def get(self, service, **kwargs):
"""Does HTTP request to BOLD webservice.
Args:
service: The BOLD API alias to interact with.
kwargs: Paramenters send by users.
Returns:
A Response class containing parsed data as attribute `items`.
"""
params = ''
if service == 'call_id':
sequence = utils._prepare_sequence(kwargs['seq'])
params = _urlencode({'db': kwargs['db'], 'sequence': sequence})
if service == 'call_taxon_search':
if kwargs['fuzzy'] is True:
fuzzy = 'true'
else:
fuzzy = 'false'
params = _urlencode({
'taxName': kwargs['taxonomic_identification'],
'fuzzy': fuzzy,
})
if service == 'call_taxon_data':
if kwargs['include_tree'] is False:
params = _urlencode({
'taxId': kwargs['tax_id'],
'dataTypes': kwargs['data_type'],
})
else:
params = _urlencode({
'taxId': kwargs['tax_id'],
'dataTypes': kwargs['data_type'],
'includeTree': 'true',
})
if service == 'call_specimen_data' or service == 'call_sequence_data' or \
service == 'call_full_data' or service == 'call_trace_files':
payload = dict()
for k, v in kwargs.items():
if v is not None and k != 'url':
payload[k] = v
params = _urlencode(payload)
url = kwargs['url'] + "?" + params
req = _Request(url, headers={'User-Agent': 'BiopythonClient'})
handle = _urlopen(req)
response = Response()
if service == 'call_trace_files':
binary_result = handle.read()
response._parse_data(service, binary_result)
else:
result = _as_string(handle.read())
response._parse_data(service, result)
return response
def qblast(
program,
database,
sequence,
url_base=NCBI_BLAST_URL,
auto_format=None,
composition_based_statistics=None,
db_genetic_code=None,
endpoints=None,
entrez_query='(none)',
expect=10.0,
filter=None,
gapcosts=None,
genetic_code=None,
hitlist_size=50,
i_thresh=None,
layout=None,
lcase_mask=None,
matrix_name=None,
nucl_penalty=None,
nucl_reward=None,
other_advanced=None,
perc_ident=None,
phi_pattern=None,
query_file=None,
query_believe_defline=None,
query_from=None,
query_to=None,
searchsp_eff=None,
service=None,
threshold=None,
ungapped_alignment=None,
word_size=None,
alignments=500,
alignment_view=None,
descriptions=500,
entrez_links_new_window=None,
expect_low=None,
expect_high=None,
format_entrez_query=None,
format_object=None,
format_type='XML',
ncbi_gi=None,
results_file=None,
show_overview=None,
megablast=None,
template_type=None,
template_length=None,
):
"""BLAST search using NCBI's QBLAST server or a cloud service provider.
Supports all parameters of the qblast API for Put and Get.
Please note that BLAST on the cloud supports the NCBI-BLAST Common
URL API (http://ncbi.github.io/blast-cloud/dev/api.html). To
use this feature, please set url_base to
'http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi' and
format_object='Alignment'. For more details, please see
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
Some useful parameters:
- program blastn, blastp, blastx, tblastn, or tblastx (lower case)
- database Which database to search against (e.g. "nr").
- sequence The sequence to search.
- ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
- descriptions Number of descriptions to show. Def 500.
- alignments Number of alignments to show. Def 500.
- expect An expect value cutoff. Def 10.0.
- matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
- filter "none" turns off filtering. Default no filtering
- format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
- entrez_query Entrez query to limit Blast search
- hitlist_size Number of hits to return. Default 50
- megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
- service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
https://ncbi.github.io/blast-cloud/dev/api.html
"""
import time
programs = ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx']
if program not in programs:
raise ValueError("Program specified is %s. Expected one of %s" %
(program, ", ".join(programs)))
