def onpicture():
#filenameImage='F:/Aotu3DImage/'+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
#filenameIma='F:/Aotu3DImage/'+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
width = G.windowWidth
height = G.windowHeight
width = width - 3
height = height - 3
#log.message(filenameImage)
#mh.grabScreen(0,0,width,height,filenameImage)
img = grabMyScreen(0, 0, width, height)
#log.message(str(imgs))
#img=cv2.imread(filenameImage)
height, width = img.shape[:2]
#print height,width
for i in range(height):
for j in range(width):
r, b, g = img[i][j]
rb = abs(r - b)
rg = abs(r - g)
bg = abs(b - g)
if rb < 10 and rg < 10 and bg < 10:
img[i][j] = [0, 0, 0]
else:
img[i][j] = [255, 255, 255]
# cv2.imwrite(filenameIma,img)
imsave = normalize.Normalize(img)
delt = findcontours.GetDeltValue(imsave, filepicture)
return delt
def dayinpicture():
filenameImage='F:/Aotu3DImage/'+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
filenameIma='F:/Aotu3DImage/'+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
width = G.windowWidth;
height = G.windowHeight;
width = width - 3;
height = height - 3;
#log.message(filenameImage)
#mh.grabScreen(0,0,width,height,filenameImage)
#img=cv2.imread(filenameImage)
img=grabMyScreen(0,0,width,height)
height1,width1=img.shape[:2]
#print height,width
for i in range(height1):
for j in range(width1):
r,b,g= img[i][j]
rb=abs(r-b)
rg=abs(r-g)
bg=abs(b-g)
if rb<10 and rg<10 and bg<10:
img[i][j]=[0,0,0]
else:
img[i][j]=[255,255,255]
imsave=normalize.Normalize(img)
cv2.imwrite(filenameIma,imsave)
def plotnormalizedplane(self, axis, pos):
""" FUNCTION plotsimpleplane
Plots a plane defined by axis and pos, where axis is a principal direction
INPUT:
integer: axis, the direction normal of plane to plot
integer: pos, the index of the line/plane intersection
"""
plane_dim = np.delete(self.f_size, axis)
X, Y = np.mgrid[-1:1:complex(0, plane_dim[0]),
-1:1:complex(0, plane_dim[1])]
if axis == 0:
#plt.matshow(self.f_field[pos,:,:], cmap='hot')
Z = self.f_field[pos, :, :]
if axis == 1:
#plt.matshow(self.f_field[:,pos,:], cmap='hot')
Z = self.f_field[:, pos, :]
if axis == 2:
#plt.matshow(self.f_field[:,:,pos], cmap='hot')
Z = self.f_field[:, :, pos]
pcm = plt.pcolormesh(X,
Y,
Z,
norm=nz.Normalize(midpoint=0.),
cmap='RdBu_r')
plt.colorbar(pcm, extend='both')
def onClicked(event):
width = G.windowWidth;
height = G.windowHeight;
width = width - 3;
height = height - 3;
log.message(str(width))
log.message(str(height))
for value in range(5,100,5):
chushihua()
a5[0]=value-50
bvhanniu()
gui3d.app.do(AotuPose1("Change pose", self, self.currentPose, fileout))
#anim = self.loadBvh(fileout, convertFromZUp="auto")
filenameImage='F:/Aotu3DImage/'+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
filenameIma='F:/Aotu3DImage/'+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
width = G.windowWidth;
height = G.windowHeight;
width = width - 3;
height = height - 3;
#log.message(filenameImage)
mh.grabScreen(0,0,width,height,filenameImage)
img=cv2.imread(filenameImage)
