"orthomcl" python multithreading loading to mysql database table
1
1
Entering edit mode
11 weeks ago
seok1213neo ▴ 10

while using orthomcl,

i am planning to load my local data into the similarsequence table.

but the problem is that my data is too large, it will take forever to load my data.

so i tried the code below to do some multithreading.

import threading
import os

class Worker(threading.Thread):
    def __init__(self, name):
        super().__init__()
        self.name = name

    def run(self):
        os.system ('/bin/bash -c "./orthomclLoadBlast ./orthomcl.config ./similarSequence_ar.txt"')

threads = []
for i in range(3):
    thread = Worker(i)
    thread.start()
    threads.append(thread)

for thread in threads:
    thread.join()

would this work for multithreading? increase my cpu usage and decrease my working time?

please help me i am running outta time

thank you!

mysql multiprocessing orthomcl multithreading • 204 views
ADD COMMENT
1
Entering edit mode
11 weeks ago

Your code will always execute the same piece of bash script, just three times, you would need to split the ./similarSequence_ar.txt into three pieces and then give each worker one piece. You could also use PorthoMCL, a parallel re-implementation of OrthoMCL to speed things up: https://github.com/etabari/PorthoMCL

I would personally recommend Orthofinder, it's much much much much faster than OrthoMCL, and doesn't require MySQL.

ADD COMMENT
1
Entering edit mode

I would personally recommend Orthofinder

I was going to say that. I spent quite some time trying to make OrthoMCL work to no avail. Besides, I think the development of OrthoMCL is kind of dead.

ADD REPLY

Login before adding your answer.

Traffic: 1525 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6