Man page - bp_bioflat_index(1)

Packages contas this manual

Package:  bioperl
apt-get install bioperl

Manuals in package:
• bp_process_sgd(1)
• bp_genbank2gff3(1)
• bp_make_mrna_protein(1)
• bp_search2alnblocks(1)
• bp_seqret(1)
• bp_fetch(1)
• bp_seqretsplit(1)
• bp_mrtrans(1)
• bp_index(1)
• bp_extract_feature_seq(1)
• bp_seqcut(1)
• bp_nexus2nh(1)
• bp_aacomp(1)
• bp_gccalc(1)
• bp_unflatten_seq(1)
• bp_local_taxonomydb_query(1)
• bp_dbsplit(1)
• bp_process_gadfly(1)
• bp_oligo_count(1)
• bp_nrdb(1)
• bp_seqpart(1)
• bp_tree2pag(1)
• bp_taxonomy2tree(1)
• bp_filter_search(1)
• bp_bioflat_index(1)
• bp_taxid4species(1)
• bp_split_seq(1)
• bp_find-blast-matches(1)
• bp_mask_by_search(1)
• bp_mutate(1)
• bp_seqconvert(1)
• bp_search2gff(1)
• bp_fastam9_to_table(1)
• bp_seq_length(1)
• bp_biogetseq(1)
• bp_translate_seq(1)
• bp_search2table(1)
• bp_sreformat(1)
• bp_revtrans-motif(1)
• bp_search2tribe(1)
Documentations in package:
• bioperl

Manual

 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.

 bp_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".

     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