height1,width1=img.shape[:2]
#print height,width
for i in range(height1):
for j in range(width1):
r,b,g= img[i][j]
rb=abs(r-b)
rg=abs(r-g)
bg=abs(b-g)
if rb<10 and rg<10 and bg<10:
img[i][j]=[0,0,0]
else:
img[i][j]=[255,255,255]
imsave=normalize.Normalize(img)
cv2.imwrite(filenameIma,imsave)
cv2.imshow("img",imsave)
cv2.waitKey(10)
delt5=onpicture()
if delt5<=deltvalue5[0]:
deltvalue5[0]=delt5
deltva5[0]=value-50
num5=(deltva5[0]+50)/5
result=cv2.imread(fileResult+str(num5)+'.png')
cv2.imshow("Result",result)
cv2.waitKey(0)
log.message(deltvalue5)
log.message(num5)
def __init__(self, config, cons):
assert config['bit_depth'] >= 1
assert config['pixels_per_cycle'] >= 1
self.bd = config['bit_depth']
self.ps = config['pixels_per_cycle']
self.axi_lite = config['support_axi_lite']
enc_out_bits = min(31, 16 + self.bd) * self.ps
#pixels in
self.pixels_in = Array(
Signal(self.bd, name="pixel_in") for _ in range(self.ps))
#enc out
self.enc_out = Signal(enc_out_bits)
self.enc_out_ctr = Signal(max=enc_out_bits + 1)
# valid in & out
self.valid_in = Signal(1)
self.valid_out = Signal(1)
# end
self.end_out = Signal(1)
self.fend_out = Signal(1)
if self.ps == 4:
self.predictor = predictor_p1_c4_px4.PredictorP1C4Px4(config, cons)
else:
self.predictor = predictor_p1_c4_pix1_2.PredictorP1C4Pix12(
config, cons)
self.difference = difference.Difference(config, cons)
self.normalize = normalize.Normalize(config, cons)
self.encode = encode.Encode(config, cons)
#create a merge layer only if more than one pixel per cycle
if self.ps > 1:
self.merge = merge.Merge(config, cons)
self.signals = signals.Signals(config, cons)
if self.axi_lite:
self.core_axi_lite = core_axi_lite.CoreAxiLite(config, cons)
else:
self.register_file = register_file.RegisterFile()
self.force_end = force_end.ForceEnd(config, cons)
self.ios = \
[pixel_in for pixel_in in self.pixels_in] + \
[self.enc_out, self.enc_out_ctr] + \
[self.valid_in, self.valid_out] + \
[self.end_out, self.fend_out]
def onClicked(event):
log.message('start...')
for slider in self.sliders:
for valuenum in range(0, 105, 5):
valuenums = valuenum / 100.000000
slider.update()
#log.message(slider.modifier.getValue())
#if slider.enabledCondition:
#log.message(slider)
slider.modifier.setValue(valuenums)
#log.message(slider.modifier.getValue())
sli = modifierslider.ModifierSlider(slider.modifier)
value = slider.modifier.getValue()
valuesli = sli.getValue()
#sli.onChanging(slider.modifier.getValue())
action = humanmodifier.ModifierAction(
slider.modifier, value, valuesli, sli.update)
log.message(str(valuesli))
log.message(str(value))
if valuesli != value:
G.app.do(action)
else:
action.do()
filenameImage = 'F:/Aotu3DImage/' + str(
time.strftime("%Y-%m-%d_%H.%M.%S")) + '.png'
filenameIma = 'F:/Aotu3DImage/' + str(
time.strftime("%Y-%m-%d_%H.%M.%S")) + '.png'
filenameIma1 = 'F:/Aotu3DImage/result' + str(
time.strftime("%Y-%m-%d_%H.%M.%S")), '.png'
width = G.windowWidth
height = G.windowHeight
width1 = width - 3
height1 = height - 3
#log.message(filenameImage)
