marker name not in first columns
When the GWAS input file is formated in such a way that the markername field is not the first retained field, it is not used as index and the merging with the reference panel remove all SNP.
For instance with the files (I checked the SNPs in the file, they should be retained by the pre-processing) GWAS_labels.tsv example_Fail_colOrder.tsv I obtained the stdout:
The pre-processing scriptgive the output:
processing GWAS: Paternoster_allergy
SNP CHR BP EFFECT_ALLELE OTHER_ALLELE BETA SE PVALUE DIRECTION RS_ID 1000G_ALLELE 1000G_ALLELE_FREQ N
a1 3
a2 4
z 5
se 6
pval 7
snpid 9
n 12
dtype: int64
SNPs 0
Traceback (most recent call last):
File "./main_preprocessing_AV_addingStudies_Nov2018.py", line 63, in
mgwas = jp.map_reference.compute_snp_alignement(mgwas)
File "/mnt/PCMA/1._DATA/JASS_Pre-processing/jass_preprocessing/map_reference/map_reference.py", line 85, in compute_snp_alignement
mgwas['a1'] = mgwas.a1.str.upper()
File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 3614, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'a1'