python 'gnomAD_DB'

Hello. I have a question about 'gnomAD_DB' package of Python.

How to save query result as csv file?

This is my code.

test_df = db.get_info_from_df(dummy_var_df, "AF")

I want to make the result of 'test_df' into a csv file. What should I do?

test_df.to_csv('my_data.csv', index =  False)

I tried running the code above, but it doesn't seem to save. I can't find the file.

Please help me.

gnomad_db python

• 1,059 views • link

written 3.0 years ago by sooni •

The function get_info_from_df returns a Pandas Series, so your code is correct. Could you post the output of dummy_var_df.shape and len(test_df) ?

• 0 views • link

written 3.0 years ago by Shred

I use 'jupyter notebook'. I tried running both codes, but no information came up. What should I do in this case?

enter image description here

The image above is my jupyter notebook window.

• 0 views • link

written 3.0 years ago by sooni •

0 answers

No answers yet.

More posts like this

matching gnomAD allele frequency
written 3.0 years ago by sooni •

Is there a way to find the allele frequency of gnomAD db with the rsID of my SNP data using gnomAD db in Python or …
Bowtie2 and subprocess issue
written 4.0 years ago by robjohn70000

Hi, I tried running bowtie2 in python using subprocess without any success. Codes: REFGENOME='/path-to-genome/genome.fasta' P1='/path-to-fastq/P1.fastq.bz2' P2='/path-to-fastq/P2.fastq.bz2' cmd=['bowtie2','--quiet','-p','10','--dovetail','--no-head','--no-sq','-x',REFGENOME,'-1',P1,'-2',P2,'-S', 'out.sam'] subprocess.Popen(cmd, shell=True) Error: No index, query, or …
How to save to CSV file scRNA-seq datasets obtained by R-package "scRNAseq"
written 4.3 years ago by Alexander •

There is R-package with collections of scRNA-seq datasets: https://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html I am Python user and know nothing about R, but want to use some of that …
How to save DEXSeq result to a .csv file ?
written 5.4 years ago by Aynur •

Hello, I am doing alternative exon usage analysis using DEXSeq and following this documentation [DEXSeq Documentation][1] After testing the result, how do I save me …
Accessing UNIPROT using REST API
written 8.7 years ago by Natasha •

Hello Everyone, I would like to programmatically access the entries(uniprot id,entry name,protein name,gene name,kinetics) for a given EC Number and organism of interest, using python. …
How could I add a column in CSV file?
written 8.7 years ago by MKS •

Hi, I have Data on CSV file, so i need a python code to subtract column from other one and add the result on a …
In this Python script I want to save result of print(traj_rmsd) in an output.xvg file. I am unable…
written 9.6 years ago by naveen100787 •

In this Python script I want to save result of print(traj_rmsd) in an output.xvg file. I am unable to open this file and it's showing …
how can I use Lumi package for GSE31699 file?
written 11.4 years ago by SCA •

I would like to use lumi package for normalize to http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31699 I read csv file and get a matrix file. I tried to use the …
Reindex A Vcf File / How To Handle Cosmic Vcf Files
written 13.3 years ago by secretjess

So I have managed to successfully query 1000 Genome VCF files before by following tutorials, I thought I could apply this to the COSMIC database. …
Create Blast Database From Query Result?
written 14.6 years ago by Nicholas •

<blockquote> Possible Duplicate: <a href='http://biostar.stackexchange.com/questions/15047/make-a-custom-blast-library-using-the-output-of-another-blast-result'>make a custom BLAST library using the output of another blast result</a> </blockquote> Hello, I would like to …