def test_overlaps(self):
lunch = Interval(14, 16)
meeting2 = Interval(12, 14)
meeting3 = Interval(13, 15)
self.assertFalse(meeting2.overlaps(lunch))
self.assertTrue(meeting2.overlaps(meeting3))
self.assertTrue(meeting3.overlaps(lunch))
def search_available_equips(equip_type, strDate, b_time, e_time):
if equip_type == 'MASSAGE':
print('Not Support Now!!!')
return
from interval import Interval
equipUsageURL = base_url + '/LeaseEquip/equipUsage.jsp'
payload = [('q_from_date', strDate), ('q_from_time', ''),
('q_to_date', strDate), ('q_to_time', ''),
('q_equip_type', equip_type)]
payload.extend([('ID_keyD', e) for e in meeting_rooms.keys()])
result = getSession().post(equipUsageURL, data=payload)
soup = bs(result.text, 'html.parser')
equips = [
equip.text.strip()
for equip in soup.select('div[id="equips"] td[align="center"]')
]
# print(equips)
availList = list()
for index, elem in enumerate(soup.select('td[nowrap]')):
availList.insert(index, 1)
if '目前無人預約' in elem.text:
continue
target = Interval(int(b_time), int(e_time), closed=False)
periods = [x.text.split('~') for x in elem.select('b')]
periodIntvs = [
Interval(x[0], x[1])
for x in list(map(lambda bb: [int(x) for x in bb], periods))
]
# print(equips[index])
# for pp in periodIntvs:ontext['lifespanCount'] = 0
# print(pp,'\n')
for periodIntv in periodIntvs:
if target.overlaps(periodIntv):
availList[index] = 0
break
# print(availList)
for index, avail in enumerate(availList):
if avail == 1:
print('{}\n'.format(equips[index]))
def judgeFusion_same(tmp):
tmpStrand = tmp['strand']
tmpChr = list(tmp['chr'])
tmpChr_unique = list(set(tmpChr))
tmpChr2Num = []
tmpChr_len = len(tmpChr_unique)
tmpNrow = tmp.shape[0]
tmp_query_start = tmp['query_start'].values
tmp_query_end = tmp['query_end'].values
if tmpNrow == 2:
#if len(set(tmpStrand))>1:
#return('U')
r1S = tmp['reference_start'].values[0]
r1E = tmp['reference_end'].values[0]
r2S = tmp['reference_start'].values[tmpNrow - 1]
r2E = tmp['reference_end'].values[tmpNrow - 1]
r1 = Interval(r1S, r1E, lower_closed=False)
r2 = Interval(r2S, r2E, lower_closed=False)
if r1.overlaps(r2):
#return('NC',-1)
return ('N', -1) # revised for more sensitive
type, rowID = read2ref(tmp, 'U')
return (type, rowID)
elif tmpNrow == 3:
#if len(set(tmpStrand))>1:
#return('U')
r1S = tmp['reference_start'].values[0]
r1E = tmp['reference_end'].values[0]
r2S = tmp['reference_start'].values[tmpNrow - 1]
r2E = tmp['reference_end'].values[tmpNrow - 1]
r1 = Interval(r1S, r1E, lower_closed=False)
r2 = Interval(r2S, r2E, lower_closed=False)
arr1 = np.zeros(tmpNrow - 1)
arr2 = np.zeros(tmpNrow - 1)
for j in range(1, tmpNrow):
cS1 = tmp['reference_start'].values[j]
cE1 = tmp['reference_end'].values[j]
cS2 = tmp['reference_start'].values[j - 1]
cE2 = tmp['reference_end'].values[j - 1]
c1 = Interval(cS1, cE1, lower_closed=False)
c2 = Interval(cS2, cE2, lower_closed=False)
arr1[j - 1] = r1.overlaps(c1)
arr2[j - 1] = r2.overlaps(c2)
if sum(arr1) > 0 and sum(arr2) > 0:
if arr1[0]:
return ('N', -1)
else:
type, rowID = read2ref(tmp, 'FC2')
return (type, rowID)
#return('FC2')
else:
type, rowID = read2ref(tmp, 'C2')
return (type, rowID)
