Error when running SMultiXcan.py

[dym22]

Hi there,

I successfully ran SPrediXcan on my sumstats file, but am running into the following error when attempting to run SMultiXcan:

(...)
Level 9 - Processing Thyroid
Level 9 - Processing Uterus
Level 9 - Processing Vagina
Level 9 - Processing Whole_Blood
INFO - Loading genes
INFO - Context for snp covariance
INFO - Assessing GWAS-Models SNP intersection
INFO - Processing GWAS command line parameters
INFO - Reading input gwas: /indy/storage3/dym22/CLCLP_38_modified.txt
Traceback (most recent call last):
File "/indy/storage3/dym22/MetaXcan/software/SMulTiXcan.py", line 93, in
run(args)
File "/indy/storage3/dym22/MetaXcan/software/SMulTiXcan.py", line 22, in run
context = CrossModelUtilities.context_from_args(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/indy/storage3/dym22/MetaXcan/software/metax/cross_model/Utilities.py", line 186, in context_from_args
intersection = GWASAndModels.gwas_model_intersection(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/indy/storage3/dym22/MetaXcan/software/metax/misc/GWASAndModels.py", line 36, in gwas_model_intersection
gwas= GWASUtilities.load_plain_gwas_from_args(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/indy/storage3/dym22/MetaXcan/software/metax/gwas/Utilities.py", line 116, in load_plain_gwas_from_args
files = [_l(x) for x in files]
^^^^^^^^^^^^^^^^^^^^^^
File "/indy/storage3/dym22/MetaXcan/software/metax/gwas/Utilities.py", line 116, in
files = [_l(x) for x in files]
^^^^^
File "/indy/storage3/dym22/MetaXcan/software/metax/gwas/Utilities.py", line 109, in
_l = lambda x: GWAS.load_gwas(x, gwas_format, skip_until_header=args.skip_until_header,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/indy/storage3/dym22/MetaXcan/software/metax/gwas/GWAS.py", line 103, in load_gwas
d = pandas.read_table(source, separator)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: read_table() takes 1 positional argument but 2 were given

These are the flags I am using:
python ${PATH_TO_METAXCAN}/SMulTiXcan.py
--models_folder ${EQTL_DIR}
--models_name_pattern "mashr_(.).db"
--snp_covariance gtex_v8_expression_mashr_snp_smultixcan_covariance.txt.gz
--metaxcan_folder ${METAXCAN_OUTPUT_DIR}
--metaxcan_filter "SPrediXcan_(.).csv"
--metaxcan_file_name_parse_pattern "SPrediXcan_(.*).csv"
--gwas_folder /indy/storage3/dym22
--gwas_file_pattern "CLCLP_38_modified.txt"
--snp_column VARIANT
--effect_allele_column A1
--non_effect_allele_column A2
--or_column OR
--pvalue_column P
--keep_non_rsid
--model_db_snp_key varID
--cutoff_condition_number 30
--verbosity 7
--throw
--output ${OUTPUT_DIR}/smultixcan_output.txt

I have been unable to find any similar issues reported on the GitHub or in Google Groups. If anyone is able to provide assistance/guidance, it would be much appreciated. Thank you!

[Hanuphant]

Is there any update on this issue? I have been facing it as well and was wondering what's going on with the positional arguments. Most suggest that being a class instance, we need to add self as an argument as well. But I feel that might unnecessarily break the code.

What would you all suggest?

[Hanuphant]

Implemented a fix that you can use or alternatively, it worked with Python v.3.6.8

#183 (comment)