dnanexus/openbio

OpenBio

This is a space for open bioinformatics projects in which DNAnexus employees have an organizational role. To check out a particular project, please click on the appropriate link below!

As-Is Software Disclaimer

This content in this repository is delivered "As-Is". Notwithstanding anything to the contrary, DNAnexus will have no warranty, support, liability or other obligations with respect to Materials provided hereunder.

Downloading Content from OpenBio to a JupyterLab Instance

To download the entire OpenBio repository in your JupyterLab instance, copy the cloning link and use git clone <cloning link> from your terminal or Bash notebook/console.

git clone https://github.com/dnanexus/OpenBio.git

The cloning link may be found by clicking on the "Code" drop down menu in Github and following instructrutions.

To download a particular notebook from the OpenBio repository, copy the link address of the raw version of that notebook and download the notebook from your terminal or Bash notebook/console, use wget <link address of notebook>:

wget https://raw.githubusercontent.com/dnanexus/OpenBio/master/dx-toolkit/dx_extract_dataset_bash.ipynb

Uploading Content from a JupyterLab Instance to a Project on the Platform

To upload a file to your project, use CLI dx-toolbox command, dx upload <file_name>.

dx upload BGEN_import.ipynb

To upload a folder to your project, use CLI dx-toolbox command, dx upload -r <folder_name>.

dx upload -r OpenBio

openbio's Issues

Extracting data with R in jupyterlab

Hi I am trying to follow this notebook for extracting data from the dataset : dx_extract_dataset_r.ipynb

But when I try the following lines of code:

cmd <- paste("dx extract_dataset", dataset, " --fields", field_list, "-o extracted_data.csv")
system(cmd)

data_df <- read_csv("extracted_data.csv", show_col_types = FALSE)
head(data_df)

I get an error:

Error: 'extracted_data.csv' does not exist in current working directory ('/opt/notebooks').

Even when I change the output to the following /mnt/project/Outs/extracted_data.csv I get the same error.

How can I extract the data ? Thanks

Jupyter notebooks available?

I see a list of Jupyter notebooks listed here:

• https://github.com/dnanexus/OpenBio/blob/master/UKB_notebooks/notebook_description.tsv

But this repository doesn't seem to contain the actual notebooks (are they located in a different repo?)

e.g. pheno_geno_linker_R.ipynb

ukb-rap-pheno-basic.ipynb

Hello, I have always used this notebook to extract variables from my UKBB project.

Today when I try to run the exact same script, when I get to finding field names for a given id, this error occurs.

#Age when attending assessment centre has multiple instances (visits):
field_names_for_id('21003')
This error occurs:
/tmp/ipykernel_631/339987039.py:7: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. return sorted(fields, key=lambda f: LooseVersion(f.name))

Then when I try to retrieve the fields i get this error:
df = participant.retrieve_fields(names=field_names, engine=dxdata.connect())
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/cluster/dnax/jars/dnanexus-api-0.1.0-SNAPSHOT-jar-with-dependencies.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/cluster/spark/jars/log4j-slf4j-impl-2.17.2.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).

Can you please advise?
Thank you,
Alyssa