I want to write a function in Python for a tab delimited file I am dealing
with,to filter out values from a column, and put that parameter as a command
line option while running the script.
So,if the limit is 10,the filter out all the rows with values less than 10.
Also,I want to check if the number entered is numeric or not else display the
message "its not numeric".
So,the command line would be:
python script.py file --quality [limit]
The Python script:
import sys
arg = []
for a in sys.argv:
arg.append(a)
quality = arg[2]
To be more specific,the file I am dealing with is a Samfile,and using package
Pysam,which has mapping quality limits in the 5th column.
https://media.readthedocs.org/pdf/pysam/latest/pysam.pdf
Commandline:
python script.py samfile --quality [limit]
I am reading the samfile using this:
samfile = pysam.Samfile(arg[1], "rb" )
mapqlim = arg[2]
I am a Python beginner,but saw one of the modules,argparse. How can I
accomplish this using argparse in Python?
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