# HG changeset patch
# User niels
# Date 1557743859 14400
# Node ID 856448f167da13c0e966f8b64e837d817086a7c7
# Parent  0925376a262409871e3254d61eaa44c5d51679b7
Uploaded

diff -r 0925376a2624 -r 856448f167da annovar_yaml/AnnovarArguments.yml
--- a/annovar_yaml/AnnovarArguments.yml	Mon May 06 08:11:46 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-GENERAL:
-  - APPLICATION: 'annovar'
-    PATHSCRIPTS: '/home/cog/snouwens/Desktop/Files/Test_YAML/scripts/'
-    CODING_ANNOVAR: 'coding_annovar.pl '
-    TABLE_ANNOVAR: 'table_annovar.pl '
-    LOCATION_DATABASE: '/home/cog/snouwens/Desktop/Files/Test_YAML/database/'
-    DOT2UNDERLINE:
-      yes: '--dot2underline '
-      no: ''
-    NASTRING: '--nastring . '
-    OTHERINFO:
-      yes: '--otherinfo '
-      no: ''
-    POLISH:
-      yes: '--polish '
-      no: ''
-    REMOVE:
-      yes: '--remove '
-      no: ''
-    THREAD: '--thread 8 '
-    INPUTFORMAT:
-      vcfinput: '--vcfinput '
-    SPECIES:
-      human: 'humandb '
-      mouse: 'mousedb '
-    BUILD: '--buildver hg19 '
-ANALYSIS:
-  DATABASES:
-    - NAME: 'cosmic84'
-      PROTOCOL: 'cosmic'
-      VERSION: '84'
-      COMMENT: '20190221' 
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'f'
-      COLSWANTED: '--colswanted 4 '
-    - NAME: 'refgene19'
-      PROTOCOL: 'refgene'
-      VERSION: '19' 
-      COMMENT: '20190210'  
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'g'
-      HGVS:
-        yes: '--hgvs '
-        no: ''
-      SPLICING: '--splicing 6 '
-      EXONSPLIC:  
-        yes: '--exonicsplicing '
-        no: ''
diff -r 0925376a2624 -r 856448f167da annovar_yaml/AnnovarInput.yml
--- a/annovar_yaml/AnnovarInput.yml	Mon May 06 08:11:46 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-GENERAL:
-  - APPLICATION: 'annovar'
-    PATHSCRIPTS: '/home/cog/snouwens/Desktop/Files/Test_YAML/scripts'
-    CODING_ANNOVAR: 'coding_annovar.pl'
-    TABLE_ANNOVAR: 'table_annovar.pl'
-    LOCATION_DATABASE: '/home/cog/snouwens/Desktop/Files/Test_YAML/databases'
-    DOT2UNDERLINE: 'yes'
-    NASTRING: '.'
-    OTHERINFO: 'yes'
-    POLISH: 'yes'
-    REMOVE: 'yes'
-    THREAD: '8'
-    INPUTFORMAT: 'vcfinput'
-    SPECIES: 'human'
-    BUILD: 'hg19'
-ANALYSIS:
-  DATABASES:
-  - NAME: 'cosmic84'
-    PROTOCOL: 'cosmic'
-    VERSION: '84'
-    COMMENT: '20190221'
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    OPERATION: 'f' 
-    COLSWANTED: '4'
-  - NAME: 'refgene19'
-    PROTOCOL: 'refgene'
-    VERSION: '19' 
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    COMMENT: '20190210'
-    OPERATION: 'g'
-    HGVS: 'yes'
-    SPLICING: '6'
-    EXONSPLIC: 'yes'
diff -r 0925376a2624 -r 856448f167da annovar_yaml/YAML_annovar.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annovar_yaml/YAML_annovar.yml	Mon May 13 06:37:39 2019 -0400
@@ -0,0 +1,66 @@
+GENERAL:
+  - APPLICATION: 'annovar'
+    PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
+    CODING_ANNOVAR: 'coding_annovar.pl'
+    TABLE_ANNOVAR: 'table_annovar.pl'
+    LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
+    DOT2UNDERLINE: 'yes'
+    NASTRING: '.'
+    OTHERINFO: 'yes'
+    POLISH: 'yes'
+    REMOVE: 'yes'
+    THREAD: '8'
+    INPUTFORMAT: 'vcfinput'
+    SPECIES: 'human'
+    BUILD: 'hg19'
+ANALYSIS:
+  DATABASES:
+  - NAME: 'cosmic84'
+    PROTOCOL: 'cosmic'
+    VERSION: '84'
+    COMMENT: '20190221'
+    AVAILABLE: 'yes'
+    REQUIRED: 'yes'
+    OPERATION: 'f' 