# Format the "Put" command, which sends search requests to qblast.
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
# Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
# To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
# (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
parameters = [
('AUTO_FORMAT', auto_format),
('COMPOSITION_BASED_STATISTICS', composition_based_statistics),
('DATABASE', database),
('DB_GENETIC_CODE', db_genetic_code),
('ENDPOINTS', endpoints),
('ENTREZ_QUERY', entrez_query),
('EXPECT', expect),
('FILTER', filter),
('GAPCOSTS', gapcosts),
('GENETIC_CODE', genetic_code),
('HITLIST_SIZE', hitlist_size),
('I_THRESH', i_thresh),
('LAYOUT', layout),
('LCASE_MASK', lcase_mask),
('MEGABLAST', megablast),
('MATRIX_NAME', matrix_name),
('NUCL_PENALTY', nucl_penalty),
('NUCL_REWARD', nucl_reward),
('OTHER_ADVANCED', other_advanced),
('PERC_IDENT', perc_ident),
('PHI_PATTERN', phi_pattern),
('PROGRAM', program),
# ('PSSM',pssm), - It is possible to use PSI-BLAST via this API?
('QUERY', sequence),
('QUERY_FILE', query_file),
('QUERY_BELIEVE_DEFLINE', query_believe_defline),
('QUERY_FROM', query_from),
('QUERY_TO', query_to),
# ('RESULTS_FILE',...), - Can we use this parameter?
('SEARCHSP_EFF', searchsp_eff),
('SERVICE', service),
('TEMPLATE_TYPE', template_type),
('TEMPLATE_LENGTH', template_length),
('THRESHOLD', threshold),
('UNGAPPED_ALIGNMENT', ungapped_alignment),
('WORD_SIZE', word_size),
('CMD', 'Put'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Send off the initial query to qblast.
# Note the NCBI do not currently impose a rate limit here, other
# than the request not to make say 50 queries at once using multiple
# threads.
request = _Request(url_base, message, {"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
# Format the "Get" command, which gets the formatted results from qblast
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
rid, rtoe = _parse_qblast_ref_page(handle)
parameters = [
('ALIGNMENTS', alignments),
('ALIGNMENT_VIEW', alignment_view),
('DESCRIPTIONS', descriptions),
('ENTREZ_LINKS_NEW_WINDOW', entrez_links_new_window),
('EXPECT_LOW', expect_low),
('EXPECT_HIGH', expect_high),
('FORMAT_ENTREZ_QUERY', format_entrez_query),
('FORMAT_OBJECT', format_object),
('FORMAT_TYPE', format_type),
('NCBI_GI', ncbi_gi),
('RID', rid),
('RESULTS_FILE', results_file),
('SERVICE', service),
('SHOW_OVERVIEW', show_overview),
('CMD', 'Get'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Poll NCBI until the results are ready.
# https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
# 1. Do not contact the server more often than once every 10 seconds.
# 2. Do not poll for any single RID more often than once a minute.
# 3. Use the URL parameter email and tool, so that the NCBI
# can contact you if there is a problem.
# 4. Run scripts weekends or between 9 pm and 5 am Eastern time
# on weekdays if more than 50 searches will be submitted.
# --
# Could start with a 10s delay, but expect most short queries
# will take longer thus at least 70s with delay. Therefore,
# start with 20s delay, thereafter once a minute.
delay = 20 # seconds
while True:
current = time.time()
wait = qblast._previous + delay - current
if wait > 0:
time.sleep(wait)
qblast._previous = current + wait
else:
qblast._previous = current
# delay by at least 60 seconds only if running the request against the public NCBI API
if delay < 60 and url_base == NCBI_BLAST_URL:
# Wasn't a quick return, must wait at least a minute
delay = 60
request = _Request(url_base, message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
results = _as_string(handle.read())
# Can see an "\n\n" page while results are in progress,
# if so just wait a bit longer...
if results == "\n\n":
continue
# XML results don't have the Status tag when finished
if "Status=" not in results:
break
i = results.index("Status=")
j = results.index("\n", i)
status = results[i + len("Status="):j].strip()
if status.upper() == "READY":
break
return StringIO(results)
def qblast(program, database, sequence, url_base=NCBI_BLAST_URL,
auto_format=None, composition_based_statistics=None,
db_genetic_code=None, endpoints=None, entrez_query='(none)',
expect=10.0, filter=None, gapcosts=None, genetic_code=None,
hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None,
matrix_name=None, nucl_penalty=None, nucl_reward=None,
other_advanced=None, perc_ident=None, phi_pattern=None,
query_file=None, query_believe_defline=None, query_from=None,
query_to=None, searchsp_eff=None, service=None, threshold=None,
ungapped_alignment=None, word_size=None,
alignments=500, alignment_view=None, descriptions=500,
entrez_links_new_window=None, expect_low=None, expect_high=None,
format_entrez_query=None, format_object=None, format_type='XML',
ncbi_gi=None, results_file=None, show_overview=None, megablast=None,
):
"""Do a BLAST search using the QBLAST server at NCBI or a cloud service
provider.
