07-28-2009
Getting Rid of Having to Write to Flat Files
Ok,
so i've been having to write to flat files lately and then making my script read information from the flat file and then work off of that.
i dont want to keep doing that because i believe it creates a mess. i like to keep my work all to one script instead of having that one script create temp files.
so, is there there a way to write the informationn that would have been written to a flat file to the memory and work off the memory as if it were a flat file?
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LEARN ABOUT DEBIAN
bp_bioflat_index
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)