add multiprocessing change to python3 #3
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…ts in order to make it multiprocessing this should allow a time clean up
…r with multiprocessing
… going to test on eight core machine
… far the faster of the ways it'll most like run faster on more cores
…nt for returning to any output file found this was redundants, add in a proper timed trail for a single core usage on 1.fa time trails into the readme file multiproccessing is done
SaberYoun6
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Jun 1, 2020
chopSEQ.py
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| #Reference: https://stackoverflow.com/questions/287871/print-in-terminal-with-colors-using-pyton | ||
| #this allow the multiprocessor call and allow for the ability to print out the results | ||
| with concurrent.futures.ProcessPoolExecutor() as executor: | ||
| results =[executor.submit(process_seq_records, seq_record, forward_primer, reverse_primer, verbosity, minimum_read_length_threshold, maximum_read_length_threshold) for seq_record in SeqIO.parse(input_file,"fasta")] | ||
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| for seq_record in SeqIO.parse(input_file,"fasta"): | ||
| if verbosity: | ||
| print('\x1b[6;37;40m' + str(seq_record.id) + '\x1b[0m') | ||
| forward_orientation_forward_primer_alignment=pairwise2.align.localms(str(seq_record.seq),forward_primer,primer_match_score, primer_mismatch_score, primer_open_gap_score, primer_extend_gap_score, one_alignment_only=1) | ||
| forward_orientation_reverse_primer_alignment=pairwise2.align.localms(str(seq_record.seq),str(Seq(reverse_primer).reverse_complement()),primer_match_score,primer_mismatch_score, primer_open_gap_score, primer_extend_gap_score, one_alignment_only=1) | ||
| reverse_orientation_forward_primer_alignment=pairwise2.align.localms(str(seq_record.seq),reverse_primer,primer_match_score,primer_mismatch_score, primer_open_gap_score, primer_extend_gap_score, one_alignment_only=1) | ||
| reverse_orientation_reverse_primer_alignment=pairwise2.align.localms(str(seq_record.seq),str(Seq(forward_primer).reverse_complement()),primer_match_score,primer_mismatch_score, primer_open_gap_score, primer_extend_gap_score, one_alignment_only=1) | ||
| for resultant in concurrent.futures.as_completed(results): | ||
| print(resultant.result()) |
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This is microprocessing changing list comprehension for the reading in of the file in.
…single core add in new things to help to tell you how many processor a machine has
…misspelled one of them
… 0 or -negative processors
…rted to try and speed up the timing
…to send and error to the system call if you tried to access all the cores in your system it would have of dumped you to the usages and then exited the program
…oing to run a combined file time trail
…realized you cannot have zero processor being called and wanted all the threads to be called
… didn't bold instead left with *** ##:##***
I'm trying to manage any security concern that might come up
Create SECURITY.md
Create codeql-analysis.yml
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made it executable, change the script to python3 and add in multiprocessing through a list comprehension. add in a git ignore and an actual license and an AUTHORS pages as well. I'm not a fan of indentions so I changed it to be spaces instead.