Need help for Genome program

[Ciprofloxacin]

Hi, I'm Ciprofloxacin. I was writing program to find which genes in the PSSD group are differ than control group. That medicines are not only altering one system or gene. We can find a cure more easily while knowing which genes and systems are altered.
I had wrote a program and it works well. But just one PC is not have enough capacity to finish it before weeks or even months. So I wrote another program to calculate only control group to get help from other members too.
(more information about what we trying to do: https://en.wikipedia.org/wiki/Genome-wi ... tion_study)
Steps:
- https://opensnp.org/genotypes This is site that peoples uploading their genom files. You can download how much you want. Just ANCESTRY and 23ANDME files are supported.
- These files are normally have random extensions( for example .5236). You have to change their extensions to ".txt".
- After downloading, change their name to 0, 1, 2, etc. Files must be like that finally: 0.txt 1.txt 2.txt etc..
- Move all the files and my script into same folder.
- Run by clicking it twice (It's different in linux. You have to open terminal and enter "python Genome_control.py")
- Upload log file here after finished. We finally merge all the logs (I finished log merger script) and comparise them with PSSD group.

There is video too how to do it:

https://youtu.be/nIpa7THV3zE

Program Links:
Python version: 2.7.15 ----> https://www.python.org/ftp/python/2.7.1 ... 2.7.15.msi (Windows 32 bit) https://www.python.org/ftp/python/2.7.1 ... .amd64.msi (Windows 64 bit)
Python coming as default on Linux. You don't have to do anything.

Universal: https://drive.google.com/file/d/10F2JXt ... sp=sharing
Linux / Cython compiled (much faster) : https://drive.google.com/file/d/1DnGCge ... sp=sharing
Windows / Cython compiled : .....

We must do it in sync. I will take volunteers names and write them here. Results may be wrong if we process same genomes more than one.

List:

[Timm Thaler]

So I don't need to install Linux?
My Laptop is not great, how many files is a good number to download, if I want to run it over night?

[Jaxx]

Please align with Ghost how to set this up, it doesnt make sense to have 2 initiatives in parallel.

Nice progress though!

[Ciprofloxacin]

So I don't need to install Linux?
My Laptop is not great, how many files is a good number to download, if I want to run it over night?

Yes, you don’t have to.
I can’t predict. But 6 or 7 files should be enough.
I forget to say, the script is accelerating after a certain percentage. Because it caching all the lines to not to scan them again. That percentage is 100 / file_count.

[GIXXER]

How big of a computer would be needed to do this?

[Ciprofloxacin]

How big of a computer would be needed to do this?

There is no minimum requirements. You can either run with 5 files or 20 files. But of course don’t do it without at least 5 file. If we get much log contain few control group count, It would be inefficient.

[Timm Thaler]

I am currently on vacation, but you can count on me to help in a weeks time!

[Vox]

I can help

[Ghost]

This is awesome. Keep up the work. I'll be spending a lot of time on this project this weekend. I've been analyzing some results.

However, WE NEED MORE GENOMES. I don't know what I need to do to get more, but I may increase my incentives / punishments to do so. What we have now simply isn't enough.

[Janie]

Just sent back yesterday my sample to the laboratory. I will send you the raw data as soon as I get it. I'm a tipical PSSD case from 11 escitalopram pills