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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 |