accession, $is_gene,$is_metabolite,$symbol,$full_name,$synonym,$species_name,$ncbi_id) = split("\t", $entry); @@ -123,6 +121,7 @@ sub importGeneInformation(){ #gets synonym_id. The function returns the id if exists already. else, inserts synonym and returns the id. $synonym_id = getSynonymId($synonym); + print "synonym_id:$synonym_id\t"; #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='$accession' "; @@ -137,7 +136,7 @@ sub importGeneInformation(){ } executeDbQuery($query); $object_id = getObjectIdFromAccession($accession); - + print "object id: $object_id\n"; #next, insert object_id and synonym_id into object_synonym table. $query = "INSERT INTO Object_synonym(`object_id`,`synonym_id`) VALUES ('$object_id','$synonym_id')"; executeDbQuery($query); @@ -155,9 +154,7 @@ if($#ARGV != 1){ $optionId = $ARGV[0]; $fileName = $ARGV[1]; $curatorId = ""; -$labName = ""; -$userName = ""; -$dbh = setUpDBConnection(); + switch($optionId){ #import gene information - accession id, synonym etc case "1" -- 2.34.1