+    COLSWANTED: '4'
+  - NAME: 'refgene19'
+    PROTOCOL: 'refgene'
+    VERSION: '19' 
+    AVAILABLE: 'yes'
+    REQUIRED: 'yes'
+    COMMENT: '20190210'
+    OPERATION: 'g'
+    HGVS: 'yes'
+    SPLICING: '6'
+    EXONSPLIC: 'yes'
+  - NAME: 'ncbiRefSeq_UMCU'
+    PROTOCOL: 'ncbiRefSeq'
+    VERSION: '_UMCU'
+    AVAILABLE: 'yes'
+    REQUIRED: 'yes'
+    COMMENT: "100519"
+    OPERATION: 'g'
+    HGVS: 'yes'
+    SPLICING: '6'
+    EXONSPLIC: 'yes'
+  - NAME: 'avsnp150'
+    PROTOCOL: 'avsnp'
+    VERSION: '150'
+    AVAILABLE: 'yes'
+    REQUIRED: 'yes'
+    OPERATION: 'f'
+    COLSWANTED: '1'
+  - NAME: 'clinvar_20180603'
+    PROTOCOL: 'clinvar'
+    VERSION: '_20180603'
+    AVAILABLE: 'yes'
+    REQUIRED: 'yes'
+    OPERATION: 'f'
+    COLSWANTED: '5'
+  - NAME: 'class100519'
+    PROTOCOL: 'class'
+    VERSION: '100519'
+    AVAILABLE: 'yes'
+    REQUIRED: 'yes'
+    OPERATION: 'f'
+    COLSWANTED: '1'
diff -r 0925376a2624 -r 856448f167da annovar_yaml/YAML_arguments_annovar.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annovar_yaml/YAML_arguments_annovar.yml	Mon May 13 06:37:39 2019 -0400
@@ -0,0 +1,111 @@
+GENERAL:
+  - APPLICATION: 'annovar'
+    PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
+    CODING_ANNOVAR: 'coding_annovar.pl '
+    TABLE_ANNOVAR: 'table_annovar.pl '
+    LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
+    DOT2UNDERLINE:
+      yes: '--dot2underline '
+      no: ''
+    NASTRING: '--nastring . '
+    OTHERINFO:
+      yes: '--otherinfo '
+      no: ''
+    POLISH:
+      yes: '--polish '
+      no: ''
+    REMOVE:
+      yes: '--remove '
+      no: ''
+    THREAD: '--thread 8 '
+    INPUTFORMAT:
+      vcfinput: '--vcfinput '
+    SPECIES:
+      human: 'humandb '
+      mouse: 'mousedb '
+    BUILD: '--buildver hg19 '
+ANALYSIS:
+  DATABASES:
+    - NAME: 'cosmic84'
+      PROTOCOL: 'cosmic'
+      VERSION: '84'
+      COMMENT: '20190221' 
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 4 '
+    - NAME: 'refgene19'
+      PROTOCOL: 'refgene'
+      VERSION: '19' 
+      COMMENT: '20190210'  
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'g'
+      HGVS:
+        yes: '--hgvs '
+        no: ''
+      SPLICING: '--splicing 6 '
+      EXONSPLIC:  
+        yes: '--exonicsplicing '
+        no: ''
+    - NAME: 'ncbiRefSeq_UMCU'
+      PROTOCOL: 'ncbiRefSeq'
+      VERSION: '_UMCU'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      COMMENT: "100519"
+      OPERATION: 'g'
+      HGVS:
+        yes: '--hgvs '
+        no: ''
+      SPLICING: '--splicing 6 '
+      EXONSPLIC:
+        yes: '--exonicsplicing '
+        no: ''
+    - NAME: 'avsnp150'
+      PROTOCOL: 'avsnp'
+      VERSION: '150'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 1 '
+    - NAME: 'clinvar_20180603'
+      PROTOCOL: 'clinvar'
+      VERSION: '_20180603'
+      COMMENT: 'blah'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 5 '
+    - NAME: 'class100519'
+      PROTOCOL: 'class'
+      VERSION: '100519'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 1 '
+      
diff -r 0925376a2624 -r 856448f167da annovar_yaml/annovar_yaml.pl
--- a/annovar_yaml/annovar_yaml.pl	Mon May 06 08:11:46 2019 -0400
+++ b/annovar_yaml/annovar_yaml.pl	Mon May 13 06:37:39 2019 -0400
@@ -5,7 +5,7 @@
 use YAML::Tiny;
 use YAML::XS 'LoadFile';
 use Data::Dumper;
-use Data::YAML::Writer;
+#use Data::YAML::Writer;
 use Getopt::Long;
 use strict;
 
