.\" Automatically generated by Pod::Man 4.11 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "BP_FETCH 1p" .TH BP_FETCH 1p "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" bp_fetch.pl \- fetches sequences from bioperl indexed databases .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& bp_fetch.pl swiss:ROA1_HUMAN \& \& bp_fetch.pl net::genbank:JX295726 \& \& bp_fetch.pl net::genpept:ROA1_HUMAN \& \& bp_fetch.pl ace::myserver.somewhere.edu,21000:X56676 \& \& bp_fetch.pl \-fmt GCG swiss:ROA1_HUMAN .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Fetches sequences using the \s-1DB\s0 access systems in Bioperl. The most common use of this is to bp_fetch sequences from bioperl indices built using bpindex.pl, or to fetch sequences from the \s-1NCBI\s0 website .PP The format for retrieving sequences is delibrately like the \&\s-1GCG/EMBOSS\s0 format like the following: .PP .Vb 1 \& db:name .Ve .PP with the potential of putting in a 'meta' database type, being .PP .Vb 1 \& meta::db:name .Ve .PP The meta information can be one of three types .PP .Vb 3 \& local \- local indexed flat file database \& net \- networked http: based database \& ace \- ACeDB database .Ve .PP This information defaults to 'local' for database names with no meta db information .SH "OPTIONS" .IX Header "OPTIONS" .Vb 4 \& \-fmt \- Output format \& Fasta (default), EMBL, Raw, swiss or GCG \& \-acc \- string is an accession number, not an \& id. .Ve .PP options only for expert use .PP .Vb 4 \& \-dir \- directory to find the index files \& (overrides BIOPERL_INDEX environment variable) \& \-type \- type of DBM file to open \& (overrides BIOPERL_INDEX_TYPE environment variable) .Ve .SH "ENVIRONMENT" .IX Header "ENVIRONMENT" bp_index and bp_fetch coordinate where the databases lie using the environment variable \s-1BIOPERL_INDEX.\s0 This can be overridden using the \&\-dir option. The index type (\s-1SDBM\s0 or DB_File or another index file) is controlled by the \s-1BIOPERL_INDEX_TYPE\s0 variable. This defaults to SDBM_File .SH "USING IT YOURSELF" .IX Header "USING IT YOURSELF" bp_fetch is a wrapper around the bioperl modules which support the Bio::DB::BioSeqI abstract interface. These include: .PP .Vb 1 \& Author Code \& \& James Gilbert \- Fasta indexer, Abstract indexer \& Aaron Mackay \- GenBank and GenPept DB access \& Ewan Birney \- EMBL .dat indexer \& Many people \- SeqIO code .Ve .PP These modules can be used directly, which is far better than using this script as a system call or a pipe to read from. Read the source code for bp_fetch to see how it is used. .SH "EXTENDING IT" .IX Header "EXTENDING IT" bp_fetch uses a number of different modules to provide access to databases. Any module which subscribes to the Bio::DB::BioSeqI interface can be used here. For flat file indexers, this is best done by extending Bio::Index::Abstract, as is done in Bio::Index::EMBL and Bio::Index::Fasta. For access to other databases you will need to roll your own interface. .PP For new output formats, you need to add a new SeqIO module. The easiest thing is to look at Bio::SeqIO::Fasta and figure out how to hack it for your own format (call it something different obviously). .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "Mailing Lists" User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Reporting Bugs" .IX Subsection "Reporting Bugs" Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR" .IX Header "AUTHOR" Ewan Birney