search

berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
MIT License
6 stars 6 forks source link

Creating fire plot takes too much time #50

Closed ghost closed 7 years ago

ghost commented 7 years ago

during processing3 in WGseq the function allelic_ratios_WGseq lines 196-237 takes to much time and causes the whole process to be very slow, the process is stuck especially on the num2str function we should change it, maybe use scanf with %d. profile_results.zip

darrenabbey commented 7 years ago

That is a very good idea. That section of code was written with convenience in mind, not processing speed.

On Sep 27, 2016 6:13 AM, "GuyKha" notifications@github.com wrote:

during processing3 in WGseq the function allelic_ratios_WGseq lines 196-237 takes to much time and causes the whole process to be very slow, the process is stuck especially on the num2str function we should change it, maybe use scanf with %d. profile_results.zip https://github.com/berman-lab/ymap/files/495306/profile_results.zip

attached a the profiler output

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/berman-lab/ymap/issues/50, or mute the thread https://github.com/notifications/unsubscribe-auth/AKPuRKH6Zp9mWEB9Znv2ZGZi3csyi3RIks5quPpJgaJpZM4KHip7 .

ghost commented 7 years ago

I have updated the code to work with text scan to process the putative or trimmed SNPs file which greatly improved the running time (profile_results2.zip).

As you can see the strcmp to check for comment lines took also very long time so I have changed it too and now there is no explicit check for comment line and it's implied by not finding the current chromosome in the chromosome list and the profile results show great improvement - profile_results3.zip

darrenabbey commented 7 years ago

I originally wanted there to be an explicit comment indicator, but it does make sense the way you have done it. It now should more robustly fail well under the input of malformatted text.

I'm glad there has been such a speed improvement.

On Nov 13, 2016 11:49 PM, "GuyKha" notifications@github.com wrote:

I have updated the code to work with text scan to process the putative or trimmed SNPs file which greatly improved the running time ( profile_results2.zip https://github.com/berman-lab/ymap/files/588445/profile_results2.zip).

As you can see the strcmp to check for comment lines took also very long time so I have changed it too and now there is no explicit check for comment line and it's implied by not finding the current chromosome in the chromosome list and the profile results show great improvement - profile_results3.zip https://github.com/berman-lab/ymap/files/588455/profile_results3.zip

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/berman-lab/ymap/issues/50#issuecomment-260253710, or mute the thread https://github.com/notifications/unsubscribe-auth/AKPuRJ_QyyI1DnRx5RCJZZhHLLv-am9aks5q9_aAgaJpZM4KHip7 .

ghost commented 7 years ago

Fixed by commits 0776c0ae3489f8d114fe1a63022f22f13c01de4f and c40c3d313e1b688d3d846aab29287c5418d6b207