@@ -22,7 +22,7 @@
 my $edit = "0";
 my $run = "0";
 my $application = "0";
-my $parameter_yml = "AnnovarArguments.yml";
+my $parameter_yml = "YAML_arguments_annovar.yml";
 my $inyml;
 my $outyml;
 my $invcf;
@@ -422,75 +422,126 @@
 #foreach (@parameters_test) {
 #print "value: $_\n";
 #}  
-
-
 #my $test_hash = $yml_hash->{ }{map};
 
 #print "value: $yml_hash->{ANALYSIS}{DATABASES}\n";
 
+#Fill hashes with input yaml files
 openyml_read ($parameter_yml);
 openyml_read ($inyml);
 load ($inyml, %yml_hash, $yml_hash);
 load_arguments ($parameter_yml, %yml_hash_arguments, $yml_hash_arguments);
 
-#foreach my $find_parameter (@{$yml_hash->{GENERAL}}) {
-#  print "each: $find_parameter\n";
-#  print "TESTINGTESTING_hash: $find_parameter->{SPECIES}\n";
-#}
-
 #Building annovar command:
 my $application = 'annovar';
+
+my $ncbiRefSeq = 'ncbiRefSeq';
 my $cosmic = 'cosmic';
-my $refgene = 'refgene';
+my $dbsnp = 'avsnp';
+my $clinvar = 'clinvar';
+my $class = 'class';
+
+my $ncbiRefSeq_version = '_UMCU';
 my $cosmic_version = '84';
-my $refgene_version = '19';
-my $invcf = "test.vcf ";
+my $dbsnp_version = '150';
+my $clinvar_version = '_20180603';
+my $class_version = '100519';
+
+#species input fixed
 my $input_annovar_species = "human";
-my $outvcf = "out.vcf ";
+
+#Defined in input
+#my $invcf = "/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/input_vcfs/prepared_vcfs/PA-AI-201812-154T_norm_2.vcf ";
+#my $outvcf = "/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/input_vcfs/prepared_vcfs/PA-AI-201812-154T_norm_2_out.vcf ";
+
 my $language = 'perl ';
+
 my $parse1 = 'parse1';
 my $parse2 = 'parse2';
+
 my $application_path = "$application,APPLICATION,GENERAL";
+
+my $ncbiRefSeq_path = "$ncbiRefSeq$ncbiRefSeq_version,NAME,ANALYSIS,DATABASES";
 my $cosmic_path = "$cosmic$cosmic_version,NAME,ANALYSIS,DATABASES";
-my $refgene_path = "$refgene$refgene_version,NAME,ANALYSIS,DATABASES";
+my $dbsnp_path = "$dbsnp$dbsnp_version,NAME,ANALYSIS,DATABASES";
+my $clinvar_path = "$clinvar$clinvar_version,NAME,ANALYSIS,DATABASES";
+my $class_path = "$class$class_version,NAME,ANALYSIS,DATABASES";
 
