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bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.
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% bp_load_gff.pl -d testdb -u user -p pw
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--dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
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dna1.fa dna2.fa features1.gff features2.gff ...
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This script loads a Bio::DB::GFF database with the features contained
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in a list of GFF files and/or FASTA sequence files. You must use the
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exact variant of GFF described in L<Bio::DB::GFF>. Various
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command-line options allow you to control which database to load and
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whether to allow an existing database to be overwritten.
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This script uses the Bio::DB::GFF interface, and so works with all
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database adaptors currently supported by that module (MySQL, Oracle,
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PostgreSQL soon). However, it is slow. For faster loading, see the
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MySQL-specific L<bp_bulk_load_gff.pl> and L<bp_fast_load_gff.pl> scripts.
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If the filename is given as "-" then the input is taken from standard
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input. Compressed files (.gz, .Z, .bz2) are automatically
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FASTA format files are distinguished from GFF files by their filename
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extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
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uppercase variants are treated as FASTA files. Everything else is
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treated as a GFF file. If you wish to load -fasta files from STDIN,
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then use the -f command-line swith with an argument of '-', as in
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gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
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On the first load of a database, you will see a number of "unknown
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table" errors. This is normal.
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About maxfeature: the default value is 100,000,000 bases. If you have
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features that are close to or greater that 100Mb in length, then the
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value of maxfeature should be increased to 1,000,000,000, or another
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=head1 COMMAND-LINE OPTIONS
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Command-line options can be abbreviated to single-letter options.
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e.g. -d instead of --database.
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--dsn <dsn> Data source (default dbi:mysql:test)
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--adaptor <adaptor> Schema adaptor (default dbi::mysqlopt)
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--user <user> Username for mysql authentication
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--pass <password> Password for mysql authentication
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--fasta <path> Fasta file or directory containing fasta files for the DNA
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--create Force creation and initialization of database
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--maxfeature Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
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--group A list of one or more tag names (comma or space separated)
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to be used for grouping in the 9th column.
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--upgrade Upgrade existing database to current schema
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--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
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--quiet No progress reports
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--summary Generate summary statistics for drawing coverage histograms.
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This can be run on a previously loaded database or during
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L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<bp_load_gff.pl>
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Lincoln Stein, lstein@cshl.org
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Copyright (c) 2002 Cold Spring Harbor Laboratory
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This library is free software; you can redistribute it and/or modify
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it under the same terms as Perl itself. See DISCLAIMER.txt for
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disclaimers of warranty.
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my ($DSN,$ADAPTOR,$CREATE,$USER,$PASSWORD,$FASTA,$UPGRADE,$MAX_BIN,$GROUP_TAG,$MUNGE,$QUIET,$SUMMARY_STATS);
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GetOptions ('dsn:s' => \$DSN,
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'adaptor:s' => \$ADAPTOR,
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'p|password:s' => \$PASSWORD,
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'upgrade' => \$UPGRADE,
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'maxbin|maxfeature:s' => \$MAX_BIN,
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'group:s' => \$GROUP_TAG,
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'gff3_munge' => \$MUNGE,
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'summary' => \$SUMMARY_STATS,
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'create' => \$CREATE) or (system('pod2text',$0), exit -1);
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# some local defaults
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$DSN ||= 'dbi:mysql:test';
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$ADAPTOR ||= 'dbi::mysqlopt';
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$MAX_BIN ||= 1_000_000_000; # to accomodate human-sized chromosomes
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push @args,(-user=>$USER) if defined $USER;
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push @args,(-pass=>$PASSWORD) if defined $PASSWORD;
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push @args,(-preferred_groups=>[split(/[,\s+]+/,$GROUP_TAG)]) if defined $GROUP_TAG;
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push @args,(-create=>1) if $CREATE;
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push @args,(-write=>1);
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my $db = Bio::DB::GFF->new(-adaptor=>$ADAPTOR,-dsn => $DSN,@args)
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or die "Can't open database: ",Bio::DB::GFF->error,"\n";
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$db->gff3_name_munging(1) if $MUNGE;
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$MAX_BIN ? $db->initialize(-erase=>1,-MAX_BIN=>$MAX_BIN) :
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warn qq(expect to see several "table already exists" messages\n);
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my $dbi = $db->dbh; # get the raw database handle
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my ($count) = $dbi->selectrow_array('SELECT COUNT(*) FROM fnote');
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if (defined($count) && $count > 0) {
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warn qq(fnote table detected. Translating into fattribute table. This may take a while.\n);
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$dbi->do("INSERT INTO fattribute VALUES (1,'Note')") or die "failed: ",$dbi->errstr;
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$dbi->do("INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) SELECT fnote.fid,1,fnote FROM fnote") or die "failed: ",$dbi->errstr;
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warn qq(Schema successfully upgraded. You might want to drop the fnote table when you're sure everything's working.\n);
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if (/\.(fa|fasta|dna|seq|fast)$/i) {
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for my $file (@gff) {
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warn "$file: loading...\n";
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my $loaded = $db->load_gff($file,!$QUIET);
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warn "$file: $loaded records loaded\n";
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unshift @fasta,$FASTA if defined $FASTA;
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for my $file (@fasta) {
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warn "Loading fasta ",(-d $file?"directory":"file"), " $file\n";
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my $loaded = $db->load_fasta($file,!$QUIET);
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warn "$file: $loaded records loaded\n";
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if ($SUMMARY_STATS) {
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warn "Building summary statistics for coverage histograms...\n";
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$db->build_summary_statistics;
added
removed
scripts/Bio-DB-GFF/bp_load_gff.pl