mh.grabScreen(0, 0, width, height, filenameImage)
img = cv2.imread(filenameImage)
height1, width1 = img.shape[:2]
#print height,width
for i in range(height1):
for j in range(width1):
r, b, g = img[i][j]
rb = abs(r - b)
rg = abs(r - g)
bg = abs(b - g)
if rb < 10 and rg < 10 and bg < 10:
img[i][j] = [0, 0, 0]
else:
img[i][j] = [255, 255, 255]
imsave = normalize.Normalize(img)
cv2.imwrite(filenameIma, imsave)
#cv2.imshow("img",imsave)
# cv2.waitKey(10)
delt = onpicture()
log.message(str(delt))
if delt <= deltvalue[0]:
deltvalue[0] = delt
deltva[0] = valuenums
num = deltva[0] * 20 + 1
result = cv2.imread(fileResult + str(num) + '.png')
cv2.imshow("Result", result)
cv2.waitKey(0)
log.message(deltvalue)
log.message(num)
slider.modifier.setValue(valuenums)
#log.message(slider.modifier.getValue())
sli = modifierslider.ModifierSlider(slider.modifier)
value = slider.modifier.getValue()
valuesli = sli.getValue()
#sli.onChanging(slider.modifier.getValue())
action = humanmodifier.ModifierAction(slider.modifier, value,
valuesli, sli.update)
G.app.do(action)
mh.grabScreen(0, 0, width, height, filenameImage)
imgw = cv2.imread(filenameImage)
height1, width1 = imgw.shape[:2]
#print height,width
for i in range(height1):
for j in range(width1):
r, b, g = imgw[i][j]
rb = abs(r - b)
rg = abs(r - g)
bg = abs(b - g)
if rb < 10 and rg < 10 and bg < 10:
imgw[i][j] = [0, 0, 0]
else:
imgw[i][j] = [255, 255, 255]
imsavew = normalize.Normalize(imgw)
cv2.imwrite(filenameIma1, imsavew)
import gi
import utest
import normalize
import pathway_enrichment #08/22/2018 by Ivan
import anova
import tnseq_stats
methods = {}
methods["example"] = example.ExampleAnalysis()
methods["gumbel"] = gumbel.GumbelAnalysis()
methods["binomial"] = binomial.BinomialAnalysis()
methods["griffin"] = griffin.GriffinAnalysis()
methods["hmm"] = hmm.HMMAnalysis()
methods["resampling"] = resampling.ResamplingAnalysis()
methods["tn5gaps"] = tn5gaps.Tn5GapsAnalysis()
methods["rankproduct"] = rankproduct.RankProductAnalysis()
methods["utest"] = utest.UTestAnalysis()
methods["GI"] = gi.GIAnalysis()
methods["anova"] = anova.AnovaAnalysis()
#methods["mcce"] = mcce.MCCEAnalysis()
#methods["mcce2"] = mcce2.MCCE2Analysis()
#methods["motifhmm"] = motifhmm.MotifHMMAnalysis()
methods["normalize"] = normalize.Normalize()
methods["pathway_enrichment"] = pathway_enrichment.GSEAAnalysis()
methods["tnseq_stats"] = tnseq_stats.TnseqStats()
# EXPORT METHODS
import norm
export_methods = {}
export_methods["norm"] = norm.NormAnalysis()
def onClicked(event):
#chushihua()
width = G.windowWidth;
height = G.windowHeight;
width = width - 3;
height = height - 3;
log.message(str(width))
log.message(str(height))
OrigalIm = cv2.imread(filepicture) #先读目标图像
for value in range(61,71,10):
a8[0]=value-50
bvhanniu()
gui3d.app.do(AotuPose1("Change pose", self, self.currentPose, fileout))
anim = self.loadBvh(fileout, convertFromZUp="auto")
#cv2.waitKey(10)
#filenameImage=fileResult+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
filenameImage=fileResult+str(a8[0])+'DegreeLLeg.png'