-#(sub, key, database/applicatie, APPLICATION/NAME, GENERAL/ANALYSIS;DATABASE)
-
+#blocks to build command
 my @command_building_blocks = ( 
 "$language",
 "$parse1,PATHSCRIPTS,$application_path",
-"$parse1,CODING_ANNOVAR,$application_path",
+"$parse1,TABLE_ANNOVAR,$application_path",
 "$invcf",
 "$parse1,LOCATION_DATABASE,$application_path",
 "$parse1,SPECIES,$application_path",
 "$parse1,BUILD,$application_path",
 "$parse1,REMOVE,$application_path",
 "--protocol \'",
-"$parse2,PROTOCOL,$cosmic_path",
-",",
-"$parse2,PROTOCOL,$refgene_path",
+"$parse2,NAME,$ncbiRefSeq_path",
+"\,",
+"$parse2,NAME,$cosmic_path",
+"\,",
+"$parse2,NAME,$dbsnp_path",
+"\,",
+"$parse2,NAME,$clinvar_path",
+"\,",
+"$parse2,NAME,$class_path",
 "\' ",
 "--operation \'",
+"$parse2,OPERATION,$ncbiRefSeq_path",
+"\'",
+"\,",
+"\'",
 "$parse2,OPERATION,$cosmic_path",
-",",
-"$parse2,OPERATION,$refgene_path",
+#"\'\,\'",
+"\'",
+"\,",
+"\'",
+"$parse2,OPERATION,$dbsnp_path",
+#"\'\,\'",
+"\'",
+"\,",
+"\'",
+"$parse2,OPERATION,$clinvar_path",
+#"\'\,\'",
+"\'",
+"\,",
+"\'",
+"$parse2,OPERATION,$class_path",
 "\' ",
 "$parse1,DOT2UNDERLINE,$application_path",
 "$parse1,OTHERINFO,$application_path",
 "$parse1,NASTRING,$application_path",
 "$parse1,INPUTFORMAT,$application_path",
 "--arg \'",
-"$parse2,COLSWANTED,$cosmic_path",
+"$parse2,HGVS,$ncbiRefSeq_path",
+"$parse2,SPLICING,$ncbiRefSeq_path",
+"$parse2,EXONSPLIC,$ncbiRefSeq_path",
+#"\'\,\'",
 "\'",
-",",
+"\,",
+"\'",
+"$parse2,COLSWANTED,$cosmic_path",
+#"\'\,\'",
+"\'",
+"\,",
 "\'",
-"$parse2,HGVS,$refgene_path",
-"$parse2,SPLICING,$refgene_path",
-"$parse2,EXONSPLIC,$refgene_path",
+"$parse2,COLSWANTED,$dbsnp_path",
+#"\'\,\'",
+"\'",
+"\,",
+"\'",
+"$parse2,COLSWANTED,$clinvar_path",
+#"\'\,\'",
+"\'",
+"\,",
+"\'",
+"$parse2,COLSWANTED,$class_path",
 "\' ",
 "$parse1,THREAD,$application_path",
 "$parse1,POLISH,$application_path",
-"-out $outvcf "); 
+"-outfile $outvcf "); 
 
 print "\n";
 
