1BP_FETCH(1) User Contributed Perl Documentation BP_FETCH(1)
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6 bp_fetch.pl - fetches sequences from bioperl indexed databases
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9 bp_fetch.pl swiss:ROA1_HUMAN
10 bp_fetch.pl net::genbank:X47072
12 bp_fetch.pl net::genpept:ROA1_HUMAN
14 bp_fetch.pl ace::myserver.somewhere.edu,21000:X56676
16 bp_fetch.pl -fmt GCG swiss:ROA1_HUMAN
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20 Fetches sequences using the DB access systems in Bioperl. The most com‐
21 mon use of this is to fetch sequences from bioperl indices built using
22 bpindex.pl, or to fetch sequences from the NCBI website
23 The format for retrieving sequences is delibrately like the GCG/EMBOSS
25 format like the following:
26 db:name
28 with the potential of putting in a 'meta' database type, being
30 meta::db:name
32 The meta information can be one of three types
34 local - local indexed flat file database
36 net - networked http: based database
37 ace - ACeDB database
38 This information defaults to 'local' for database names with no meta db
40 information
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43 -fmt <format> - Output format
44 Fasta (default), EMBL, Raw, swiss or GCG
45 -acc - string is an accession number, not an
46 id.
47 options only for expert use
49 -dir <dir> - directory to find the index files
51 (overrides BIOPERL_INDEX environment varaible)
52 -type <type> - type of DBM file to open
53 (overrides BIOPERL_INDEX_TYPE environment variable)
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56 bp_index and bp_fetch coordinate where the databases lie using the
57 enviroment variable BIOPERL_INDEX. This can be overridden using the
58 -dir option. The index type (SDBM or DB_File or another index file) is
59 controlled by the BIOPERL_INDEX_TYPE variable. This defaults to
60 SDBM_File
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63 bp_fetch is a wrapper around the bioperl modules which support the
64 Bio::DB::BioSeqI abstract interface. These include:
65 Author Code
67 James Gilbert - Fasta indexer, Abstract indexer
69 Aaron Mackay - GenBank and GenPept DB access
70 Ewan Birney - EMBL .dat indexer
71 Many people - SeqIO code
72 These modules can be used directly, which is far better than using this
74 script as a system call or a pipe to read from. Read the source code
75 for bp_fetch to see how it is used.
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78 bp_fetch uses a number of different modules to provide access to data‐
79 bases. Any module which subscribes to the Bio::DB::BioSeqI interface
80 can be used here. For flat file indexers, this is best done by extend‐
81 ing Bio::Index::Abstract, as is done in Bio::Index::EMBL and
82 Bio::Index::Fasta. For access to other databases you will need to roll
83 your own interface.
84 For new output formats, you need to add a new SeqIO module. The easiest
86 thing is to look at Bio::SeqIO::Fasta and figure out how to hack it for
87 your own format (call it something different obviously).
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90 Mailing Lists
91 User feedback is an integral part of the evolution of this and other
93 Bioperl modules. Send your comments and suggestions preferably to the
94 Bioperl mailing list. Your participation is much appreciated.
95 bioperl-l@bioperl.org - General discussion
97 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
98 Reporting Bugs
100 Report bugs to the Bioperl bug tracking system to help us keep track of
102 the bugs and their resolution. Bug reports can be submitted via the
103 web:
104 http://bugzilla.open-bio.org/
106
108 Ewan Birney <birney@ebi.ac.uk>
109perl v5.8.8 2007-05-07 BP_FETCH(1)