Supports all parameters of the qblast API for Put and Get.
Please note that BLAST on the cloud supports the NCBI-BLAST Common
URL API (http://ncbi.github.io/blast-cloud/dev/api.html). To
use this feature, please set url_base to
'http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi' and
format_object='Alignment'. For more details, please see
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
Some useful parameters:
- program blastn, blastp, blastx, tblastn, or tblastx (lower case)
- database Which database to search against (e.g. "nr").
- sequence The sequence to search.
- ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
- descriptions Number of descriptions to show. Def 500.
- alignments Number of alignments to show. Def 500.
- expect An expect value cutoff. Def 10.0.
- matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
- filter "none" turns off filtering. Default no filtering
- format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
- entrez_query Entrez query to limit Blast search
- hitlist_size Number of hits to return. Default 50
- megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
- service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
"""
import time
assert program in ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx']
# Format the "Put" command, which sends search requests to qblast.
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
# Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
# To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
# (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
parameters = [
('AUTO_FORMAT', auto_format),
('COMPOSITION_BASED_STATISTICS', composition_based_statistics),
('DATABASE', database),
('DB_GENETIC_CODE', db_genetic_code),
('ENDPOINTS', endpoints),
('ENTREZ_QUERY', entrez_query),
('EXPECT', expect),
('FILTER', filter),
('GAPCOSTS', gapcosts),
('GENETIC_CODE', genetic_code),
('HITLIST_SIZE', hitlist_size),
('I_THRESH', i_thresh),
('LAYOUT', layout),
('LCASE_MASK', lcase_mask),
('MEGABLAST', megablast),
('MATRIX_NAME', matrix_name),
('NUCL_PENALTY', nucl_penalty),
('NUCL_REWARD', nucl_reward),
('OTHER_ADVANCED', other_advanced),
('PERC_IDENT', perc_ident),
('PHI_PATTERN', phi_pattern),
('PROGRAM', program),
# ('PSSM',pssm), - It is possible to use PSI-BLAST via this API?
('QUERY', sequence),
('QUERY_FILE', query_file),
('QUERY_BELIEVE_DEFLINE', query_believe_defline),
('QUERY_FROM', query_from),
('QUERY_TO', query_to),
# ('RESULTS_FILE',...), - Can we use this parameter?
('SEARCHSP_EFF', searchsp_eff),
('SERVICE', service),
('THRESHOLD', threshold),
('UNGAPPED_ALIGNMENT', ungapped_alignment),
('WORD_SIZE', word_size),
('CMD', 'Put'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Send off the initial query to qblast.
# Note the NCBI do not currently impose a rate limit here, other
# than the request not to make say 50 queries at once using multiple
# threads.
request = _Request(url_base,
message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
# Format the "Get" command, which gets the formatted results from qblast
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
rid, rtoe = _parse_qblast_ref_page(handle)
parameters = [
('ALIGNMENTS', alignments),
('ALIGNMENT_VIEW', alignment_view),
('DESCRIPTIONS', descriptions),
('ENTREZ_LINKS_NEW_WINDOW', entrez_links_new_window),
('EXPECT_LOW', expect_low),
('EXPECT_HIGH', expect_high),
('FORMAT_ENTREZ_QUERY', format_entrez_query),
('FORMAT_OBJECT', format_object),
('FORMAT_TYPE', format_type),
('NCBI_GI', ncbi_gi),
('RID', rid),
('RESULTS_FILE', results_file),
('SERVICE', service),
('SHOW_OVERVIEW', show_overview),
('CMD', 'Get'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Poll NCBI until the results are ready. Use a backoff delay from 2 - 120 second wait
delay = 2.0
previous = time.time()
while True:
current = time.time()
wait = previous + delay - current
if wait > 0:
time.sleep(wait)
previous = current + wait
else:
previous = current
if delay + .5 * delay <= 120:
delay += .5 * delay
else:
delay = 120
request = _Request(url_base,
message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
results = _as_string(handle.read())
