| Previous changeset 4:0925376a2624 (2019-05-06) Next changeset 6:a55510bb8478 (2019-05-14) |
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Commit message:
Uploaded |
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modified:
annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml |
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added:
annovar_yaml/YAML_annovar.yml annovar_yaml/YAML_arguments_annovar.yml |
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removed:
annovar_yaml/AnnovarArguments.yml annovar_yaml/AnnovarInput.yml |
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| 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 |
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| @@ -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: '' |
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| 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 |
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| @@ -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' |
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| 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 |
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| @@ -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' |
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| 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 |
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| @@ -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 ' + |
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| 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 |
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| @@ -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 { |
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| 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 |
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| @@ -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> |