#filenameIma=fileResult+str(time.strftime("%Y-%m-%d_%H.%M.%S"))+'.png'
filenameIma=fileResult+str(a8[0])+'DegreeLLeg.png'
width = G.windowWidth;
height = G.windowHeight;
Xdel=600 #原图为800x600 减除后为200x150
Ydel=450
width = width - Xdel;
height = height - Ydel;
#log.message(filenameImage)
#mh.grabScreen(300,225,width,height,filenameImage) #存盘
mh.grabScreen(Xdel/2,Ydel/2,width,height,filenameImage) #不存盘，全在内在操作，提高速度
log.message("Saved screengrab to %s", filenameImage)
img=cv2.imread(filenameImage) #存盘
height1,width1=img.shape[:2]
#print height,width
for i in range(height1):
for j in range(width1):
r,b,g= img[i][j]
rb=abs(r-b)
rg=abs(r-g)
bg=abs(b-g)
if rb<10 and rg<10 and bg<10:
img[i][j]=[0,0,0]
else:
img[i][j]=[255,255,255]
imsave=normalize.Normalize(img)
cv2.imwrite(filenameIma,imsave)
#cv2.imshow("img",imsave)
#cv2.waitKey(10)
#delt8=findcontours.GetDeltValue(imsave,OrigalIm) #onpicture()
delt8=findcontours.CalDiff(imsave,OrigalIm)
log.debug('delt8 (%d Degree): = %f', a8[0], delt8)
if delt8<=deltvalue8[0]:
deltvalue8[0]=delt8
deltva8[0]=value-50
filenameImaFit=filenameIma
bvhanniu(filepicbvh)
gui3d.app.do(AotuPose1("Change pose", self, self.currentPose, filepicbvh))
anim = self.loadBvh(filepicbvh, convertFromZUp="auto")
imsavefit=imsave
gui3d.app.do(AotuPose1("Change pose", self, self.currentPose, filepicbvh))
anim = self.loadBvh(filepicbvh, convertFromZUp="auto")
a8[0]= deltva8[0] #需要更新，不然后面姿态重置了
bvhanniu()
num1=(deltva8[0]+50)/5
#result=cv2.imread(fileResult+str(num1)+'.png')
#result=cv2.imread(filenameImaFit)
result =imsavefit
result2=cv2.imread(filepicture)
cv2.imshow("Result",result)
cv2.imshow("Original",result2)
#cv2.waitKey(10)
log.message(deltvalue8)
log.message(num1)
imsavefit = None
def pipeline(gse, output='zrb_pipeline_bern_result'):
with open(output, "a", encoding='utf-8') as out:
# title=['gse','gsm','text','bern_text','cell line','organism','cell type','method','source name','tissue','treatment','disease','bern_zrb_disease','bern_zrb_disease_id','bern_zrb_drug','bern_zrb_drug_id','bern_zrb_gene','bern_zrb_gene_id']
title = [
'gse', 'gsm', 'text', 'bern_text', 'cell line', 'organism',
'cell type', 'method', 'source name', 'tissue', 'treatment',
'disease', 'library_strategy', 'bern_disease_str',
'bern_disease_id_str', 'normolize_disease_id_name',
'normolize_disease_name', 'bern_drug_str', 'bern_drug_id_str',
'normolize_drug_id_name', 'normolize_drug_name',
'bern_gene_str', 'bern_gene_id_str', 'normolize_gene_id_name',
'normolize_gene_name', 'knock_out/knock_down', 'knock_in',
'knock', 'over_expression', 'cell_line_text_regex',
'cell_line_bern_text_regex', 'gsm_rrid_cell_line',
'gsm_rrid_disease'
]
title_line = "\t".join(title)
out.write(title_line)
out.write('\n')
# file_list=[]
file_list = [x for x in os.listdir('gse') if x.startswith(gse)]
if not file_list:
print('+++ no GSE samples')
return (None)
# print(file_list)
for i_file in file_list:
file_path = os.path.join(os.path.abspath('.'), 'gse')
file_path_need = os.path.join(file_path, i_file)
