Package TogoWS

TogoWS fetch entry (returns a handle).

db - database (string), see list below.
id - identier (string) or a list of identifiers (either as a list of
     strings or a single string with comma separators).
format - return data file format (string), options depend on the database
         e.g. "xml", "json", "gff", "fasta", "ttl" (RDF Turtle)
field - specific field from within the database record (string)
        e.g. "au" or "authors" for pubmed.

At the time of writing, this includes the following:

KEGG: compound, drug, enzyme, genes, glycan, orthology, reaction,
      module, pathway
DDBj: ddbj, dad, pdb
NCBI: nuccore, nucest, nucgss, nucleotide, protein, gene, onim,
      homologue, snp, mesh, pubmed
EBI:  embl, uniprot, uniparc, uniref100, uniref90, uniref50

For the current list, please see http://togows.dbcls.jp/entry/

This function is essentially equivalent to the NCBI Entrez service
EFetch, available in Biopython as Bio.Entrez.efetch(...), but that
does not offer field extraction.

TogoWS search count (returns an integer).

db - database (string), see http://togows.dbcls.jp/search
query - search term (string)

You could then use the count to download a large set of search results in
batches using the offset and limit options to Bio.TogoWS.search(). In
general however the Bio.TogoWS.search_iter() function is simpler to use.

TogoWS search iteratating over the results (generator function).

db - database (string), see http://togows.dbcls.jp/search
query - search term (string)
limit - optional upper bound on number of search results
batch - number of search results to pull back each time talk to
        TogoWS (currently limited to 100).

You would use this function within a for loop, e.g.

>>> for id in search_iter("pubmed", "lung+cancer+drug", limit=10):
...     print id #maybe fetch data with entry?

Internally this first calls the Bio.TogoWS.search_count() and then
uses Bio.TogoWS.search() to get the results in batches.

TogoWS search (returns a handle).

This is a low level wrapper for the TogoWS search function, which
can return results in a several formats. In general, the search_iter
function is more suitable for end users.

db - database (string), see http://togows.dbcls.jp/search/
query - search term (string)
offset, limit - optional integers specifying which result to start from
        (1 based) and the number of results to return.
format - return data file format (string), e.g. "json", "ttl" (RDF)
         By default plain text is returned, one result per line.

At the time of writing, TogoWS applies a default count limit of 100
search results, and this is an upper bound. To access more results,
use the offset argument or the search_iter(...) function.

TogoWS supports a long list of databases, including many from the NCBI
(e.g. "ncbi-pubmed" or "pubmed", "ncbi-genbank" or "genbank", and
"ncbi-taxonomy"), EBI (e.g. "ebi-ebml" or "embl", "ebi-uniprot" or
"uniprot, "ebi-go"), and KEGG (e.g. "kegg-compound" or "compound").
For the current list, see http://togows.dbcls.jp/search/

The NCBI provide the Entrez Search service (ESearch) which is similar,
available in Biopython as the Bio.Entrez.esearch() function.

See also the function Bio.TogoWS.search_count() which returns the number
of matches found, and the Bio.TogoWS.search_iter() function which allows
you to iterate over the search results (taking care of batching for you).

TogoWS convert (returns a handle).

data - string or handle containing input record(s)
in_format - string describing the input file format (e.g. "genbank")
out_format - string describing the requested output format (e.g. "fasta")

For a list of supported conversions (e.g. "genbank" to "fasta"), see
http://togows.dbcls.jp/convert/

Note that Biopython has built in support for conversion of sequence and
alignnent file formats (functions Bio.SeqIO.convert and Bio.AlignIO.convert)