scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl

   1 #!/usr/bin/perl
   2
   3 use strict;
   4 use warnings;
   5
   6 ## Used to output the 'usage' message
   7 use Pod::Usage;
   8
   9 ## Used to parse command line options
  10 use Getopt::Long;
  11
  12 ## Used to create temporary files, if necessary
  13 use File::Spec;
  14
  15 ## BioPerl!
  16 use Bio::DB::SeqFeature::Store;
  17 use Bio::DB::SeqFeature::Store::GFF3Loader;
  18
  19
  20
  21 ## The available options. Note, these defaults are 'hard coded' into
  22 ## the USAGE POD, so if you change one of the defaults (you shouldn't),
  23 ## you should update the USAGE.
  24
  25 my $DSN                 = 'dbi:mysql:test';
  26 my $SFCLASS             = 'Bio::DB::SeqFeature';
  27 my $ADAPTOR             = 'DBI::mysql';
  28 my $NAMESPACE;
  29 my $VERBOSE             = 1;
  30 my $FAST                = 0;
  31 my $TMP                 = File::Spec->tmpdir();
  32 my $IGNORE_SEQREGION    = 0;
  33 my $CREATE              = 0;
  34 my $USER                = '';
  35 my $PASS                = '';
  36 my $COMPRESS            = 0;
  37 my $INDEX_SUB           = 1;
  38 my $NOALIAS_TARGET      = 0;
  39 my $SUMMARY_STATS       = 0;
  40 my $NOSUMMARY_STATS  = 0;
  41 my $FTS = 0;
  42
  43 ## Two flags based on http://stackoverflow.com/questions/1232116
  44 ## how-to-create-pod-and-use-pod2usage-in-perl
  45 my $opt_help;
  46 my $opt_man;
  47
  48 GetOptions( 'd|dsn=s'                   => \$DSN,
  49             's|seqfeature=s'            => \$SFCLASS,
  50             'n|namespace=s'             => \$NAMESPACE,
  51             'a|adaptor=s'               => \$ADAPTOR,
  52             'v|verbose!'                => \$VERBOSE,
  53             'f|fast'                    => \$FAST,
  54             'T|temporary-directory=s'   => \$TMP,
  55             'i|ignore-seqregion'        => \$IGNORE_SEQREGION,
  56             'c|create'                  => \$CREATE,
  57             'u|user=s'                  => \$USER,
  58             'p|password=s'              => \$PASS,
  59             'z|zip'                     => \$COMPRESS,
  60             'S|subfeatures!'            => \$INDEX_SUB,
  61
  62             ## Any good single letter choices here?
  63             'noalias-target'            => \$NOALIAS_TARGET,
  64             'summary'                   => \$SUMMARY_STATS,
  65         'N|nosummary'    => \$NOSUMMARY_STATS,
  66             'fts'                       => \$FTS,
  67
  68             ## I miss '--help' when it isn't there!
  69             'h|help!'                   => \$opt_help,
  70             'm|man!'                    => \$opt_man,
  71           )
  72   or pod2usage( -message =>
  73                 "\nTry 'bp_seqfeature_load.pl --help' for more information\n",
  74                 -verbose => 0,
  75                 -exitval => 2,
  76               );
  77
  78 ## Should we output usage information?
  79 pod2usage( -verbose => 1 ) if $opt_help;
  80 pod2usage( -verbose => 2 ) if $opt_man;
  81
  82 ## Did we get any files to process?
  83 @ARGV
  84   or pod2usage( -message =>
  85                 "\nYou need to pass some GFF or fasta files to load\n",
  86                 -verbose => 0,
  87                 -exitval => 2,
  88               );
  89
  90 pod2usage( -message => "\n--fts requires --create\n",
  91            -verbose => 0,
  92            -exitval => 2,
  93 ) if ($FTS and not $CREATE);
  94
  95
  96 ## POD
  97
  98 =head1 NAME
  99
 100 bp_seqfeature_load.pl - Load GFF into a SeqFeature database
 101
 102 =head1 DESCRIPTION
 103
 104 Pass any number of GFF or fasta format files (or GFF with embedded
 105 fasta) to load the features and sequences into a SeqFeature
 106 database. The database (and adaptor) to use is specified on the
 107 command line. Use the --create flag to create a new SeqFeature
 108 database.
 109
 110 =head1 SYNOPSIS
 111
 112  bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]
 113
 114 Try 'bp_seqfeature_load.pl --help' or '--man' for more information.
 115
 116 =head1 OPTIONS
 117
 118 =over 4
 119
 120 =item -d, --dsn
 121
 122 DBI data source (default dbi:mysql:test)
 123
 124 =item -n, --namespace
 125
 126 The table prefix to use (default undef) Allows several independent
 127 sequence feature databases to be stored in a single database
 128
 129 =item -s, --seqfeature
 130
 131 The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)
 132
 133 =item -a, --adaptor
 134
 135 The storage adaptor (class) to use (default DBI::mysql)
 136
 137 =item -v, --verbose
 138
 139 Turn on verbose progress reporting (default true) Use --noverbose to
 140 switch this off.