dom = xml.dom.minidom.parse(file_path_need)
def move_break(need_list):
for i in range(len(need_list)):
need_list[i] = re.sub("\n", "", need_list[i])
need_list[i] = re.sub("\s+", " ", need_list[i])
return need_list
#单独获取测序方法
Platform = dom.getElementsByTagName("Platform")
p_technology_list = []
for i_p in range(Platform.length):
try:
p_technology = dom.getElementsByTagName(
"Platform")[i_p].getElementsByTagName(
"Technology")[0].childNodes[0].data
p_technology_list.append(p_technology)
except:
p_technology_list.append("null")
p_technology_set = set(p_technology_list)
p_technology_list = list(p_technology_set)
p_technology_list = move_break(p_technology_list)
#print(p_technology_set)
#print(p_technology_list)
p_technology_all = ",".join(str(x) for x in p_technology_list)
#extract sample tags
#extract sample tags
sample = dom.getElementsByTagName("Sample")
#sample_list=[]
#sample_data_list=[]
sample_char_list = []
#sample_table_list=[]
for i_s in range(sample.length):
output_list = []
try:
s_number = sample[i_s].getAttribute("iid")
except:
s_number = "null"
try:
s_title = sample[i_s].getElementsByTagName(
"Title")[0].childNodes[0].data
except:
s_title = sample[i_s] = "null"
try:
s_channel = sample[i_s].getElementsByTagName(
"Channel-Count")[0].childNodes[0].data
except:
s_channel = "null"
try:
s_source = sample[i_s].getElementsByTagName(
"Source")[0].childNodes[0].data
except:
s_source = "null"
try:
s_organism = sample[i_s].getElementsByTagName(
"Organism")[0].childNodes[0].data
except:
s_organism = "null"
#会出现换行符
try:
s_treatment = sample[i_s].getElementsByTagName(
"Treatment-Protocol")[0].childNodes[0].data
except:
s_treatment = "null"
#print(s_title)
#会出现换行符
try:
s_growth = sample[i_s].getElementsByTagName(
"Growth-Protocol")[0].childNodes[0].data
except:
s_growth = "null"
try:
s_molecule = sample[i_s].getElementsByTagName(
"Molecule")[0].childNodes[0].data
except:
s_molecule = "null"
try:
s_extract = sample[i_s].getElementsByTagName(
"Extract-Protocol")[0].childNodes[0].data
except:
s_extract = "null"
try:
s_label = sample[i_s].getElementsByTagName(
"Label")[0].childNodes[0].data
except:
s_label = "null"
#换行符会出现在句字中，用空格代替，再将多个空格替换成一个空格
try:
s_data_processing = sample[i_s].getElementsByTagName(
"Data-Processing")[0].childNodes[0].data
except:
s_data_processing = "null"
try:
s_library_strategy = sample[i_s].getElementsByTagName(
"Library-Strategy")[0].childNodes[0].data
except:
s_library_strategy = "null"
try:
s_description = sample[i_s].getElementsByTagName(
"Description")[0].childNodes[0].data
except:
s_description = "null"
try:
s_platform_ref = sample[i_s].getElementsByTagName(
"Platform-Ref")[0].childNodes[0].data
except:
s_platform_ref = "null"
try:
s_Last_Update_Date = sample[i_s].getElementsByTagName(
"Last-Update-Date")[0].childNodes[0].data
except:
s_Last_Update_Date = "null"
try:
s_Release_Date = sample[i_s].getElementsByTagName(
"Release-Date")[0].childNodes[0].data
except:
s_Release_Date = "null"
#SAGE 特有的
try:
s_anchor = sample[i_s].getElementsByTagName(
