search

statgen / locuszoom-standalone

Create regional association plots from GWAS or meta-analysis
http://locuszoom.org/
58 stars 19 forks source link

Error with SNP=NA and chr/start/end specified #3

Open fsakhtari opened 7 years ago

fsakhtari commented 7 years ago

Hello, I believe that there is a bug in Locuszoom version 1.4 ("05/01/2017"). If no SNP is specified, and the region is specified using the chr/start/end, then the region is now defined as 'chr16:69234563-70257828' . Now the following lines in m2zfast.py, evaluates this as a SNP even though it is not because of the '.*' line 99 : RE_SNP_1000G = re.compile("(chr)?([0-9a-zA-z]+):([0-9]+).*") line 282: elif RE_SNP_1000G.search(string): return TRUE

This leads to problems later as this SNP does not have a position, etc... I was able to fix this by changing the following: line 99 in m2zfast.py: RE_SNP_1000G = re.compile("(chr)?([0-9a-zA-z]+):([0-9]+)$") I was running the standalone locus zoom version in batch mode with a metal and a hitspec file. I've attached edited relevant versions of these files along with the locuszoom log output and error.

Error: File "/usr/local/locuszoom/bin/../src/m2zfast.py", line 1968, in runAll if refsnp.pos is None: AttributeError: 'str' object has no attribute 'pos'

This prevents running locus zoom with SNP=NA and chr/start/end specified. A workaround is to specify a SNP in the region which will then be used as the reference SNP along with the chr/start/end.

My fix above works for the scenario I mention but has not been unit tested. In my organization, this software is installed on a server shared by a large number of people who want to run published software. Hence, I can only make this change in my private copy of locuszoom. Would it be possible to provide a patch release with this fix?

Attachment with metal, hit spec and locus zoom log -
Archive.zip

welchr commented 7 years ago

Indeed sounds like a bug. Will take a look at patching in your change shortly. Does your organization accept hotfixes, or do they require that it be a new "release" from the software publisher's website? Any idea how they verify new releases?

fsakhtari commented 7 years ago

Hi Ryan,Thank you for looking into this. I work for North Carolina State University. I am a graduate student there. We'd be OK with a hotfix or patch release. We just need to specify the LocusZoom version number that we used to generate the plots in our research articles for publications.The server on which the software is installed is mainly for student use, so the new releases aren't verified as such. It is up to the end user like myself to ensure that it works as expected. Thanks,Farida Akhtari

On Tuesday, July 18, 2017 10:03 AM, Ryan Welch <notifications@github.com> wrote:

Indeed sounds like a bug. Will take a look at patching in your change shortly. Does your organization accept hotfixes, or do they require that it be a new "release" from the software publisher's website? Any idea how they verify new releases?— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.