get_novel() raises TypeError: got multiple values for keyword argument 'build' when build = "19"

[sarahjang15]

First of all, thank you very much for developing and maintaining gwaslab — it has been extremely helpful for GWAS post-analysis workflows.

While using Sumstats.get_novel(), I encountered a TypeError when explicitly passing the build argument. The error seems to occur because build is passed both from self.meta["gwaslab"]["genome_build"] and again via **kwargs.

In addition, I noticed that the handling of genome build differs depending on whether efo is provided. In util_in_get_sig.py, when efo == False, targ_build can be set to "19" (see the following line in the code):

gwaslab/src/gwaslab/util/util_in_get_sig.py

Line 1034 in 14517fa

if efo != False:

However, when efo != False, this option appears to be disabled, even though the documentation states that GWAS Catalog data is available for both build 19 and 38.

Error message

TypeError: gwaslab.util.util_in_get_sig.getnovel() got multiple values for keyword argument 'build'

Reproducible example

sumstat_gl.get_novel(
    known=None,
    efo=[
       'EFO_0004330', 'EFO_0006781', 'EFO_0006782'
    ],
    only_novel=False,
    windowsizekb_for_novel=1000,
    windowsizekb=500,
    sig_level=5e-8,
    if_get_lead=True,
    group_key=None,
    use_p=False,
    anno=False,
    wc_correction=False,
    source="refseq",
    gwascatalog_source="NCBI",
    output_known=False,
    verbose=True,
    build='19'
)

Environment

• gwaslab version: 3.6.15
• Python version: 3.10.11

Please let me know if I am misunderstanding the intended design, or if there is a recommended way to use genome build 19 when using get_novel() with EFO-based novelty checking.
Thank you for your time.

[Cloufield]

Hi,
Thank you so much for the feedback.
I checked the update logs and found that there are errors in get_novel docs. Currently, it only works for build="38".
(I overlooked the extra functionality overstated by the LLM when updating the documentation... )
Since i am also updating it to use GWAS Catalog v2 API, I will let you know when it is finished.