bp_seqfeature_load(1p) [debian man page]
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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BP_FAST_LOAD_GFF(1p) User Contributed Perl Documentation BP_FAST_LOAD_GFF(1p) NAME
bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files. SYNOPSIS
% bp_fast_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ... DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained in a list of GFF files and/or FASTA sequence files. You must use the exact variant of GFF described in Bio::DB::GFF. Various command-line options allow you to control which database to load and whether to allow an existing database to be overwritten. This script is similar to load_gff.pl, but is much faster. However, it is hard-coded to use MySQL and probably only works on Unix platforms due to its reliance on pipes. See bp_load_gff.pl for an incremental loader that works with all databases supported by Bio::DB::GFF, and bp_bulk_load_gff.pl for a fast MySQL loader that supports all platforms. NOTES If the filename is given as "-" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically uncompressed. FASTA format files are distinguished from GFF files by their filename extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their uppercase variants are treated as FASTA files. Everything else is treated as a GFF file. If you wish to load -fasta files from STDIN, then use the -f command-line swith with an argument of '-', as in gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f - The nature of the load requires that the database be on the local machine and that the indicated user have the "file" privilege to load the tables and have enough room in /usr/tmp (or whatever is specified by the $TMPDIR environment variable), to hold the tables transiently. If your MySQL is version 3.22.6 and was compiled using the "load local file" option, then you may be able to load remote databases with local data using the --local option. About maxfeature: the default value is 100,000,000 bases. If you have features that are close to or greater that 100Mb in length, then the value of maxfeature should be increased to 1,000,000,000. This value must be a power of 10. If the list of GFF or fasta files exceeds the kernel limit for the maximum number of command-line arguments, use the --long_list /path/to/files option. The adaptor used is dbi::mysqlopt. There is currently no way to change this. COMMAND-LINE OPTIONS Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database. --database <dsn> Mysql database name --create Reinitialize/create data tables without asking --local Try to load a remote database using local data. --user Username to log in as --fasta File or directory containing fasta files to load --password Password to use for authentication --long_list Directory containing a very large number of GFF and/or FASTA files --maxfeature Set the value of the maximum feature size (default 100Mb; must be a power of 10) --group A list of one or more tag names (comma or space separated) to be used for grouping in the 9th column. --gff3_munge Activate GFF3 name munging (see Bio::DB::GFF) --summary Generate summary statistics for drawing coverage histograms. This can be run on a previously loaded database or during the load. --Temporary Location of a writable scratch directory SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl AUTHOR
Lincoln Stein, lstein@cshl.org Copyright (c) 2002 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. perl v5.14.2 2012-03-02 BP_FAST_LOAD_GFF(1p)