# Can see an "\n\n" page while results are in progress,
# if so just wait a bit longer...
if results == "\n\n":
continue
# XML results don't have the Status tag when finished
if "Status=" not in results:
break
i = results.index("Status=")
j = results.index("\n", i)
status = results[i + len("Status="):j].strip()
if status.upper() == "READY":
break
return StringIO(results)
def qblast(
program,
database,
sequence,
auto_format=None,
composition_based_statistics=None,
db_genetic_code=None,
endpoints=None,
entrez_query='(none)',
expect=10.0,
filter=None,
gapcosts=None,
genetic_code=None,
hitlist_size=50,
i_thresh=None,
layout=None,
lcase_mask=None,
matrix_name=None,
nucl_penalty=None,
nucl_reward=None,
other_advanced=None,
perc_ident=None,
phi_pattern=None,
query_file=None,
query_believe_defline=None,
query_from=None,
query_to=None,
searchsp_eff=None,
service=None,
threshold=None,
ungapped_alignment=None,
word_size=None,
alignments=500,
alignment_view=None,
descriptions=500,
entrez_links_new_window=None,
expect_low=None,
expect_high=None,
format_entrez_query=None,
format_object=None,
format_type='XML',
ncbi_gi=None,
results_file=None,
show_overview=None,
megablast=None,
):
"""Do a BLAST search using the QBLAST server at NCBI.
Supports all parameters of the qblast API for Put and Get.
Some useful parameters:
program blastn, blastp, blastx, tblastn, or tblastx (lower case)
database Which database to search against (e.g. "nr").
sequence The sequence to search.
ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
descriptions Number of descriptions to show. Def 500.
alignments Number of alignments to show. Def 500.
expect An expect value cutoff. Def 10.0.
matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
filter "none" turns off filtering. Default no filtering
format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
entrez_query Entrez query to limit Blast search
hitlist_size Number of hits to return. Default 50
megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
"""
import time
assert program in ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx']
# Format the "Put" command, which sends search requests to qblast.
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
# Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
# To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
# (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
parameters = [
('AUTO_FORMAT', auto_format),
('COMPOSITION_BASED_STATISTICS', composition_based_statistics),
('DATABASE', database),
('DB_GENETIC_CODE', db_genetic_code),
('ENDPOINTS', endpoints),
('ENTREZ_QUERY', entrez_query),
('EXPECT', expect),
('FILTER', filter),
('GAPCOSTS', gapcosts),
('GENETIC_CODE', genetic_code),
('HITLIST_SIZE', hitlist_size),
('I_THRESH', i_thresh),
('LAYOUT', layout),
('LCASE_MASK', lcase_mask),
('MEGABLAST', megablast),
('MATRIX_NAME', matrix_name),
('NUCL_PENALTY', nucl_penalty),
('NUCL_REWARD', nucl_reward),
('OTHER_ADVANCED', other_advanced),
('PERC_IDENT', perc_ident),
('PHI_PATTERN', phi_pattern),
('PROGRAM', program),
#('PSSM',pssm), - It is possible to use PSI-BLAST via this API?
('QUERY', sequence),
('QUERY_FILE', query_file),
('QUERY_BELIEVE_DEFLINE', query_believe_defline),
('QUERY_FROM', query_from),
('QUERY_TO', query_to),
#('RESULTS_FILE',...), - Can we use this parameter?
('SEARCHSP_EFF', searchsp_eff),
('SERVICE', service),
('THRESHOLD', threshold),
('UNGAPPED_ALIGNMENT', ungapped_alignment),
('WORD_SIZE', word_size),
('CMD', 'Put'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Send off the initial query to qblast.
