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Merge pull request #3494 from solgenomics/fix_vcf_format
Fix vcf format in the VCF download. Transpose introduces some issues, also trailing tabs.
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,138 @@ | ||
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| =head1 NAME | ||
| load_dbxref.pl - a script to link marker_names with cvterm for external database link, this script uses the nd_protocolprop table | ||
| with a typdef_id | ||
| =head1 SYNOPSYS | ||
| load_locus_publications.pl -p [person_id] -H [hostname] -D [database name] -c dbxref -j protocol_id file | ||
| where file contains a column with marker names | ||
| if marker_name does not exist then do not insert | ||
| nd_protocolprop format { dbxref: dbxref_name, marker: {array of marker_names} } | ||
| To use an existing protocol (not create a new nd_protocol name entry), use -j protocol_id | ||
| =head1 COMMAND-LINE OPTIONS | ||
| ARGUMENTS | ||
| -H host name (required) e.g. "localhost" | ||
| -D database name (required) e.g. "cxgn_cassava" | ||
| -j protocol_id (Will associate genotype data to an existing nd_protocol_id) | ||
| =head1 AUTHOR | ||
| Clay Birkett <[email protected]> | ||
| =cut | ||
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| use strict; | ||
| use warnings; | ||
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| use Getopt::Std; | ||
| use File::Slurp qw | slurp |; | ||
| use CXGN::DB::InsertDBH; | ||
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| our %opts; | ||
| getopts('p:H:D:j:', \%opts); | ||
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| my $file = shift; | ||
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| my @lines = slurp($file); | ||
| chomp(@lines); | ||
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| my $dbh = CXGN::DB::InsertDBH->new( { dbname => $opts{D}, | ||
| dbhost => $opts{H}, | ||
| }); | ||
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| my $sth; | ||
| my @row; | ||
| my $alias; | ||
| my $count; | ||
| my $count_add; | ||
| my $marker_id; | ||
| my %alias_list; | ||
| my %marker_list; | ||
| my %unique_list; | ||
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| my $protocol_id = $opt_j; | ||
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| #if protocol_id provided, a new one will not be created | ||
| if ($protocol_id){ | ||
| my $protocol = CXGN::Genotype::Protocol->new({ | ||
| bcs_schema => $schema, | ||
| nd_protocol_id => $protocol_id | ||
| }); | ||
| $organism_species = $protocol->species_name; | ||
| $obs_type = $protocol->sample_observation_unit_type_name if !$obs_type; | ||
| } | ||
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| ##get list of current alias entries | ||
| ##use (marker_id, alias) as unique key so we don't duplicate entries | ||
| my $key; | ||
| $count = 0; | ||
| $sth = $dbh->prepare("SELECT alias, marker_id, preferred from marker_alias"); | ||
| $sth->execute(); | ||
| while (@row = $sth->fetchrow_array()) { | ||
| $count++; | ||
| $alias = $row[0]; | ||
| if ($row[2]) { | ||
| $marker_list{$alias} = $row[1]; | ||
| } else { | ||
| $alias_list{$alias} = $row[1]; | ||
| } | ||
| $key = $row[0] . $row[1]; | ||
| $unique_list{$key} = 1; | ||
| } | ||
| print "$count from marker_alias\n"; | ||
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| $count = 0; | ||
| $sth = $dbh->prepare("INSERT into marker_alias (marker_id, alias, preferred) values (?, ?, ?)"); | ||
| foreach my $l (@lines) { | ||
| $count++; | ||
| push (@marker_list, $alias); | ||
| } | ||
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| my ($marker_name, $alias) = split /\t/, $l; | ||
| my @alias_list = split /\|/, $alias; | ||
| if (exists($marker_list{$marker_name})) { | ||
| $marker_id = $marker_list{$marker_name}; | ||
| foreach (@alias_list) { | ||
| $key = $_ . $marker_id; | ||
| if (exists($unique_list{$key})) { | ||
| } else { | ||
| $count_add++; | ||
| $sth->execute($marker_id, $_, 0); | ||
| $alias_list{$_} = $marker_id; | ||
| } | ||
| } | ||
| } else { | ||
| $sth2 = $dbh->prepare("INSERT into marker (dummy_field) values (null) RETURNING marker_id"); | ||
| $sth2->execute(); | ||
| ($marker_id) = $sth2->fetchrow_array(); | ||
| $sth2 = $dbh->prepare("INSERT into marker_alias (marker_id, alias, preferred) values (?, ?, ?)"); | ||
| $sth2->execute($marker_id, $marker_name, 1); | ||
| print "added marker $marker_name $marker_id\n"; | ||
| foreach (@alias_list) { | ||
| $key = $_ . $marker_id; | ||
| if (exists($unique_list{$key})) { | ||
| } else { | ||
| $count_add++; | ||
| $sth->execute($marker_id, $_, 0); | ||
| $alias_list{$_} = $marker_id; | ||
| } | ||
| print "added alias $_\n"; | ||
| } | ||
| last; | ||
| } | ||
| } | ||
| print "$count total $count_add added\n"; | ||
| $dbh->commit(); | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| #!/usr/bin/env perl | ||
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| =head1 NAME | ||
| AddVcfType.pm | ||
| =head1 SYNOPSIS | ||
| mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F] | ||
| This patch add new cvterm vcf_snp_dbxref to nd_protocol | ||
| =head1 DESCRIPTION | ||
| This dbpatch adds vcf_snp_dbxref to nd_protocol and nd_protocolprop to provide external links to marker_names | ||
| =head1 AUTHOR | ||
| Clay Birkett<[email protected]> | ||
| =head1 COPYRIGHT & LICENSE | ||
| Copyright 2010 Boyce Thompson Institute for Plant Research | ||
| This program is free software; you can redistribute it and/or modify | ||
| it under the same terms as Perl itself. | ||
| =cut | ||
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| package AddVcfType; | ||
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| use Moose; | ||
| use Bio::Chado::Schema; | ||
| use Try::Tiny; | ||
| extends 'CXGN::Metadata::Dbpatch'; | ||
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| has '+description' => ( default => <<'' ); | ||
| This patch add new cvterm vcf_snp_dbxref to nd_protocol | ||
| has '+prereq' => ( | ||
| default => sub { | ||
| [], | ||
| }, | ||
| ); | ||
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| sub patch { | ||
| my $self=shift; | ||
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| print STDOUT "Executing the patch:\n " . $self->name . ".\n\nDescription:\n ". $self->description . ".\n\nExecuted by:\n " . $self->username . " ."; | ||
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| print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n"; | ||
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| print STDOUT "\nExecuting the SQL commands.\n"; | ||
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| my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } ); | ||
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| my $term = 'vcf_snp_dbxref'; | ||
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| $schema->resultset("Cv::Cvterm")->create_with( { | ||
| name => $term, | ||
| cv => 'protocol_property', } | ||
| ); | ||
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| print "You're done!\n"; | ||
| } | ||
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| #### | ||
| 1; # | ||
| #### |
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