I trimmed my Illumina short reads, forward and reverse, by using Trimmomatic. The Trimmomatic's outputs were: paired_1 - unpaired_1, and paired_2 - unpaired_2.fastq.gz files. I want to know how big was the impact of trimming by counting the number of reads and bases of each file in my directory. I had made a script to count the number of bases and reads for each file in my directory; however, I have problems in
if __name__=='__main__'. When I do the for loop I don't know the order of the files that will be run, how can I make it to call the files by the order I see from the screen? Additionally, I also need help with correcting the script as I don't get any stdout.
Thank you in advance for your help.
#!/usr/bin/env python from sys import argv import os def get_num_bases(file_content): total =  for linenumber, line in enumerate(file_content): mod=linenumber%4 if mod==0: ID = line.strip()[1:] #print(ID) if mod==1: seq = line.strip() counting = 0 counting += seq.count("T")+ seq.count("A") + seq.count("C") + seq.count("G") total.append(counting) allbases = sum(total) print("Number of bases are: " , allbases) def get_num_reads(file_content): total_1 =  for line in file_content: num_reads = 0 num_reads += content.count(line) total_1.append(num_reads) print("Number of reads are: ", sum(total_1)/int(4)) if __name__=='__main__': path = os.getcwd() dir_files = os.listdir(path) list_files =  for file in dir_files: if file.endswith("fastq.gz"): if file not in list_files: file_content = open(file, "r").readlines() list_files.append(file) print("This is the filename: ", file, get_num_bases(file_content), get_num_reads(file_content))