"Anchor")[0].childNodes[0].data
s_anchor = "(SAGE_anchor)" + s_anchor
except:
s_anchor = "(SAGE_anchor)null"
try:
s_type = sample[i_s].getElementsByTagName(
"Type")[0].childNodes[0].data
s_type = "(SAGE_type)" + s_type
except:
s_type = "(SAGE_type)null"
try:
s_tag_count = sample[i_s].getElementsByTagName(
"Tag-Count")[0].childNodes[0].data
s_tag_count = "(SAGE_count)" + s_tag_count
except:
s_tag_count = "(SAGE_count)null"
try:
s_tag_length = sample[i_s].getElementsByTagName(
"Tag-Length")[0].childNodes[0].data
s_tag_length = "(SAGE_len)" + s_tag_length
except:
s_tag_length = "(SAGE_len)null"
#把characteristic放在最后，是因为characteristic对每个GSE是不同的
chr_str = ''
try:
s_char_array = sample[i_s].getElementsByTagName(
"Characteristics")
for i in range(s_char_array.length):
s_char_tag = s_char_array[i].getAttribute("tag")
#text里面有换行符
s_char_text = s_char_array[i].childNodes[0].data
if not s_char_tag:
s_char_tag = 'characteristics'
chr_str = chr_str + "'" + s_char_tag + "'" + ":" + "'" + s_char_text + "'" + ","
s_char = "[char]({}){}".format(s_char_tag, s_char_text)
sample_char_list.append(s_char)
s_char_need = "*#*#*#".join(sample_char_list)
sample_char_list = []
except:
s_char_need = "null"
chr_str = re.sub(r'\n', '', chr_str)
chr_str = re.sub(r'\s+', ' ', chr_str)
output_col_1 = "{" + chr_str + "'organism':" + "'" + s_organism + "'" + ",'source name':" + "'" + s_source + "'" + ", 'title':" + "'" + s_title + "'" + ", 'last update date':" + "'" + s_Last_Update_Date + "'" + ", 'release date': " + "'" + s_Release_Date + "'" + ", 'method': " + "'" + p_technology_all + "'" + "}"
output_list.append(gse)
output_list.append(s_number)
output_list.append(output_col_1)
#output_list.append(virus_name)
#换行符和多个空格的问题
sample_single = s_number + "*#*#*#" + s_title + "*#*#*#" + s_channel + "*#*#*#" + s_source + "*#*#*#" + s_organism + "*#*#*#" + s_treatment + "*#*#*#" + s_growth + "*#*#*#" + s_molecule + "*#*#*#" + s_extract + "*#*#*#" + s_label + "*#*#*#" + s_data_processing + "*#*#*#" + s_library_strategy + "*#*#*#" + s_description + "*#*#*#" + s_platform_ref + "*#*#*#" + s_Last_Update_Date + "*#*#*#" + s_Release_Date + "*#*#*#" + s_anchor + "*#*#*#" + s_type + "*#*#*#" + s_tag_count + "*#*#*#" + s_tag_length + "*#*#*#" + s_char_need
sample_single_list = [sample_single]
sample_single_list = move_break(sample_single_list)
sample_single = sample_single_list[0]
output_list.append(sample_single)
#print("sample_single:{}".format(sample_single))
#zrb_bern=query_raw(output_col_1)
#print(sample_list_all)
hdq_bern = query_raw(sample_single)
#extract characteristic alone
# line_list=line.split('\t')
# line_text=line_list[0]
#line_dict={}
line_text_list = output_col_1.split(',')
line_dict = {}
match_list = [
'cell line', 'organism', 'cell type', 'method',
'source name', 'tissue', 'disease', 'treatment'
]
for i in line_text_list:
i = re.sub("'", "", i)
i = re.sub(r"\{", "", i)
i = re.sub(r"\}", "", i)
i = re.sub(r'"', "", i)
i = i.strip()
dcit_list = i.split(':')
#line_dict[str(dcit_list[0])]=str(dcit_list[1])
