cre | excel report generation using data from bcbio variant2 | Genomics library

by naumenko-sa Shell Version: v.0.0.6 License: MIT

X-Ray Key Features Code Snippets(2)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | cre Summary

cre is a Shell library typically used in Artificial Intelligence, Genomics applications. cre has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Excel variant report generator and scripts to process WES data (cram/bam/fastq -> variant calls -> annotated variant calls -> prioritized variants -> excel report). Uses results from bcbio variant2 germline variant calling pipeline.

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Quality

Security

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Support

cre has a low active ecosystem.

It has 6 star(s) with 7 fork(s). There are 2 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 0 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of cre is v.0.0.6

Quality

cre has 0 bugs and 0 code smells.

Security

cre has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

cre code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

cre is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

cre releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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cre Key Features

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cre Examples and Code Snippets

6. Step 5 in detail

Shell

Lines of Code : 7

License : Permissive (MIT)

Copy

cat ${family}-ensemble.db.txt | cut -f 23,24  | sed 1d | sed s/chr// > ${family}-ensemble.db.txt.positions
    bcftools view -R ${family}-ensemble.db.txt.positions -o ${family}.vcf.gz -O z ${family}-ensemble-annotated-decomposed.vcf.gz


vcf.freeb

1. Installation

Shell

Lines of Code : 4

License : Permissive (MIT)

Copy

export PATH=[installation_path]/tools/bcbio/bin:[installation_path]/tools/bcbio/anaconda/bin:$PATH
export PYTHONPATH=[installation_path]/tools/bcbio/anaconda/lib/python2.7:$PYTHONPATH

cd
git clone https://github.com/naumenko-sa/cre

Community Discussions

Trending Discussions on cre

Does CRAN (or any of its relatives) have an API?

Converting dict to DataFrame gives too many rows

How to label xAxis with series data using Highcharts?

Read Authors@R field from DESCRIPTION of R package as vector

How to migrate 'current' mysql timestamp value to postgreSQL

how to split a column in dataframe into list of tuple

Multiple inputs into new prompt & Powershell -run as and -nonewwindow issue

Multiple "if" condition for R-Shiny Calculator App

How to lowercase a variable expansion

Expanding variables in Powershell, to Linux commands

QUESTION

Does CRAN (or any of its relatives) have an API?

Asked 2022-Mar-22 at 16:11

I am interested in retieving machine readable meta information about R packages.

For example, when I go to CRAN I can see a short description about the package, before I download it: https://cran.r-project.org/web/packages/MASS/

I could not find any way to retrieve a different output from the CRAN server than HTML. I would like to avoid parsing HTML and instead somehow retrieve meta information about packages in a more convenient format (e.g., JSON).

I saw that each R package (at least to my knowledge) has a yaml-like (?) description text inside its source code package (the file is called DESCRIPTION). However, so far I could only find this kind of description inside tar archives, which means that I would have to download the package before I can access its description.

Here an example of the DESCRIPTION from the MASS package:

...

ANSWER

Answered 2022-Mar-22 at 14:38

An acceptable solution is the METACRAN API that is available here: https://crandb.r-pkg.org/

Source https://stackoverflow.com/questions/71573982

QUESTION

Converting dict to DataFrame gives too many rows

Asked 2021-Dec-01 at 20:03

I am trying to convert a dict to Pandas DataFrame as the following:

...

ANSWER

Answered 2021-Dec-01 at 20:03

You're not doing anything wrong. