| Previous changeset 14:94ddfdeb1d38 (2019-05-14) Next changeset 16:fe3deb1dc20b (2019-06-07) |
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Commit message:
Uploaded |
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modified:
annovar_yaml/YAML_annovar.yml annovar_yaml/YAML_arguments_annovar.yml annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml |
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| diff -r 94ddfdeb1d38 -r 7f4fb56714e8 annovar_yaml/YAML_annovar.yml --- a/annovar_yaml/YAML_annovar.yml Tue May 14 07:49:56 2019 -0400 +++ b/annovar_yaml/YAML_annovar.yml Fri Jun 07 09:23:41 2019 -0400 |
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| @@ -3,7 +3,7 @@ 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/' + LOCATION_DATABASE: ' /hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/' DOT2UNDERLINE: 'yes' NASTRING: '.' OTHERINFO: 'yes' @@ -16,6 +16,7 @@ ANALYSIS: DATABASES: - NAME: 'cosmic84' + ALIAS: 'N/A' PROTOCOL: 'cosmic' VERSION: '84' COMMENT: '20190221' @@ -24,6 +25,7 @@ OPERATION: 'f' COLSWANTED: '4' - NAME: 'refgene19' + ALIAS: 'N/A' PROTOCOL: 'refgene' VERSION: '19' AVAILABLE: 'yes' @@ -34,6 +36,7 @@ SPLICING: '6' EXONSPLIC: 'yes' - NAME: 'ncbiRefSeq_UMCU' + ALIAS: 'Annotation' PROTOCOL: 'ncbiRefSeq' VERSION: '_UMCU' AVAILABLE: 'yes' @@ -44,6 +47,7 @@ SPLICING: '6' EXONSPLIC: 'yes' - NAME: 'avsnp150' + ALIAS: 'dbSNP' PROTOCOL: 'avsnp' VERSION: '150' AVAILABLE: 'yes' @@ -51,6 +55,7 @@ OPERATION: 'f' COLSWANTED: '1' - NAME: 'clinvar_20180603' + ALIAS: 'N/A' PROTOCOL: 'clinvar' VERSION: '_20180603' AVAILABLE: 'yes' @@ -58,6 +63,7 @@ OPERATION: 'f' COLSWANTED: '5' - NAME: 'class100519' + ALIAS: 'Class' PROTOCOL: 'class' VERSION: '100519' AVAILABLE: 'yes' |
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| diff -r 94ddfdeb1d38 -r 7f4fb56714e8 annovar_yaml/YAML_arguments_annovar.yml --- a/annovar_yaml/YAML_arguments_annovar.yml Tue May 14 07:49:56 2019 -0400 +++ b/annovar_yaml/YAML_arguments_annovar.yml Fri Jun 07 09:23:41 2019 -0400 |
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| @@ -3,7 +3,7 @@ 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/' + LOCATION_DATABASE: ' /hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/' DOT2UNDERLINE: yes: '--dot2underline ' no: '' @@ -27,6 +27,7 @@ ANALYSIS: DATABASES: - NAME: 'cosmic84' + ALIAS: 'N/A' PROTOCOL: 'cosmic' VERSION: '84' COMMENT: '20190221' @@ -39,6 +40,7 @@ OPERATION: 'f' COLSWANTED: '--colswanted 4 ' - NAME: 'refgene19' + ALIAS: 'N/A' PROTOCOL: 'refgene' VERSION: '19' COMMENT: '20190210' @@ -57,6 +59,7 @@ yes: '--exonicsplicing ' no: '' - NAME: 'ncbiRefSeq_UMCU' + ALIAS: 'Annotation' PROTOCOL: 'ncbiRefSeq' VERSION: '_UMCU' AVAILABLE: @@ -75,6 +78,7 @@ yes: '--exonicsplicing ' no: '' - NAME: 'avsnp150' + ALIAS: 'dbSNP' PROTOCOL: 'avsnp' VERSION: '150' AVAILABLE: @@ -86,6 +90,7 @@ OPERATION: 'f' COLSWANTED: '--colswanted 1 ' - NAME: 'clinvar_20180603' + ALIAS: 'N/A' PROTOCOL: 'clinvar' VERSION: '_20180603' COMMENT: 'blah' @@ -98,6 +103,7 @@ OPERATION: 'f' COLSWANTED: '--colswanted 5 ' - NAME: 'class100519' + ALIAS: 'Class' PROTOCOL: 'class' VERSION: '100519' AVAILABLE: |
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| diff -r 94ddfdeb1d38 -r 7f4fb56714e8 annovar_yaml/annovar_yaml.pl --- a/annovar_yaml/annovar_yaml.pl Tue May 14 07:49:56 2019 -0400 +++ b/annovar_yaml/annovar_yaml.pl Fri Jun 07 09:23:41 2019 -0400 |
| [ |