# Note the NCBI do not currently impose a rate limit here, other
# than the request not to make say 50 queries at once using multiple
# threads.
request = _Request("http://blast.ncbi.nlm.nih.gov/Blast.cgi", message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
# Format the "Get" command, which gets the formatted results from qblast
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
rid, rtoe = _parse_qblast_ref_page(handle)
parameters = [
('ALIGNMENTS', alignments),
('ALIGNMENT_VIEW', alignment_view),
('DESCRIPTIONS', descriptions),
('ENTREZ_LINKS_NEW_WINDOW', entrez_links_new_window),
('EXPECT_LOW', expect_low),
('EXPECT_HIGH', expect_high),
('FORMAT_ENTREZ_QUERY', format_entrez_query),
('FORMAT_OBJECT', format_object),
('FORMAT_TYPE', format_type),
('NCBI_GI', ncbi_gi),
('RID', rid),
('RESULTS_FILE', results_file),
('SERVICE', service),
('SHOW_OVERVIEW', show_overview),
('CMD', 'Get'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Poll NCBI until the results are ready. Use a backoff delay from 2 - 120 second wait
delay = 2.0
previous = time.time()
while True:
current = time.time()
wait = previous + delay - current
if wait > 0:
time.sleep(wait)
previous = current + wait
else:
previous = current
if delay + .5 * delay <= 120:
delay += .5 * delay
else:
delay = 120
request = _Request("http://blast.ncbi.nlm.nih.gov/Blast.cgi", message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
results = _as_string(handle.read())
# Can see an "\n\n" page while results are in progress,
# if so just wait a bit longer...
if results == "\n\n":
continue
# XML results don't have the Status tag when finished
if "Status=" not in results:
break
i = results.index("Status=")
j = results.index("\n", i)
status = results[i + len("Status="):j].strip()
if status.upper() == "READY":
break
return StringIO(results)
def qblast(
program,
database,
sequence,
url_base=NCBI_BLAST_URL,
auto_format=None,
composition_based_statistics=None,
db_genetic_code=None,
endpoints=None,
entrez_query="(none)",
expect=10.0,
filter=None,
gapcosts=None,
genetic_code=None,
hitlist_size=50,
i_thresh=None,
layout=None,
lcase_mask=None,
matrix_name=None,
nucl_penalty=None,
nucl_reward=None,
other_advanced=None,
perc_ident=None,
phi_pattern=None,
query_file=None,
query_believe_defline=None,
query_from=None,
query_to=None,
searchsp_eff=None,
service=None,
threshold=None,
ungapped_alignment=None,
word_size=None,
short_query=None,
alignments=500,
alignment_view=None,
descriptions=500,
entrez_links_new_window=None,
expect_low=None,
expect_high=None,
format_entrez_query=None,
format_object=None,
format_type="XML",
ncbi_gi=None,
results_file=None,
show_overview=None,
megablast=None,
template_type=None,
template_length=None,
):
"""BLAST search using NCBI's QBLAST server or a cloud service provider.
Supports all parameters of the old qblast API for Put and Get.
Please note that NCBI uses the new Common URL API for BLAST searches
on the internet (http://ncbi.github.io/blast-cloud/dev/api.html). Thus,
some of the parameters used by this function are not (or are no longer)
officially supported by NCBI. Although they are still functioning, this
may change in the future.
The Common URL API (http://ncbi.github.io/blast-cloud/dev/api.html) allows
doing BLAST searches on cloud servers. To use this feature, please set
``url_base='http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi'``
and ``format_object='Alignment'``. For more details, please see
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
Some useful parameters:
- program blastn, blastp, blastx, tblastn, or tblastx (lower case)
- database Which database to search against (e.g. "nr").
- sequence The sequence to search.
- ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
- descriptions Number of descriptions to show. Def 500.
- alignments Number of alignments to show. Def 500.
- expect An expect value cutoff. Def 10.0.
- matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
- filter "none" turns off filtering. Default no filtering
- format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
- entrez_query Entrez query to limit Blast search
- hitlist_size Number of hits to return. Default 50
- megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
- short_query TRUE/FALSE whether to adjust the search parameters for a
short query sequence. Note that this will override
manually set parameters like word size and e value. Turns
off when sequence length is > 30 residues. Default: None.
- service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
https://ncbi.github.io/blast-cloud/dev/api.html
"""
import time
programs = ["blastn", "blastp", "blastx", "tblastn", "tblastx"]
if program not in programs:
raise ValueError("Program specified is %s. Expected one of %s" %
(program, ", ".join(programs)))
# SHORT_QUERY_ADJUST throws an error when using blastn (wrong parameter
# assignment from NCBIs side).
# Thus we set the (known) parameters directly:
if short_query and program == "blastn":
short_query = None
# We only use the 'short-query' parameters for short sequences:
if len(sequence) < 31:
expect = 1000
word_size = 7
nucl_reward = 1
filter = None
lcase_mask = None
warnings.warn(
'"SHORT_QUERY_ADJUST" is incorrectly implemented '
"(by NCBI) for blastn. We bypass the problem by "
"manually adjusting the search parameters. Thus, "
"results may slightly differ from web page "
"searches.", BiopythonWarning)
