def analysis(paths_dict, cov, ident, collapsed, absence, height, width): #statsA + statisticsA
cov = int(cov.get())
ident = int(ident.get())
collapsed = int(collapsed.get())
absence = int(absence.get())
height =int(height.get())
width = int(width.get())
savepath = paths_dict[SAVEPATH]
#openpath = paths_dict[OPENPATH]
try:
facade.analysis(savepath, cov, ident, collapsed, absence, sys.stderr)
except Exception as e:
_display(str(e))
sys.stderr.write(str(e)+"\n")
tkMessageBox.showinfo("ORTHOPROK","analysis is done!!")
# load the protein listbox with data
df_protein = pd.read_csv(analyzer.get_file5(savepath))
protein_list= df_protein.ix[:,2::].columns.tolist()
for item in protein_list:
protein_listbox1.insert(END,item)
novi = Toplevel()
image = Image.open(analyzer.get_tmpfiles(savepath) +'graphic_stats.tif')
photo = ImageTk.PhotoImage(image)
#image not visual
canvas = Canvas(novi, width = (width*100), height = (height*100),
scrollregion = (0,0,(width*100),(height*100)))
canvas.create_image(0, 0,image = photo, anchor="nw")
canvas.photo = photo
hbar=Scrollbar(novi,orient=HORIZONTAL)
hbar.pack(side=BOTTOM,fill=X)
hbar.config(command=canvas.xview)
vbar=Scrollbar(novi,orient=VERTICAL)
vbar.pack(side=RIGHT,fill=Y)
vbar.config(command=canvas.yview)
canvas.config(width=900,height=600)
canvas.config(xscrollcommand=hbar.set, yscrollcommand=vbar.set)
canvas.pack(side=LEFT,expand=True,fill=BOTH)
canvas.pack(expand = YES, fill = BOTH)
return
def get_all_text(self, post):
"""
Obtain all the text of a submission, including its comments.
If a comment is passed, its parent submission will be determined.
:param post: The comment of submission to obtain the thread's text
from.
:return: A cleaned up version of all the text within the thread, ready
for further analysis.
"""
all_text = ''
# Get the parent submission of a comment
if isinstance(post, praw.objects.Comment):
submission_id = post.link_id[3:]
post = self.reddit.get_submission(submission_id=submission_id)
submission_text = post.selftext
submission_title = post.title
''.join((all_text, submission_title + '\n', submission_text + '\n'))
comments = self.get_comments(post)
for comment in comments:
''.join((all_text, comment.body + '\n'))
clean_content = Analyzer.clean_up(all_text)
return clean_content
def Blast (paths_dict, REDO):
sys.stderr.write("Starting Blast command...\n")
querypath = paths_dict[QUERYPATH]
savepath = paths_dict[SAVEPATH]
openpath = paths_dict[OPENPATH]
utils.change_extension_fasta(openpath)
utils.change_extension_fasta(querypath)
queryDir = querypath+"/"
subjectDir = openpath+"/"
outputDir = analyzer.get_outputfolder(savepath)
#creates output directory in project directory
# newpath = savepath+"/output"
# if not os.path.exists(newpath):
# os.makedirs(newpath)
if not os.path.exists(outputDir):
os.makedirs(outputDir)
facade.Blast(queryDir, subjectDir, outputDir,
known_query_list, known_target_list,
REDO , _display, sys.stderr) # CPC2018
tkMessageBox.showinfo("ORTHOPROK","Blast is finished!!")
displayedText.set('Blast is done!!')
sys.stderr.write("Finished Blast command\n")
return
def is_recipe(self, content):
"""
Calls Analyzer method to check if a body of text has the qualities of a
recipe.
:param content: The body of text to analyze.
"""
return Analyzer.determine_if_recipe(content)
def check_post(self, post):
"""Checks a post for qualities of a recipe.
:param post: The post to get the comments from.
"""
if isinstance(post, praw.objects.Submission):
content = post.selftext
url = post.permalink
else: # Comment
content = post.body
submission_id = post.link_id[3:]
parent_post = self.reddit.get_submission(
submission_id=submission_id)
url = parent_post.permalink + post.id
clean_content = Analyzer.clean_up(content)
if self.is_recipe(clean_content):
print("Got a recipe!! Mama mia! " + str(datetime.now()))
all_text = self.get_all_text(post)
author = post.author.name
karma = post.score
date_posted = post.created
post_id = post.id
title = Analyzer.determine_title(post)
ingredients = Analyzer.get_ingredients(content)
instructions = Analyzer.get_instructions(content)
recipe_type = Analyzer.determine_type(all_text)
post_info = PostInfo(author, karma, date_posted, post_id, url)
refined_post = RefinedPost(title, ingredients, instructions,
recipe_type)
recipe = Recipe(post_info, refined_post)
self.recipe_handler.add(recipe)
def main():
analyzer = stat.Analyzer(len(sys.argv), sys.argv)
analyzer.run()