@@ -504,34 +555,7 @@
 my $in_lookup;
 my ($pattern1, $pattern2, $pattern3, $pattern4, $pattern5);
 
-#Defin input yml
-
-#####################################
-
-print "Loading all yml hashes...\n";
-
-#$in = $inyml;
-#openyml_read($in);
-#$in = $inyml;
-#load($in);
-
-#$in = $inyml;
-#openyml_read($in);
-#$in = $inyml;
-#load_edit($in);
-
-#$in = $parameter_yml;
-#openyml_read($in);
-#$in = $parameter_yml;
-#load_arguments($in);
-
-######################################
-
-#foreach my $find_parameter (@{$yml_hash->{GENERAL}}) {
-#  print "each: $find_parameter\n";
-#  print "TESTINGTESTING_hash: $find_parameter->{SPECIES}\n";
-#}
-
+#Empty command
 my $test_command = "";
 
 foreach (@command_building_blocks) {
@@ -576,13 +600,9 @@
 
 print "\n";
 print "Resulting in following command: $test_command\n";
+system ($test_command);
 print "Job done program stopping.\n";
 
-
-#print "#####\n";
-#print "testing_stuff...\n";
-#print "#####\n";
-
 #testing parse2
 #%in = $inyml;
 #$pattern1 = "PROTOCOL";
@@ -608,7 +628,6 @@
 #!!!END OF SCRIPT!!!#
 ####################
 
-
 #############
 #SUBROUTINES#
 #############
@@ -630,13 +649,6 @@
 #############
 sub parse2 { 
 
-#Loading yml files for processing:
-
-#openyml_read ($_[0]);
-#openyml_read ($_[1]);
-#load ($_[0], %yml_hash, $yml_hash);
-#load_arguments ($_[1], %yml_hash_arguments, $yml_hash_arguments);
-
 #presetting variables
 $input = '';
 %input = '';
@@ -655,10 +667,8 @@
 my $pattern4 = $_[5];
 my $pattern5 = $_[6];
 
-
 print "Searching for matching parameter for: $pattern1...";
 
-
 for my $test_value_ANALYSIS (@{$yml_hash->{$pattern4}{$pattern5}}) {
   $count_key = 0;
   foreach my $key (keys $test_value_ANALYSIS) {
@@ -719,14 +729,6 @@
 #############
 sub parse1 {
 
-#print "element 0: $_[0]\n";
-#print "element 1: $_[1]\n";
-
-#openyml_read ($_[0], );
-#openyml_read ($_[1], );
-#load ($_[0], %yml_hash, $yml_hash);
-#load_arguments ($_[1], %yml_hash_arguments, $yml_hash_arguments);
-
 #presetting variables
 %input = '';
 $lookup = '';
@@ -743,13 +745,6 @@
 my $pattern3 = $_[4];
 my $pattern4 = $_[5];
 
-#print "element 2: $_[2]\n";
-#print "element 3: $_[3]\n";
-#print "element 4: $_[4]\n";
-#print "element 5: $_[5]\n";
-
-
-
 print "Searching for matching parameter for: $pattern1...";
 
 foreach my $find_parameter (@{$yml_hash->{$pattern4}}) {
@@ -845,6 +840,7 @@
 }
 
 #############
+#pen(FILE, '<', "$inyml") or die "Could not open file '$inyml' $!";
 ##
 ##############
 sub load {
diff -r 0925376a2624 -r 856448f167da annovar_yaml/annovar_yaml.xml
--- a/annovar_yaml/annovar_yaml.xml	Mon May 06 08:11:46 2019 -0400
+++ b/annovar_yaml/annovar_yaml.xml	Mon May 13 06:37:39 2019 -0400
@@ -20,6 +20,6 @@
         <data name="output" format="vcf"/>
     </outputs>
     <help><![CDATA[
-        TODO: Fill in help.
+        TODO: Fill in help for Annovar YAML tool.
     ]]></help>
 </tool>