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Old 2012-11-16, 18:57   #1
Greebley's Avatar
May 2009
Dedham Massachusetts USA

84310 Posts
Default Could use some scripting help (windows)

Currently, I have a very primitive way of submitting sequences to the database (this is a *.bat file on windows). For example:

aliqueit -c 60 6261388
aliqueit -s 0 6261388
aliqueit -c 60 6261822
aliqueit -s 0 6261822

Each number is listed separately (I create the list using emacs macros so long lists isn't an issue).

This has some major weaknesses for new sequences like ones over 6 million. The biggest problem is that I hit the 3000 limit, I am not submitting the sequences to the database at all

I was thinking of splitting out the sends to the data base from the running of the sequences, but to do that I really need a way to know if I am at the 3000 limit and I need a loop like the following pseudo-code:

for each item in a list:
Check if we are at the 3000 limit. if so wait 5 min and try again
If not at the limit, submit the sequence (using aliqueit -s or some other method)

It also occurs to me that submitting from 0 each time is sending too much. An enhancement is to find the length of the sequence in the database and send only the needed part (which may be nothing in which case I can skip the sequence). I could use the current index/length for:
aliqueit -s <current index> <sequence>
I don't know how expensive it is to find the length of a sequence vs sending the whole thing, but I am thinking finding the length is cheaper. I do know the number of database queries is quite large if I submit from 0 each time.

I could look up how to loop in a batch file from the internet, but I have no idea how to find if I am at the limit (optional: or find the length of the sequence from the database).

I was wondering if anyone has done this already, or can help me do this. I will be away next week for thanksgiving and I can't respond right away, so thanks in advance for any help anyone can offer.

I do have perl, but am not proficient in it if that is better than a batch file.

Last fiddled with by Greebley on 2012-11-16 at 18:57
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Old 2012-11-16, 19:53   #2
Basketry That Evening!
Dubslow's Avatar
"Bunslow the Bold"
Jun 2011
40<A<43 -89<O<-88

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I have no idea how to do batch files, and not much better an idea how to do bash scripting (Linux equiv) either. If you have Python, I could whip up whatever you need, if nothing else occurs to you. (LaurV might be able to help with the batch scripting, or perhaps even kladner from "up north".)

For my dinky script that runs aliquot sequences, I pass the "original length" as some of the info so that it doesn't overdo the submit.
#! /usr/bin/python3
import os, sys
R = False
list = """198786   723
221130   682
229560   612
259716   991
263952   573
275880   811
280686   998
281460   828
297000   766
299184   799
306000   838
307746   918
310100   848
316350   971"""
if len(sys.argv) > 1 and sys.argv[1] == '-R':
     R = True
     first = list.split()[0]

for seq, ind in [line.split() for line in list.splitlines()]:
     if not (R and seq == first):
          os.system('wget --cache=off "{}&type=1" -O {}.elf'.format(seq, seq))
     os.system('taskset fe nice -n 19 ~/yafu/ali/aliqueit -y {} -d 120'.format(seq))
     os.system('~/yafu/ali/aliqueit -s {} {}'.format(ind, seq))
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