| b'@@ -1,4 +1,13 @@\n #/usr/bin/perl\n+#This code is using v4 of the Run_Annovar_vx.pl script!\n+\n+##################\n+#!!TEST COMMAND!!#\n+##################\n+#Following input required, input fixed currently to run limited Annovar settings\n+#perl annovar_yaml.pl --inyml YAML_annovar.yml --invcf invcf.vcf --outvcf outvcf.vcf > log.txt\n+\n+#Future prospects: ability to learn to read YAML files to pick up parameters. Manual definition of command line still required!\n \n #perl modules use\n use YAML;\n@@ -7,6 +16,9 @@\n use Data::Dumper;\n #use Data::YAML::Writer;\n use Getopt::Long;\n+use feature qw(postderef postderef_qq);\n+use feature qw(refaliasing);\n+#no warnings qw(experimental::postderef);\n use strict;\n \n #input required\n@@ -19,9 +31,12 @@\n #protocolversion [default required]\n \n #basic paramters\n+#Switch to enable disable Aliasses; enable=1 disable=0\n+my $use_alias = "1";\n my $edit = "0";\n my $run = "0";\n my $application = "0";\n+#arguments yaml file is fixed!\n my $parameter_yml = "YAML_arguments_annovar.yml";\n my $inyml;\n my $outyml;\n@@ -38,6 +53,8 @@\n my %in;\n my %in2;\n my $writer;\n+my $lookup;\n+my $data_type;\n \n #parameter applications\n my %annovarparameters_array;\n@@ -94,6 +111,9 @@\n my @match_value;\n my @readonly;\n my %editinyml;\n+my $folder_symlinks = \'0\';\n+my $path_symlinks;\n+my @softlink_building_blocks;\n \n #Fixed values for searching hashes\n my $level5 = "DATABASES";\n@@ -135,6 +155,8 @@\n \t\'splicing=s\' => \\$input_databases_splicing,\n );\n \n+chomp $invcf;\n+chomp $outvcf;\n \n #inactive options\n # \'drequired=s\' => \\$input_databases_required,\n@@ -175,9 +197,8 @@\n @readonly = ("hg19","human","mouse","mm10","annovar","VERSION","TABLE_ANNOVAR","refgene","cosmic");\n \n \n-#converting string into arrays\n+#converting input strings into input arrays\n @inprotocol = split (",", $inprotocol);\n-print "version $inprotocolversion\\n";\n @inprotocolversion = split (",", $inprotocolversion);\n @input_databases_colswanted = split (",", $input_databases_colswanted);\n @input_databases_exonicsplic = split (",", $input_databases_exonicsplic);\n@@ -356,109 +377,56 @@\n #load_arguments($in);\n #print "Finished loading arguments...\\n";\n \n-#Build command for application\n \n-################### stuff to replace with loop\n-\n-#Starting with Annovar\n-#$count = "0";\n-#foreach (@inprotocol) {\n-#$protocol .= "$_$inprotocolversion[$count]";\n-#print "protocol $inprotocol\\n";\n-#print "protocol_version $inprotocolversion\\n";\n-#if ($count+1 >= scalar @inprotocol) { } else { $protocol .= "\',\'"; };\n-#$count++; \n-#}\n-\n-#Make new array with protocol plus version\n-#@protocol = split (",", $protocol); \n-#foreach (@protocol) {\n-#print "print value: $_\\n";\n-#}\n-\n-#Required as input value, not pickup from yaml file!\n-#$operation = $input_databases_operation;\n-#$operation =~ s/,/\',\'/g;\n-\n-#$count= "0";\n-#foreach (@inprotocol) {\n-#if ( $_ =~ /refgene/ ) {\n-#print "Entering refgene...\\n";\n-#$argument .= "$yml_hash_arguments->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{HGVS}{$yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{HGVS}} ";\n-#$argument .= "--splicing $yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{SPLICING} "; \n-#$argument .= "$yml_hash_arguments->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{EXONSPLIC}{$yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{EXONSPLIC}}";\n-#if ($count+1 >= scalar @inprotocol) { } else { $argument .= "\',\'"; };\n-#} elsif ( $_ =~ /cosmic/ ) {\n-#print "Entering cosmic...\\n";\n-#$argument .= "--colswanted $yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{COLSWANTED}";\n-#if ($count+1 >= scalar @inprotocol) { } else { $argument .