_strip_and_combine ( line_list )

Combine multiple lines of content separated by spaces.

This function is used by the EventGenerator callback function to combine multiple lines of information. The lines are first stripped to remove whitepsace, and then combined so they are separated by a space. This is a simple minded way to combine lines, but should work for most cases.

download_many (
        gis,
        callback_fn,
        broken_fn=None,
        db='Nucleotide',
        delay=127.0,
        batchsize=500,
        parser=None,
        )

download_many(gis, callback_fn[, delay][, batchsize])

Download many records from GenBank. gis is a list of Genbank Gi's. Each time a record is downloaded, callback_fn is called with the text of the record. delay is the number of seconds to wait between requests. Waits 127 seconds by default. abatchsize is the number of records to request each time. Default is 500 records, which is the maximum NCBI can handle.

This does not check to make sure all gi's are returned. The client must make sure that the gi's are valid. This may be implemented in the future.

index_file (
        genbank_file,
        index_file,
        rec_to_key=None,
        )

Index a GenBank file to prepare it for use as a dictionary.

Arguments: o genbank_file - The name of the GenBank file to be index. o index_name - The name of the index file which will be created. o rec_to_key - A function object which, when called with a GenBank record object, will return a key to be used for the record. If no function is specified, then the accession numbers will be used as the keys.

index_file_db (
        genbank_file,
        db_name,
        db_directory,
        identifier="locus",
        aliases=[ "accession" ],
        keywords=[],
        always_index=0,
        )

Index a GenBank file into a database for quick loading.

WARNING: This is very experimental and subject to change. It requires the use of Andrew Dalke's mindy.

This is very similar to index_file, but uses a database instead of a flat file to store the information about the genbank_file.

Arguments:

• genbank_file - The GenBank formatted file that we want to index.

• db_name - The name of the database to create. This name will allow you to retrieve the file later.

• db_directory - The directory where the database information should be stored.

• identifier - The primary identifier used to store records in the file under. This will be used for retrieving them later.

• aliases - Secondary identifiers that point to the record. These can be used for searching if a primary identifier is not found. This is useful for GenBank since we'll index by a single identifier (the LOCUS identifier by default) but might want to search by some other identifier.

• keywords - More advanced Mindy features that I'm not positive how to make full use of right now.

• always_index - A flag indicating whether or not to index a file even if the file appears not to have changed. By default, the function will try to skip indexing if it thinks the file hasn't changed.

search_for (
        search,
        database='Nucleotide',
        max_ids=500,
        )

search_for(search[, database][, max_ids])

Search GenBank and return a list of GenBank identifiers (gi's). search is the search string used to search the database. database should be either Nucleotide or Protein. max_ids is the maximum number of ids to retrieve (default 500).