[ERROR] 'str' object has no attribute 'N' about focus

[quattro]

Hi @BinglanLi , could you output the header of the GWAS input you're using?

Thank you.

[BinglanLi]

$ focus munge SNP_gwas_mc_merge_nogc.tbl.uniq --N-col N --frq Freq1.Hapmap --p P --signed-sumstats Z,0  --output giant_bmi_gwas_focus_munge_cleaned

$ gunzip -c giant_bmi_gwas_focus_munge_cleaned.sumstats.gz | head
CHR	SNP	BP	A1	A2	Z	N
12	rs1000000	126890980	G	A	0.023	231410.000
4	rs10000010	21618674	T	C	-0.959	322079.000
4	rs10000013	37225069	A	C	-2.159	233886.000
4	rs10000017	84778125	C	T	-0.739	233146.000
3	rs1000002	183635768	C	T	2.946	233932.000
4	rs10000023	95733906	G	T	0.632	233860.000
4	rs10000029	138685624	T	C	1.369	179950.000
3	rs1000003	98342907	G	A	1.118	233852.000
4	rs10000030	103374154	A	G	-0.130	233939.000

[quattro]

HI @BinglanLi ,

I'm having trouble replicating this bug. I used the GWAS data you sent, the 1000GP3 EUR plink data as LD ref and the latest focus db using sqlite 3.28.0 (installed by conda) and found

===================================
              FOCUS v0.6            
===================================
focus finemap
	/home/rcf-40/nmancuso/projects/twas_proj/data/GWAS/focus_staging/giant_bmi_gwas_focus_munge_cleaned.part.sumstats.gz
	/home/rcf-40/nmancuso/projects/twas_proj/data/1000GP3/EUR//1000G.EUR.QC.1
	/home/rcf-40/nmancuso/projects/twas_proj/data/FOCUSdb/focus.db
	--max-genes 1
	--chr 1
	--plot

Starting log...
[...]
[2019-06-24 15:21:29 - WARNING] No GWAS SNPs with p-value < 5e-08 found at 1:48002576 - 1:48978188. Skipping
[2019-06-24 15:21:38 - INFO] Starting fine-mapping at region 1:48978188 - 1:49894177
[2019-06-24 15:21:43 - INFO] Completed fine-mapping at region 1:48978188 - 1:49894177
[2019-06-24 15:21:43 - INFO] Creating FOCUS plots at region 1:48978188 - 1:49894177
[2019-06-24 15:21:53 - INFO] Starting fine-mapping at region 1:49894177 - 1:51713726
[2019-06-24 15:21:59 - INFO] Completed fine-mapping at region 1:49894177 - 1:51713726
[2019-06-24 15:21:59 - INFO] Creating FOCUS plots at region 1:49894177 - 1:51713726
[2019-06-24 15:22:00 - WARNING] No GWAS SNPs with p-value < 5e-08 found at 1:51713726 - 1:54226262. Skipping

Can you share the installed versions of matplotlib and seaborn?

Thank you.

[BinglanLi]

Python 3.6.5 (default, Jun 19 2018, 16:28:05) [GCC 6.2.0] on linux Type "help", "copyright", "credits" or "license" for more information.

>> import matplotlib >> matplotlib.__version__

'3.1.0'

>> import seaborn >> seaborn.__version__

'0.9.0'

…

On Mon, Jun 24, 2019 at 6:24 PM Nicholas Mancuso ***@***.***> wrote: HI @BinglanLi <https://github.com/BinglanLi> , I'm having trouble replicating this bug. I used the GWAS data you sent, the 1000GP3 EUR plink data as LD ref and the latest focus db using sqlite 3.28.0 (installed by conda) and found =================================== FOCUS v0.6 =================================== focus finemap /home/rcf-40/nmancuso/projects/twas_proj/data/GWAS/focus_staging/giant_bmi_gwas_focus_munge_cleaned.part.sumstats.gz /home/rcf-40/nmancuso/projects/twas_proj/data/1000GP3/EUR//1000G.EUR.QC.1 /home/rcf-40/nmancuso/projects/twas_proj/data/FOCUSdb/focus.db --max-genes 1 --chr 1 --plot Starting log... [...] [2019-06-24 15:21:29 - WARNING] No GWAS SNPs with p-value < 5e-08 found at 1:48002576 - 1:48978188. Skipping [2019-06-24 15:21:38 - INFO] Starting fine-mapping at region 1:48978188 - 1:49894177 [2019-06-24 15:21:43 - INFO] Completed fine-mapping at region 1:48978188 - 1:49894177 [2019-06-24 15:21:43 - INFO] Creating FOCUS plots at region 1:48978188 - 1:49894177 [2019-06-24 15:21:53 - INFO] Starting fine-mapping at region 1:49894177 - 1:51713726 [2019-06-24 15:21:59 - INFO] Completed fine-mapping at region 1:49894177 - 1:51713726 [2019-06-24 15:21:59 - INFO] Creating FOCUS plots at region 1:49894177 - 1:51713726 [2019-06-24 15:22:00 - WARNING] No GWAS SNPs with p-value < 5e-08 found at 1:51713726 - 1:54226262. Skipping Can you share the installed versions of matplotlib and seaborn? Thank you. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9?email_source=notifications&email_token=AEEAARHRLKWZHEAWIUHWZFTP4FCR7A5CNFSM4HRNMIVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYOM5EA#issuecomment-505204368>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEEAARE373YRIOYWVBTKHPLP4FCR7ANCNFSM4HRNMIVA> .

-- Binglan Li Ph.D. candidate, Genomics and Computational Biology University of Pennsylvania, Ritchie Lab Mail: [email protected]

[quattro]

Hi @BinglanLi ,

Matplotlib updated their api to not accept strings for color map names. I've gone ahead and updated the requirements to use the latest version of matplotlib and fixed the bug.

Can you run the following and re-test your code to ensure it works for you?

git clone --branch dev [email protected]:bogdanlab/focus.git
cd focus
pip install -e .

Once you confirm I'll go ahead and start repacking focus and push to the master branch.

Thanks again for your useful report.

Cheers,
Nick

[Maysson]

Hi Nick,

I'm adding my comment here because I'm getting the same error when I run focus (I installed focus two days a go).

I checked the versions of matplotlib and seaborn that I have, Do I need to re-install/update them?

Python 3.6.7 | packaged by conda-forge | (default, Jul 2 2019, 02:18:42)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import matplotlib
matplotlib.version
'2.2.2'

import seaborn
/anaconda3/lib/python3.6/site-packages/ipykernel/kernelbase.py:16: VisibleDeprecationWarning: zmq.eventloop.minitornado is deprecated in pyzmq 14.0 and will be removed.
Install tornado itself to use zmq with the tornado IOLoop.

from jupyter_client.session import utcnow as now

Thanks,
Maysson

[quattro]

Hi Maysson,

How did you install focus? It currently requires matplotlib >3, which should automatically be addressed when using either pip or setup.py to install.