def custom_track_request(chromosome, startpos, endpos, request_proxy=None, *args, **kwargs):
"""
Needs request_proxy with hgsid or kwargs.hgsid
NOTE: for whatever reason, you need to set the startpos in the submit to the
startpos computed by the hgPcr tool (and referenced in sequence lookup) minus 1.
I dunno. Will write unit test to check if this ever changes.
"""
if request_proxy:
if not request_proxy.hgsid:
raise ValueError, "Cannot make custom track request without hgsid in session"
else:
hgsid = request_proxy.hgsid
else:
if not kwargs.get('hgsid', None):
raise ValueError, "Cannot make custom track request without hgsid in kwargs"
else:
hgsid = kwargs.get('hgsid')
if 'chr%s' % chromosome not in CHROMOSOME_MAXES[HG19]:
raise ValueError, "Invalid chromosome: %s" % chromosome
if startpos < 1:
startpos = 1
if endpos > CHROMOSOME_MAXES[HG19]['chr%s' % chromosome]:
endpos = CHROMOSOME_MAXES[HG19]['chr%s' % chromosome]
uri = 'hgCustom'
defaults = {'hgsid': hgsid,
'clade': MAMMAL,
'org': HUMAN,
'db': HG19,
'hgct_customText': """track name='%s'
chr%s %s %s""" % (hgsid, chromosome, startpos-1, endpos)}
req = make_request_params(defaults, **kwargs)
datagen, headers = poster_multipart_encode_patch(req)
request = urllib2.Request(make_get_request_url(BASE_URL, uri), datagen, headers)
if request_proxy is not None:
response = request_proxy.request(request)
else:
response = urllib2.urlopen(request)
response = response.read()
# hack hack hack
if "Unrecognized format line" in response or "Error line" in response or "Add Custom Tracks" in response:
# TODO: parse the error as well?
raise ValueError, "Invalid custom track specification: chr%s %s %s" % (chromosome, startpos, endpos)
return response
def table_sequence_request(chromosome, startpos, endpos, request_proxy=None, *args, **kwargs):
"""
Make table sequence request. Actually makes two requests; the two requests are
dependent (at least to generate a sequence), so they are grouped in the same
method.
Requires a request proxy with hgsid and hgct_table set *or* hgsid and track_id
kwargs set.
"""
if request_proxy:
if not request_proxy.hgsid or not request_proxy.track_id:
raise ValueError, "Required variables (hgsid, track_id) not set in session"
else:
hgsid = request_proxy.hgsid
track_id = request_proxy.track_id
elif not kwargs.get('hgsid', None) or not kwargs.get('track_id', None):
raise ValueError, "Required kwargs (hgsid, track_id) not set"
else:
hgsid = kwargs.get('hgsid')
track_id = kwargs.get('track_id')
if 'chr%s' % chromosome not in CHROMOSOME_MAXES[HG19]:
raise ValueError, "Invalid chromosome: %s" % chromosome
# zero based request
if startpos < 0:
startpos = 0
if endpos > CHROMOSOME_MAXES[HG19]["chr%s" % chromosome]:
endpos = CHROMOSOME_MAXES[HG19]["chr%s" % chromosome]
uri = "hgTables"
defaults = {'hgsid': hgsid,
'boolshad.sendToGalaxy': 0,
'boolshad.sendToGreat': 0,
'clade': MAMMAL,
'db': HG19,
'hgta_compressType': "none",
'hgta_doTopSubmit': "get output",
"hgta_outFileName": "",
"hgta_outputType": "sequence",
"hgta_regionType": "range",
"hgta_table": "ct_%s_%s" % (hgsid, track_id),
"hgta_track": "ct_%s_%s" % (hgsid, track_id),
"position": "chr%s:%s-%s" % (chromosome, startpos, endpos)}
req = make_request_params(defaults, **kwargs)
datagen, headers = poster_multipart_encode_patch(req)
request = urllib2.Request(make_get_request_url(BASE_URL, uri), datagen, headers)
if request_proxy is not None:
response = request_proxy.request(request)
else:
response = urllib2.urlopen(request)
intermediate = response.read()
intermediate_tree = BeautifulSoup(intermediate)
# TODO is this more general? (Error case in any UCSC response)
# if so, put on the request proxy
if "Error" in intermediate_tree.head.title.text or len(intermediate_tree.findAll(id='warnBox')) > 0:
raise ValueError, "Could not generate sequence from arguments to hgTables"
defaults2 = {'hgsid': hgsid,
'boolshad.hgSeq.maskRepeats': 0,
'boolshad.hgSeq.revComp': 0,
'hgSeq.casing': "upper",
'hgSeq.cdsExon': 1,
'hgSeq.padding3': 0, # these don't seem to actually work
'hgSeq.padding5': 0, # these don't seem to actually work
'hgSeq.repMasking': 'lower',
'hgta_doGenomicDna': 'get sequence'}
req = make_request_params(defaults2, **kwargs)
if request_proxy is not None:
response = request_proxy.request(make_get_request_url(BASE_URL, uri, req))
else:
response = urllib2.urlopen(make_get_request_url(BASE_URL, uri, req))
return response.read()