dcit_list[0] = re.sub("'", "", dcit_list[0])
dcit_list[0] = re.sub(r"\{", "", dcit_list[0])
dcit_list[0] = re.sub(r"\}", "", dcit_list[0])
dcit_list[0] = re.sub(r'"', "", dcit_list[0])
dcit_list[0] = str(dcit_list[0]).strip()
try:
line_dict[str(dcit_list[0])] = str(dcit_list[1])
except:
line_dict[str(dcit_list[0])] = 'null'
for i in match_list:
if i in line_dict.keys():
line_dict[i] = str(line_dict[i]).strip()
output_list.append(str(line_dict[i]))
else:
output_list.append('null')
output_list.append(s_library_strategy)
#换行符和多个空格的问题
#sample_single=s_number+"*#*#*#"+s_title+"*#*#*#"+s_channel+"*#*#*#"+s_source+"*#*#*#"+s_organism+"*#*#*#"+s_treatment+"*#*#*#"+s_growth+"*#*#*#"+s_molecule+"*#*#*#"+s_extract+"*#*#*#"+s_label+"*#*#*#"+s_data_processing+"*#*#*#"+s_description+"*#*#*#"+s_platform_ref+"*#*#*#"+s_Last_Update_Date+"*#*#*#"+s_Release_Date+"*#*#*#"+s_anchor+"*#*#*#"+s_type+"*#*#*#"+s_tag_count+"*#*#*#"+s_tag_length+"*#*#*#"+s_char_need
#zrb_bern=query_raw(output_col_1)
#print(sample_list_all)
hdq_bern = query_raw(sample_single)
#zrb_disease_str,zrb_disease_id_str,zrb_drug_str,zrb_drug_id_str,zrb_gene_str,zrb_gene_id_str=bern_list(zrb_bern)
# zrb_bern_list=[zrb_disease_str,zrb_disease_id_str,zrb_drug_str,zrb_drug_id_str,zrb_gene_str,zrb_gene_id_str]
# for i in zrb_bern_list:
# output_list.append(str(i))
hdq_disease_str, hdq_disease_id_str, hdq_drug_str, hdq_drug_id_str, hdq_gene_str, hdq_gene_id_str = bern_list(
hdq_bern)
hdq_bern_list = [
hdq_disease_str, hdq_disease_id_str, hdq_drug_str,
hdq_drug_id_str, hdq_gene_str, hdq_gene_id_str
]
test_disease = normalize.Normalize(hdq_disease_id_str)
disease_output_id_disease_name_str, disease_output_disease_name_str = test_disease.disease(
)
test_drug = normalize.Normalize(hdq_drug_id_str)
drug_output_id_drug_name_str, drug_output_drug_name_str = test_drug.drug(
)
test_gene = normalize.Normalize(hdq_gene_id_str)
gene_output_id_gene_name_str, gene_output_gene_name_str = test_gene.gene(
)
test_knock = normalize.Normalize(sample_single)
knock_out_down, knock_in, knock, over = test_knock.knock_out()
cell_line_text = normalize.Normalize(output_col_1)
cell_line_text_str = cell_line_text.cell_line()
cell_line_bern_text = normalize.Normalize(sample_single)
cell_line_bern_text_str = cell_line_bern_text.cell_line()
gsm_rrid = normalize.Normalize(s_number)
gsm_rrid_cell_line, gsm_rrid_disease = gsm_rrid.rrid_gsm()
hdq_bern_list = [
hdq_disease_str, hdq_disease_id_str,
disease_output_id_disease_name_str,
disease_output_disease_name_str, hdq_drug_str,
hdq_drug_id_str, drug_output_id_drug_name_str,
drug_output_drug_name_str, hdq_gene_str, hdq_gene_id_str,
gene_output_id_gene_name_str, gene_output_gene_name_str,
knock_out_down, knock_in, knock, over, cell_line_text_str,
cell_line_bern_text_str, gsm_rrid_cell_line,
gsm_rrid_disease
]
for j in hdq_bern_list:
output_list.append(str(j))
#for i in output_list :
line = '\t'.join(output_list)
line = line + '\n'
with open(output, "a", encoding='utf-8') as out:
out.write(line)