# Format the "Put" command, which sends search requests to qblast.
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
# Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
# To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
# (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
parameters = [
("AUTO_FORMAT", auto_format),
("COMPOSITION_BASED_STATISTICS", composition_based_statistics),
("DATABASE", database),
("DB_GENETIC_CODE", db_genetic_code),
("ENDPOINTS", endpoints),
("ENTREZ_QUERY", entrez_query),
("EXPECT", expect),
("FILTER", filter),
("GAPCOSTS", gapcosts),
("GENETIC_CODE", genetic_code),
("HITLIST_SIZE", hitlist_size),
("I_THRESH", i_thresh),
("LAYOUT", layout),
("LCASE_MASK", lcase_mask),
("MEGABLAST", megablast),
("MATRIX_NAME", matrix_name),
("NUCL_PENALTY", nucl_penalty),
("NUCL_REWARD", nucl_reward),
("OTHER_ADVANCED", other_advanced),
("PERC_IDENT", perc_ident),
("PHI_PATTERN", phi_pattern),
("PROGRAM", program),
# ('PSSM',pssm), - It is possible to use PSI-BLAST via this API?
("QUERY", sequence),
("QUERY_FILE", query_file),
("QUERY_BELIEVE_DEFLINE", query_believe_defline),
("QUERY_FROM", query_from),
("QUERY_TO", query_to),
# ('RESULTS_FILE',...), - Can we use this parameter?
("SEARCHSP_EFF", searchsp_eff),
("SERVICE", service),
("SHORT_QUERY_ADJUST", short_query),
("TEMPLATE_TYPE", template_type),
("TEMPLATE_LENGTH", template_length),
("THRESHOLD", threshold),
("UNGAPPED_ALIGNMENT", ungapped_alignment),
("WORD_SIZE", word_size),
("CMD", "Put"),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Send off the initial query to qblast.
# Note the NCBI do not currently impose a rate limit here, other
# than the request not to make say 50 queries at once using multiple
# threads.
request = _Request(url_base, message, {"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
# Format the "Get" command, which gets the formatted results from qblast
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
rid, rtoe = _parse_qblast_ref_page(handle)
parameters = [
("ALIGNMENTS", alignments),
("ALIGNMENT_VIEW", alignment_view),
("DESCRIPTIONS", descriptions),
("ENTREZ_LINKS_NEW_WINDOW", entrez_links_new_window),
("EXPECT_LOW", expect_low),
("EXPECT_HIGH", expect_high),
("FORMAT_ENTREZ_QUERY", format_entrez_query),
("FORMAT_OBJECT", format_object),
("FORMAT_TYPE", format_type),
("NCBI_GI", ncbi_gi),
("RID", rid),
("RESULTS_FILE", results_file),
("SERVICE", service),
("SHOW_OVERVIEW", show_overview),
("CMD", "Get"),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Poll NCBI until the results are ready.
# https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
# 1. Do not contact the server more often than once every 10 seconds.
# 2. Do not poll for any single RID more often than once a minute.
# 3. Use the URL parameter email and tool, so that the NCBI
# can contact you if there is a problem.
# 4. Run scripts weekends or between 9 pm and 5 am Eastern time
# on weekdays if more than 50 searches will be submitted.
# --
# Could start with a 10s delay, but expect most short queries
# will take longer thus at least 70s with delay. Therefore,
# start with 20s delay, thereafter once a minute.
delay = 20 # seconds
while True:
current = time.time()
wait = qblast._previous + delay - current
if wait > 0:
time.sleep(wait)
qblast._previous = current + wait
else:
qblast._previous = current
# delay by at least 60 seconds only if running the request against the public NCBI API
if delay < 60 and url_base == NCBI_BLAST_URL:
# Wasn't a quick return, must wait at least a minute
delay = 60
request = _Request(url_base, message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
results = _as_string(handle.read())
# Can see an "\n\n" page while results are in progress,
# if so just wait a bit longer...
if results == "\n\n":
continue
# XML results don't have the Status tag when finished
if "Status=" not in results:
break
i = results.index("Status=")
j = results.index("\n", i)
status = results[i + len("Status="):j].strip()
if status.upper() == "READY":
break
return StringIO(results)