= "\',\'"; };\n-#} \n-#$'..b':$key2:$key3:$key4:$key5:$key6:$key7:$key8 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}\\n";\n- }\n-\t\t\t\t\t\t }\n- } else {\n-\t\t\t\t\t\tmy $value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}";\n-\t\t\t\t\t\tif ( $value =~ /$pattern/ ) {\n-\t\t\t\t\t\t $match++;\n-\t\t\t\t\t\t $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}";\n- #print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}\\n";\n-\t\t\t\t\t\t}\n-\t\t\t\t\t\t#print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}\\n";\n- }\n- }\n- } else {\n-\t\t\t\t\t my $value = "$key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}";\n-\t\t\t\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t\t\t $match++;\n-\t\t\t\t\t $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}";\n- #print "value: $key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}\\n";\n-\t\t\t\t\t }\n-\t\t\t\t\t #print "value: $key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}\\n";\n- }\n- }\n- } else {\n-\t\t\t\t my $value = "$key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}";\n-\t\t\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t\t $match++;\n-\t\t\t\t $match_value = "$key1:$key2:$key3:$key4:$key5:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}";\n- #print "value: $key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}\\n";\n-\t\t\t\t }\n-\t\t\t\t #print "value: $key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}\\n";\n- }\n- }\n- } else {\n-\t\t\t my $value = "$key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}";\n-\t\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t $match++;\n-\t\t\t $match_value = "$key1:$key2:$key3:$key4:$yml_hash->{$key1}{$key2}{$key3}{$key4}";\n- #print "value: $key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}\\n";\n-\t\t\t }\n-\t\t\t #print "value: $key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}\\n";\n- }\n- }\n- } else {\n-\t\t my $value = "$key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}";\n-\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t$match++;\n-\t\t\t$match_value = "$key1:$key2:$key3:$yml_hash->{$key1}{$key2}{$key3}";\n- #print "value: $key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}\\n";\n-\t\t }\n-\t\t #print "value: $key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}\\n";\n- }\n- }\n- } else {\n-\t my $value = "$key1:$key2 $yml_hash->{$key1}{$key2}";\n-\t if ( $value =~ /$pattern/ ) {\n-\t\t$match++;\n-\t\t$match_value = "$key1:$key2:$yml_hash->{$key1}{$key2}";\n- #print "value: $key1:$key2 $yml_hash->{$key1}{$key2}\\n";\n-\t }\n-\t #print "value: $key1:$key2 $yml_hash->{$key1}{$key2}\\n";\n- }\n- }\n- } else {\n- my $value = "$key1 $yml_hash->{$key1}";\n- if ( $value =~ /$pattern/ ) {\n-\t$match++;\n-\t$match_value = "$key1:$yml_hash->{$key1}";\n- #print "value: $key1 $yml_hash->{$key1}\\n";\n- }\n- #print "value: $key1 $yml_hash->{$key1}\\n";\n- }\n-}\n-\n-print "Match: $match\\n";\n-\n-return $match;\n-return $match_value;\n-} \n' |
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| diff -r 94ddfdeb1d38 -r 7f4fb56714e8 annovar_yaml/annovar_yaml.xml --- a/annovar_yaml/annovar_yaml.xml Tue May 14 07:49:56 2019 -0400 +++ b/annovar_yaml/annovar_yaml.xml Fri Jun 07 09:23:41 2019 -0400 |
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| @@ -1,14 +1,14 @@ -<tool id="annovar_yaml" name="Annovar YAML" version="1.1"> +<tool id="annovar_yaml" name="Annovar YAML" version="1.0"> <requirements> <requirement type="package" version="5.22.0">perl</requirement> - <requirement type="package" version="1.24">perl-yaml</requirement> - <requirement type="package" version="1.70">perl-yaml-tiny</requirement> + <requirement type="package" version="1.27">perl-yaml</requirement> + <requirement type="package" version="1.73">perl-yaml-tiny</requirement> <requirement type="package" version="0.74">perl-yaml-xs</requirement> - <requirement type="package" version="2.161">perl-data-dumper</requirement> + <requirement type="package" version="2.173">perl-data-dumper</requirement> <requirement type="package" version="2.50">perl-getopt-long</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - which perl && perl $__tool_directory__/annovar_yaml.pl --invcf $vcf --inyml $yaml --outvcf $output + perl $__tool_directory__/annovar_yaml.pl --invcf $vcf --inyml $yaml --outvcf $output ]]></command> <inputs> |