 141
 142 =item -f, --fast
 143
 144 Activate fast loading. (default 0) Only available for some adaptors.
 145
 146 =item -T, --temporary-directory
 147
 148 Specify temporary directory for fast loading (default
 149 File::Spec->tmpdir())
 150
 151 =item -i, --ignore-seqregion
 152
 153 If true, then ignore ##sequence-region directives in the GFF3 file
 154 (default, create a feature for each region)
 155
 156 =item -c, --create
 157
 158 Create the database and reinitialize it (default false) Note, this
 159 will erase previous database contents, if any.
 160
 161 =item -u, --user
 162
 163 User to connect to database as
 164
 165 =item -p, --password
 166
 167 Password to use to connect to database
 168
 169 =item -z, --zip
 170
 171 Compress database tables to save space (default false)
 172
 173 =item -S, --subfeatures
 174
 175 Turn on indexing of subfeatures (default true) Use --nosubfeatures to
 176 switch this off.
 177
 178 =item --fts
 179
 180 Index the attribute table for full-text search (default false). Applicable
 181 only when --create is specified. Currently applicable to the DBI::SQLite
 182 storage adaptor only (using the most recent supported FTS indexing method,
 183 which may not be portable to older DBI::SQLite versions).
 184
 185 =item --summary
 186
 187 Generate summary statistics for coverage graphs (default false) This
 188 can be run on a previously loaded database or during the load. It will
 189 default to true if --create is used.
 190
 191 =item -N, --nosummary
 192
 193 Do not generate summary statistics to save some space and load time (default if
 194 --create is not specified, use this option to explicitly turn off summary
 195 statistics when --create is specified)
 196
 197 =item --noalias-target
 198
 199 Don't create an Alias attribute whose value is the target_id in a
 200 Target attribute (if the feature contains a Target attribute, the
 201 default is to create an Alias attribute whose value is the target_id
 202 in the Target attribute)
 203
 204 =back
 205
 206 Please see http://www.sequenceontology.org/gff3.shtml for information
 207 about the GFF3 format. BioPerl extends the format slightly by adding a
 208 ##index-subfeatures directive. Set this to a true value if you wish
 209 the database to be able to retrieve a feature's individual parts (such
 210 as the exons of a transcript) independently of the top level feature:
 211
 212   ##index-subfeatures 1
 213
 214 It is also possible to control the indexing of subfeatures on a
 215 case-by-case basis by adding "index=1" or "index=0" to the feature's
 216 attribute list. This should only be used for subfeatures.
 217
 218 Subfeature indexing is true by default. Set to false (0) to save lots
 219 of database space and speed performance. You may use --nosubfeatures
 220 to force this.
 221
 222 =cut
 223
 224
 225
 226
 227
 228 if ($FAST) {
 229   -d $TMP && -w $TMP
 230     or die "Fast loading is requested, but I cannot write into the directory $TMP";
 231   $DSN .= ";mysql_local_infile=1" if $ADAPTOR =~ /mysql/i && $DSN !~ /mysql_local_infile/;
 232 }
 233
 234 my @options;
 235 @options = ($USER,$PASS) if $USER || $PASS;
 236
 237 my $store = Bio::DB::SeqFeature::Store->new
 238 (
 239     -dsn        => $DSN,
 240     -namespace  => $NAMESPACE,
 241     -adaptor    => $ADAPTOR,
 242     -tmpdir     => $TMP,
 243     -user       => $USER,
 244     -pass       => $PASS,
 245     -write      => 1,
 246     -create     => $CREATE,
 247     -compress   => $COMPRESS,
 248     -fts        => $FTS,
 249 )
 250 or die "Couldn't create connection to the database";
 251
 252 $store->init_database('erase') if $CREATE;
 253 $SUMMARY_STATS++               if $CREATE; # this is a good thing
 254
 255 my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new
 256 (
 257     -store              => $store,
 258     -sf_class           => $SFCLASS,
 259     -verbose            => $VERBOSE,
 260     -tmpdir             => $TMP,
 261     -fast               => $FAST,
 262     -ignore_seqregion   => $IGNORE_SEQREGION,
 263     -index_subfeatures  => $INDEX_SUB,
 264     -noalias_target     => $NOALIAS_TARGET,
 265     -summary_stats      => $NOSUMMARY_STATS ? 0 : $SUMMARY_STATS,
 266 )
 267 or die "Couldn't create GFF3 loader";
 268
 269 # on signals, give objects a chance to call their DESTROY methods
 270 $SIG{TERM} = $SIG{INT} = sub {  undef $loader; undef $store; die "Aborted..."; };
 271
 272 $loader->load(@ARGV);
 273
 274 exit 0;