def get_L1_templates(L1_cols, step_choose, template_path, model_path):
'''
descript:
将词列数据和分词列数据组合使用，按不同的特征函数的数量创建L1模板，
对不同的模板用 template_L1_w:i_s:j 命名
上面的 :i = 5|7|10, 对应特征函数数量
上面的 :j = 0|5|7|10, 对应特征函数数量
return:
返回模板名列表
'''
time = 0
template_list = [] #存储模板文件名的列表
# 只用word，没用分词
for i in step_choose:
type = 'L1_w' + str(i) + '_s0'
time += 1
name = 'template_' + type + '_' + str(time)
unigram = [(0, i)]
create_template.create_template(type, time, unigram) #创建模板
template_list.append(name)
# 用word和分词的数据
for i in step_choose:
for j in step_choose:
type = 'L1_w' + str(i) + '_s' + str(j)
time += 1
name = 'template_' + type + '_' + str(time)
unigram = [(0, i), (1, j), (2, j)]
create_template.create_template(type, time, unigram) #创建模板
template_list.append(name)
return template_list
def templates(self):
plates = raw_input('Do you need to create templates? (y/n): ')
if plates == 'y':
create_template()
else:
pass
def main(): # parse args opts = parse_args() # get current absolute path wd = make_abs_path(opts.project_name) # insert template create_template(opts) # chnage directory os.chdir(wd) # # make virtual environment # mkvirtualenv(opts.project_name) # initialize git repository git_init() #workon(opts.project_name) print "DONE: Your new python project and git repo have been created in '%s/'" % opts.project_name
def setup_template(templates_link,
template_file_path,
template_name='Untitled template'):
template, headers = create_template(templates_link,
template_file_path.split('.')[-1],
template_name)
template_link = template['links']['self']
image_link = headers['Location']
print(f'Successfully created template at {template_link}')
upload_image(image_link, template_file_path)
print(f'Successfully uploaded image {template_file_path} at {image_link}')
return template
def main(variant_alias_file, output, images, xlsx, sheet, pdf):
''' For each variant alias, extract the approriate variant and mutation
information and export as a variant confirmation report.
variant_alias_file: should be in a text file where each new line
contains a different variant alias or a single
variant alias.
'''
# intialise 2 objects using All_Variants & Mutation ID sheets
extract = ExtractInfo(xlsx, sheet, 2)
# open the All_Variants and Mutation ID sheet
variant_sheet = extract.open_spreadsheets()
# use the headers of the above workbooks to create a header dicts
create_variant_dict = extract.create_header_dicts(variant_sheet)
# create a template report
create_template(output)
# for each variant alias...
variant_list = [var_alias for var_alias in open(variant_alias_file, "r")]
for var_alias in tqdm.tqdm(variant_list):
var_alias = var_alias.rstrip("\n")
# Open template every iteration, otherwise information leftover from last
# iter in cells
template = openpyxl.load_workbook("test_template.xlsx")
template_sheet = template.worksheets[0]
# extract variant information from spreadsheet
variant_row = extract.get_row(variant_sheet, var_alias)
variant_info = extract.get_query_info(variant_row,variant_sheet)
# get the completed header dictionarys
variant_dict = extract.header_contents
# with the collected information, fill out the template report.
Fill = FillReport(template, template_sheet, var_alias, variant_dict, images)
Fill.fill_report()
# insert sanger trace and IGV image into the report
Fill.insert_image(var_alias+"_F", "B22", 600, 242)
Fill.insert_image(var_alias+"_R", "B22", 600, 242)
Fill.insert_image(var_alias+"_IGV", "B35", 600, 242)
# get mutation information for the given variant alias if an ID is there
Fill.pick_comment()
#print("\t".join((var_alias,variant_dict.get("Category"),
# variant_dict.get("Mutation_ID"))))
output_name = (output+str(variant_dict.get("Sample_Name"))+
"_"+str(variant_dict.get("Variant_Alias"))+"_"+
"VariantConfirmationReport"+".xlsx")
# save the filled sheet and convert to PDF
template.save(output_name)
if pdf:
Fill.convert2pdf(output_name)
# clear the dicts items
variant_dict = {key: "-" for key in variant_dict}
if __name__ == "__main__":
(inputs, success) = read_inputs()
num_subjects = len(inputs)
if success:
print("Starting processing")
for a, subject in enumerate(inputs):
# print("Processing ", subject,"|| overall Progress --> {0: >3} % done".format(((a+1)/num_subjects)*100))
images = inputs[subject]["images"]
results = inputs[subject]["results"]
templates = inputs[subject]["templates"]
templates = [cv.imread(template_path, 0) for template_path in templates]
T = []
for template in templates:
T += create_template(template)
for i, image_path in enumerate(images):
print("Processing ", subject,"|| Progress --> {0: >3} % done".format(((i+1)/len(images))*100))
image = cv.imread(i age_path)
img_gray = cv.cvtColor(image, cv.COLOR_BGR2GRAY)
probablity_maps = template_matching(img_gray, templates, threshold=0.7)
points = []
for temp_maps in probablity_maps:
for point in temp_maps:
points.append(point)
points = NMS(points)
for pt in points:
[xi, yi, ci, hi, wi] = pt
cv.rectangle(image, (xi, yi), (xi + wi, yi + hi), (0,0,255), 1)
def main(variant_alias_file, output, images, xlsx, sheet, pdf):
''' For each variant alias, extract the approriate variant and mutation
information and export as a variant confirmation report.
variant_alias_file: should be in a text file where each new line
contains a different variant alias or a single
variant alias.
'''
# intialise 2 objects using All_Variants & Mutation ID sheets
extract = ExtractInfo(xlsx, sheet, 2)
# open the All_Variants and Mutation ID sheet
variant_sheet = extract.open_spreadsheets()
# use the headers of the above workbooks to create a header dicts
create_variant_dict = extract.create_header_dicts(variant_sheet)
# create a template report
create_template(output)
# for each variant alias...
variant_list = [var_alias for var_alias in open(variant_alias_file, "r")]
for var_alias in tqdm.tqdm(variant_list):
var_alias = var_alias.rstrip("\n")
# Open template every iteration, otherwise information leftover from last
# iter in cells
template = openpyxl.load_workbook("test_template.xlsx")
template_sheet = template.worksheets[0]
# extract variant information from spreadsheet
variant_row = extract.get_row(variant_sheet, var_alias)
variant_info = extract.get_query_info(variant_row, variant_sheet)
# get the completed header dictionarys
variant_dict = extract.header_contents
# with the collected information, fill out the template report.
Fill = FillReport(template, template_sheet, var_alias, variant_dict,
images)
Fill.fill_report()
# insert sanger trace and IGV image into the report
Fill.insert_image(var_alias + "_F", "B22", 600, 242)
Fill.insert_image(var_alias + "_R", "B22", 600, 242)
Fill.insert_image(var_alias + "_IGV", "B35", 600, 242)
# get mutation information for the given variant alias if an ID is there
Fill.pick_comment()
#print("\t".join((var_alias,variant_dict.get("Category"),
# variant_dict.get("Mutation_ID"))))
output_name = (output + str(variant_dict.get("Sample_Name")) + "_" +
str(variant_dict.get("Variant_Alias")) + "_" +
"VariantConfirmationReport" + ".xlsx")
# save the filled sheet and convert to PDF
template.save(output_name)
if pdf:
Fill.convert2pdf(output_name)
# clear the dicts items
variant_dict = {key: "-" for key in variant_dict}