Comments (7)
Hi @BinglanLi , could you output the header of the GWAS input you're using?
Thank you.
from focus.
$ 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
from focus.
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.
from focus.
from focus.
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
from focus.
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
from focus.
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.
from focus.
Related Issues (20)
- unsupported operand type(s) for +: 'float' and 'str'
- [ERROR] Import submodule requires mygene and rpy2 to be installed
- [ERROR] ufunc 'isfinite' not supported for the input types HOT 2
- Please specify independent regions location or default regions with '37:EUR', etc HOT 2
- Integer column has NA values in column 3 HOT 4
- unsupported operand type(s) for +: 'float' and 'str' HOT 3
- Focus import error - "500 Server Error: Internal Server Error for url: http://mygene.info/v3/query/" HOT 2
- ERROR] MetaData.__init__() got multiple values for argument 'schema' HOT 1
- error in creating the weight database HOT 3
- symbol issue when creating weight database using Predixcan databases HOT 5
- name 'zscores' is not defined errror with when running finemap with --intercept HOT 2
- The TWAS z-score obtained by S-PrediXcan and FOCUS software is different
- [WARNING] Unable to match ENSG00000228327.3 to Ensembl ID. Using ID for symbol HOT 2
- The --prior-prob parameter set for DNA methylation based fine-mapping analysis
- p-values in the output plot is on negative natural log scale? HOT 2
- Some example files/databases unavailable
- data for re-plotting the expression correlation as in the plot output
- "block" issue on FOCUS HOT 3
- focus finemap error HOT 6
- [error] dataframe.pivot() takes 1 positional argument but 4 were given HOT 7
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from focus.