elif tmpNrow > 3:
r1S = tmp['reference_start'].values[np.where(
tmp['exon_length'].values == max(tmp['exon_length'].values))[0][0]]
r1E = tmp['reference_end'].values[np.where(
tmp['exon_length'].values == max(tmp['exon_length'].values))[0][0]]
r1 = Interval(r1S, r1E, lower_closed=False)
arr1 = np.zeros(tmpNrow)
for j in range(0, tmpNrow):
cS1 = tmp['reference_start'].values[j]
cE1 = tmp['reference_end'].values[j]
c1 = Interval(cS1, cE1, lower_closed=False)
arr1[j] = r1.overlaps(c1)
#if len(set(tmpStrand[np.array(arr1)==0]))>1 or len(set(tmpStrand[np.array(arr1)==1]))>1:
# return('U')
if sum(arr1 == 1) > (tmpNrow - 2):
return ('N', -1)
else:
targetNum = [0, 1]
for j in range(2 * tmpNrow):
targetNum.extend([0, 1])
arr1 = [int(i) for i in arr1]
targetNum = np.array(targetNum[arr1[0]:(arr1[0] + tmpNrow)])
if sum(targetNum == arr1) == tmpNrow:
if (tmp_query_start[2] - tmp_query_end[0]) > 40 and (
tmp_query_start[3] - tmp_query_end[1]
) > 40 and (tmp_query_end[1] - tmp_query_end[0]) > 40 and (
tmp_query_end[2] - tmp_query_end[1]
) > 40 and (tmp_query_end[3] - tmp_query_end[2]) > 40 and (
tmp_query_start[1] - tmp_query_end[0]) > -40 and (
tmp_query_start[2] - tmp_query_end[1]) > -40 and (
tmp_query_start[3] - tmp_query_end[2]) > -40:
type, rowID = read2ref(tmp, 'F2')
return (type, rowID)
else:
type, rowID = read2ref(tmp, 'FC2')
return (type, rowID)
else:
type, rowID = read2ref(tmp, 'C2')
return (type, rowID)
else:
return ('U', -1)
def calReadSplice(i):
tmp=FL_noDup.iloc[i,:]
readArr=[]
targetI=Interval(tmp['start']-1,tmp['end'])
tmpRegionS=tmp['chr']+':'+str(tmp['start'])+'-'+str(tmp['start'])
tmpRegionE=tmp['chr']+':'+str(tmp['end'])+'-'+str(tmp['end'])
tmpFileS=RG_tmp_outPrefix+str(i)+'_FO_s.sam'
tmpFileE=RG_tmp_outPrefix+str(i)+'_FO_e.sam'
CMDS='samtools view -h %s %s>%s' % (bamFile,tmpRegionS,tmpFileS)
CMDE='samtools view -h %s %s>%s' % (bamFile,tmpRegionE,tmpFileE)
tmpSAM_s=''
tmpSAM_e=''
isPass=True
if not os.system(CMDS):
tmpSAM_s=pysam.AlignmentFile(tmpFileS)
else:
isPass=False
if not os.system(CMDE):
tmpSAM_e=pysam.AlignmentFile(tmpFileE)
else:
isPass=False
if not isPass:
return([1,1])
readDict_tmp={}
for read in tmpSAM_s.fetch():
readDict_tmp[read.qname]=1
if read.flag & 260 >0:
continue
if dict_ID2type.__contains__(read.qname):
continue
readInfo=getReadInfo(read)
for i in range(len(readInfo[0])):
readI=Interval(readInfo[0][i],readInfo[1][i])
if readI.overlaps(targetI):
readArr.append(readInfo)
for read in tmpSAM_e.fetch():
if readDict_tmp.__contains__(read.qname):
continue
if read.flag & 260 >0:
continue
if dict_ID2type.__contains__(read.qname):
continue
readInfo=getReadInfo(read)
for i in range(len(readInfo[0])):
readI=Interval(readInfo[0][i],readInfo[1][i])
if readI.overlaps(targetI):
readArr.append(readInfo)
count_s=0
count_i=0
for readInfo in readArr:
tmpS=0
tmpI=0
if len(readInfo[0])>1:
for j in range(len(readInfo[0])-1):
readI=Interval(readInfo[1][j],readInfo[0][j+1])
if readI.overlaps(targetI):
tmpS=1
#print(readInfo)
break
else:
tmpI=1
count_s+=tmpS
count_i+=tmpI
os.system('rm %s' % tmpFileS)
os.system('rm %s' % tmpFileE)
return([count_s,count_i])
