def search_count(db, query):
"""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.
"""
global _search_db_names
if _search_db_names is None:
_search_db_names = _get_fields(_BASE_URL + "/search")
if db not in _search_db_names:
#TODO - Make this a ValueError? Right now despite the HTML website
#claiming to, the "gene" or "ncbi-gene" don't work and are not listed.
import warnings
warnings.warn("TogoWS search does not officially support database '%s'. "
"See %s/search/ for options." % (db, _BASE_URL))
url = _BASE_URL + "/search/%s/%s/count" % (db, _quote(query))
handle = _open(url)
data = handle.read()
handle.close()
try:
count = int(data.strip())
except ValueError:
raise ValueError("Expected an integer from URL %s, got: %r" % (url, data))
return count
def search_count(db, query):
"""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.
"""
global _search_db_names
if _search_db_names is None:
_search_db_names = _get_fields(_BASE_URL + "/search")
if db not in _search_db_names:
#TODO - Make this a ValueError? Right now despite the HTML website
#claiming to, the "gene" or "ncbi-gene" don't work and are not listed.
import warnings
warnings.warn(
"TogoWS search does not officially support database '%s'. "
"See %s/search/ for options." % (db, _BASE_URL))
url = _BASE_URL + "/search/%s/%s/count" % (db, _quote(query))
handle = _open(url)
data = handle.read()
handle.close()
try:
count = int(data.strip())
except ValueError:
raise ValueError("Expected an integer from URL %s, got: %r" %
(url, data))
return count
def entry(db, id, format=None, field=None):
"""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.
"""
global _entry_db_names, _entry_db_fields, fetch_db_formats
if _entry_db_names is None:
_entry_db_names = _get_entry_dbs()
if db not in _entry_db_names:
raise ValueError("TogoWS entry fetch does not officially support "
"database '%s'." % db)
if field:
try:
fields = _entry_db_fields[db]
except KeyError:
fields = _get_entry_fields(db)
_entry_db_fields[db] = fields
if db == "pubmed" and field == "ti" and "title" in fields:
#Backwards compatibility fix for TogoWS change Nov/Dec 2013
field = "title"
import warnings
warnings.warn("TogoWS dropped 'pubmed' field alias 'ti', please use 'title' instead.")
if field not in fields:
raise ValueError("TogoWS entry fetch does not explicitly support "
"field '%s' for database '%s'. Only: %s"
% (field, db, ", ".join(sorted(fields))))
if format:
try:
formats = _entry_db_formats[db]
except KeyError:
formats = _get_entry_formats(db)
_entry_db_formats[db] = formats
if format not in formats:
raise ValueError("TogoWS entry fetch does not explicitly support "
"format '%s' for database '%s'. Only: %s"
% (format, db, ", ".join(sorted(formats))))
if isinstance(id, list):
id = ",".join(id)
url = _BASE_URL + "/entry/%s/%s" % (db, _quote(id))
if field:
url += "/" + field
if format:
url += "." + format
return _open(url)
def search(db, query, offset=None, limit=None, format=None):
"""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).
"""
global _search_db_names
if _search_db_names is None:
_search_db_names = _get_fields(_BASE_URL + "/search")
if db not in _search_db_names:
#TODO - Make this a ValueError? Right now despite the HTML website
#claiming to, the "gene" or "ncbi-gene" don't work and are not listed.
import warnings
warnings.warn("TogoWS search does not explicitly support database '%s'. "
"See %s/search/ for options." % (db, _BASE_URL))
url = _BASE_URL + "/search/%s/%s" % (db, _quote(query))
if offset is not None and limit is not None:
try:
offset = int(offset)
except:
raise ValueError("Offset should be an integer (at least one), not %r" % offset)
try:
limit = int(limit)
except:
raise ValueError("Limit should be an integer (at least one), not %r" % limit)
if offset <= 0:
raise ValueError("Offset should be at least one, not %i" % offset)
if limit <= 0:
raise ValueError("Count should be at least one, not %i" % limit)
url += "/%i,%i" % (offset, limit)
elif offset is not None or limit is not None:
raise ValueError("Expect BOTH offset AND limit to be provided (or neither)")
if format:
url += "." + format
#print(url)
return _open(url)
def entry(db, id, format=None, field=None):
"""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.
"""
global _entry_db_names, _entry_db_fields, fetch_db_formats
if _entry_db_names is None:
_entry_db_names = _get_entry_dbs()
if db not in _entry_db_names:
raise ValueError("TogoWS entry fetch does not officially support "
"database '%s'." % db)
if field:
try:
fields = _entry_db_fields[db]
except KeyError:
fields = _get_entry_fields(db)
_entry_db_fields[db] = fields
if db == "pubmed" and field == "ti" and "title" in fields:
#Backwards compatibility fix for TogoWS change Nov/Dec 2013
field = "title"
import warnings
warnings.warn(
"TogoWS dropped 'pubmed' field alias 'ti', please use 'title' instead."
)
if field not in fields:
raise ValueError("TogoWS entry fetch does not explicitly support "
"field '%s' for database '%s'. Only: %s" %
(field, db, ", ".join(sorted(fields))))
if format:
try:
formats = _entry_db_formats[db]
except KeyError:
formats = _get_entry_formats(db)
_entry_db_formats[db] = formats
if format not in formats:
raise ValueError("TogoWS entry fetch does not explicitly support "
"format '%s' for database '%s'. Only: %s" %
(format, db, ", ".join(sorted(formats))))
if isinstance(id, list):
id = ",".join(id)
url = _BASE_URL + "/entry/%s/%s" % (db, _quote(id))
if field:
url += "/" + field
if format:
url += "." + format
return _open(url)
def search(db, query, offset=None, limit=None, format=None):
"""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).
"""
global _search_db_names
if _search_db_names is None:
_search_db_names = _get_fields(_BASE_URL + "/search")
if db not in _search_db_names:
#TODO - Make this a ValueError? Right now despite the HTML website
#claiming to, the "gene" or "ncbi-gene" don't work and are not listed.
import warnings
warnings.warn(
"TogoWS search does not explicitly support database '%s'. "
"See %s/search/ for options." % (db, _BASE_URL))
url = _BASE_URL + "/search/%s/%s" % (db, _quote(query))
if offset is not None and limit is not None:
try:
offset = int(offset)
except:
raise ValueError(
"Offset should be an integer (at least one), not %r" % offset)
try:
limit = int(limit)
except:
raise ValueError(
"Limit should be an integer (at least one), not %r" % limit)
if offset <= 0:
raise ValueError("Offset should be at least one, not %i" % offset)
if limit <= 0:
raise ValueError("Count should be at least one, not %i" % limit)
url += "/%i,%i" % (offset, limit)
elif offset is not None or limit is not None:
raise ValueError(
"Expect BOTH offset AND limit to be provided (or neither)")
if format:
url += "." + format
#print(url)
return _open(url)
