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BP_BIOFLAT_INDEX(1p)					User Contributed Perl Documentation				      BP_BIOFLAT_INDEX(1p)

NAME
bioflat_index.pl - index sequence files using Bio::DB::Flat DESCRIPTION
Create or update a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed. USAGE
bioflat_index.pl <options> file1 file2 file3... Options: --create Create or reinitialize the index. If not specified, the index must already exist. --format <format> The format of the sequence files. Must be one of "genbank", "swissprot", "embl" or "fasta". --location <path> Path to the directory in which the index files are stored. --dbname <name> The symbolic name of the database to be created. --indextype <type> Type of index to create. Either "bdb" or "flat". "binarysearch" is the same as "flat". Options can be abbreviated. For example, use -i for --indextype. The following environment variables will be used as defaults if the corresponding options are not provided: OBDA_FORMAT format of sequence file OBDA_LOCATION path to directory in which index files are stored OBDA_DBNAME name of database OBDA_INDEX type of index to create perl v5.14.2 2012-03-02 BP_BIOFLAT_INDEX(1p)

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BP_SEQFEATURE_LOAD(1p)					User Contributed Perl Documentation				    BP_SEQFEATURE_LOAD(1p)

NAME
bp_seqfeature_load.pl - Load GFF into a SeqFeature database DESCRIPTION
Pass any number of GFF or fasta format files (or GFF with embedded fasta) to load the features and sequences into a SeqFeature database. The database (and adaptor) to use is specified on the command line. Use the --create flag to create a new SeqFeature database. SYNOPSIS
bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]] Try 'bp_seqfeature_load.pl --help' or '--man' for more information. OPTIONS
-d, --dsn DBI data source (default dbi:mysql:test) -n, --namespace The table prefix to use (default undef) Allows several independent sequence feature databases to be stored in a single database -s, --seqfeature The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature) -a, --adaptor The storage adaptor (class) to use (default DBI::mysql) -v, --verbose Turn on verbose progress reporting (default true) Use --noverbose to switch this off. -f, --fast Activate fast loading. (default 0) Only available for some adaptors. -T, --temporary-directory Specify temporary directory for fast loading (default File::Spec->tmpdir()) -i, --ignore-seqregion If true, then ignore ##sequence-region directives in the GFF3 file (default, create a feature for each region) -c, --create Create the database and reinitialize it (default false) Note, this will erase previous database contents, if any. -u, --user User to connect to database as -p, --password Password to use to connect to database -z, --zip Compress database tables to save space (default false) -S, --subfeatures Turn on indexing of subfeatures (default true) Use --nosubfeatures to switch this off. --summary Generate summary statistics for coverage graphs (default false) This can be run on a previously loaded database or during the load. It will default to true if --create is used. --noalias-target Don't create an Alias attribute whose value is the target_id in a Target attribute (if the feature contains a Target attribute, the default is to create an Alias attribute whose value is the target_id in the Target attribute) Please see http://www.sequenceontology.org/gff3.shtml for information about the GFF3 format. BioPerl extends the format slightly by adding a ##index-subfeatures directive. Set this to a true value if you wish the database to be able to retrieve a feature's individual parts (such as the exons of a transcript) independently of the top level feature: ##index-subfeatures 1 It is also possible to control the indexing of subfeatures on a case-by-case basis by adding "index=1" or "index=0" to the feature's attribute list. This should only be used for subfeatures. Subfeature indexing is true by default. Set to false(0) to save lots of database space and speed performance. You may use --nosubfeatures to force this. perl v5.14.2 2012-03-02 BP_SEQFEATURE_LOAD(1p)
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