I have a question.
I am writing a program in Python. I am using an pileup file generated from samtools. I have loaded the file into python and I want to loop through the file to find the values in the 4th column of each line.
I have managed to do this for only one line so far using the code below...
How can I combine the code in order to loop through the entire file to find the values in the fourth column that are equal to or less than 10 ?
If the number in the fourth column is equal to or less than 10, then I want to print out this line.
This is my code so far:
# A different way to open the mpileup file. f = open("/Users/m.o.l.s/outputFile.mpileup","rt") line_1 = f.readline() print(line_1) # Split up the strings based on tabs individuals = line_1.split("\t") print(individuals) # The value we are interested in is in the 3rd index position The_Coverage = individuals print(The_Coverage) # If this number is less than 10, the row needs to be displayed if The_Coverage <= "10": print(The_Coverage) else: print("The Coverage is not less than or equal to 10")
... so this code works , but only for 1 line and I have about 200 lines in the file
Should I turn the file into a pandas data frame? I would appreciate any help possible to further this along. Best.