jass_preprocessing issueshttps://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues2018-11-21T14:25:28+01:00https://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/1Todo2018-11-21T14:25:28+01:00Hanna JULIENNETodoAdd a command line interface that launch the main_preprocessing script?Add a command line interface that launch the main_preprocessing script?https://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/2Create a command line interface for the main2018-11-23T15:59:43+01:00Hanna JULIENNECreate a command line interface for the mainput the main_preprocesing in a main functionput the main_preprocesing in a main functionHanna JULIENNEHanna JULIENNEhttps://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/3remove the subfolder to have a clean command line to install the package2018-11-23T16:00:46+01:00Hanna JULIENNEremove the subfolder to have a clean command line to install the packagehttps://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/4Ask hugues script for the reference panel2023-05-09T10:13:35+02:00Hanna JULIENNEAsk hugues script for the reference panelhttps://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/5marker name not in first columns2018-11-27T18:12:31+01:00Amaury VAYSSEmarker name not in first columnsWhen 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 SN...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](/uploads/1517fd5838bec235aab44f2d08a9bc73/GWAS_labels.tsv)
[example_Fail_colOrder.tsv](/uploads/aa4a4c7f8ae705a077d102e41ed40b24/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 <module>
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'
>>>https://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/6conditions that makes the pre-processing procedure freeze2018-11-27T19:01:45+01:00Amaury VAYSSEconditions that makes the pre-processing procedure freezeFor some in put the pre-processing procedure freeze (and ctrl+C does not work).
It seems to be when the markername field has NA values (since removing those line removed the problem), but that was not a sufficient condition to reduce th...For some in put the pre-processing procedure freeze (and ctrl+C does not work).
It seems to be when the markername field has NA values (since removing those line removed the problem), but that was not a sufficient condition to reduce the size of the illustrating files. I did not manage to make a 20 line file that replicate the bug.
I put the file that bug in PCMA/1._DATA/freeze_pre_process
The procedure output is:
```
processing GWAS: Willer_AtrialFibri
MarkerName rs_dbSNP147 CHR POS_GRCh37 A1 A2 Freq_A2 Effect_A2 StdErr Pvalue
snpid 1
a2 4
a1 5
freq 6
z 7
se 8
pval 9
dtype: int64
sys:1: DtypeWarning: Columns (1) have mixed types. Specify dtype option on import or set low_memory=False.
```https://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/7Positional index fail when some allele contain NA2021-08-09T18:37:03+02:00Hanna JULIENNEPositional index fail when some allele contain NAhttps://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/8Position index fail when allele are in lower case2021-10-01T14:27:39+02:00Hanna JULIENNEPosition index fail when allele are in lower casehttps://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing/-/issues/9Make Jass preprocessing compatible with structural variant2022-03-17T09:09:40+01:00Hanna JULIENNEMake Jass preprocessing compatible with structural variantSo far Jass prepro deals only SNPSo far Jass prepro deals only SNP