URL to Mobidetails, Merge CHROM-POS-REF-ALT columns, OMIM annotation rescue

Author: thomasguignard

wwwachab.pl

@@ -54,7 +54,7 @@
 \n--hideACMG (ACMG tab will be empty but information will be reported in the gene comment) 
 \n--gnomadGenome <comma separated list of gnomad genome annotation fields that will be displayed as gnomAD_Genome comments. First field of the list will be filtered regarding to popFreqThr argument. (default fields are hard-coded gnomAD_genome_ALL like)  > 
 \n--gnomadExome <comma separated list of gnomad exome annotation fields that will be displayed as gnomAD comments. (default fields are hard-coded gnomAD_exome_ALL like) > 
-\n--MDAPIkey <Path to File containing MobiDetails API key (default file is MD.apikey in the achab folder) >
+\n--MDAPIkey <Path to File containing only MobiDetails API key (default file is MD.apikey in the achab folder) >
 \n\n-v|--version < return version number and exit > ";
 
 my $versionOut = "achab version www:1.0.13";
@@ -961,25 +961,28 @@
 }
 
 open( MDAPIKEY , "<$mdAPIkey") or do {print "Didn't find any MoBiDetails APIkey file, expected: ".$mdAPIkey."\n"; $mdAPIkey = "";  } ;
-if ($mdAPIkey ne ""){
-	print  STDERR "Processing MDAPIKEY file ... \n" ;
-	while( <MDAPIKEY> ){
-		$md_line = $_;
-		chomp $md_line;
-		if ($md_line eq ""){
-			$mdAPIkey = "";
-			#print "DEBUG:    ".$mdAPIkey."\n";
-		}else{
-			$mdAPIkey = "https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/create_vcf_str?genome_version=hg19&api_key=".$md_line."&vcf_str=";
+#checkif file is empty
+if (-z $mdAPIkey){
+	$mdAPIkey = "";
+	print "The MoBiDetails APIkey file: ".$mdAPIkey. " is empty. Please fill it";
+}else{
+	if ($mdAPIkey ne ""){
+		print  STDERR "Processing MDAPIKEY file ... \n" ;
+		while( <MDAPIKEY> ){
+			$md_line = $_;
+			chomp $md_line;
+			if ($md_line eq ""){
+				$mdAPIkey = "";
+			}else{
+				$mdAPIkey = "https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/create_vcf_str?genome_version=hg19&api_key=".$md_line."&vcf_str=";
+			}
 		}
 	}
 }
 close(MDAPIKEY);
 
 
 
-
-
 #Hash of 81 ACMG incidentalome genes secondary findings SF v3.2 according to  https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/
 my %ACMGgene = ("ACTA2" =>1,"ACTC1" =>1,"ACVRL1" =>1,"APC" =>1,"APOB" =>1,"ATP7B" =>1,"BAG3" =>1,"BMPR1A" =>1,"BRCA1" =>1,"BRCA2" =>1,"BTD" =>1,"CACNA1S" =>1,"CALM1" =>1,"CALM2" =>1,"CALM3" =>1,"CASQ2" =>1,"COL3A1" =>1,"DES" =>1,"DSC2" =>1,"DSG2" =>1,"DSP" =>1,"ENG" =>1,"FBN1" =>1,"FLNC" =>1,"GAA" =>1,"GLA" =>1,"HFE" =>1,"HNF1A" =>1,"KCNH2" =>1,"KCNQ1" =>1,"LDLR" =>1,"LMNA" =>1,"MAX" =>1,"MEN1" =>1,"MLH1" =>1,"MSH2" =>1,"MSH6" =>1,"MUTYH" =>1,"MYBPC3" =>1,"MYH11" =>1,"MYH7" =>1,"MYL2" =>1,"MYL3" =>1,"NF2" =>1,"OTC" =>1,"PALB2" =>1,"PCSK9" =>1,"PKP2" =>1,"PMS2" =>1,"PRKAG2" =>1,"PTEN" =>1,"RB1" =>1,"RBM20" =>1,"RET" =>1,"RPE65" =>1,"RYR1" =>1,"RYR2" =>1,"SCN5A" =>1,"SDHAF2" =>1,"SDHB" =>1,"SDHC" =>1,"SDHD" =>1,"SMAD3" =>1,"SMAD4" =>1,"STK11" =>1,"TGFBR1" =>1,"TGFBR2" =>1,"TMEM127" =>1,"TMEM43" =>1,"TNNC1" =>1,"TNNI3" =>1,"TNNT2" =>1,"TP53" =>1,"TPM1" =>1,"TRDN" =>1,"TSC1" =>1,"TSC2" =>1,"TTN" =>1,"TTR" =>1,"VHL" =>1,"WT1" =>1);