Datasets:

---

thisisanshgupta

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Pycode

like 1

for subline in indexqc:

straindata = [x.rstrip() for x in subline.rstrip().split(""\t"")]

# Try and replicate the Illumina rules to create file names from ""Sample_Name""

samplename = samplenamer(straindata, 1)

# Use the sample number -1 as the index in the list of objects created in parsesamplesheet

strainindex = int(straindata[0]) - 1

# Set run to the .run object of self.samples[index]

run = self.samples[strainindex].run

# An assertion that compares the sample computer above to the previously entered sample name

# to ensure that the samples are the same

assert self.samples[strainindex].name == samplename, \

""Sample name {} does not match object name {}"" \

.format(self.samples[strainindex].name, samplename)

# Extract and format the percent of reads (passing filter) associated with each sample

# noinspection PyTypeChecker

percentperstrain = float(""{:.2f}"".format(float(straindata[5])))

# Calculate the number of reads passing filter associated with each sample:

# percentage of reads per strain times the total reads passing filter divided by 100

numberofclusterspf = int(percentperstrain * tclusterspf / 100)

# Update the object with the variables

run.SampleNumber = straindata[0]

run.NumberofClustersPF = numberofclusterspf

run.TotalClustersinRun = tclusterspf

run.PercentOfClusters = percentperstrain

run.flowcell = self.flowcell

run.instrument = self.instrument

else:

strainindex = 0

for i in range(len(self.samples)):

# Set run to the .run object of self.samples[index]

run = self.samples[strainindex].run

# Update the object with the variables

run.SampleNumber = strainindex + 1

run.NumberofClustersPF = 'NA'

run.TotalClustersinRun = 'NA'

run.PercentOfClusters = 'NA'

run.flowcell = self.flowcell

run.instrument = self.instrument

strainindex += 1"

5,"def fix_raw_path(path):

""""""Prettify name of path

:param path: path to fix

:return: Good name for path

""""""

double_path_separator = PATH_SEPARATOR + PATH_SEPARATOR

while path.find(

double_path_separator) >= 0: # there are double separators

path = path.replace(double_path_separator,

PATH_SEPARATOR) # remove double path separator

if is_folder(path) and not path.endswith(""/""):

path = path + ""/""

return path"

6,"def remove_year(name):

""""""Removes year from input

:param name: path to edit

:return: inputs with no years

""""""

for i in range(len(

name) - 3): # last index is length - 3 - 1 = length - 4

if name[i: i + 4].isdigit():

name = name[:i] + name[i + 4:]

return remove_year(

name) # if there is a removal, start again

return name"

7,"def remove_brackets(name):

""""""Removes brackets form input

:param name: path to fix

:return: inputs with no brackets

""""""

name = re.sub(

r""([(\[]).*?([)\]])"",

r""\g<1>\g<2>"",

name

) # remove anything in between brackets

brackets = ""()[]{}"" # list of brackets

for bracket in brackets:

name = name.replace(bracket, """")

return name"

8,"def extract_name_max_chars(name, max_chars=64, blank="" ""):

""""""Extracts max chars in name truncated to nearest word

:param name: path to edit

:param max_chars: max chars of new name

:param blank: char that represents the blank between words

:return: Name edited to contain at most max_chars

""""""

new_name = name.strip()

if len(new_name) > max_chars:

new_name = new_name[:max_chars] # get at most 64 chars

if new_name.rfind(blank) > 0:

new_name = new_name[:new_name.rfind(blank)] # nearest word

return new_name"

9,"def prettify(name, blank="" ""):

""""""Prettify name of path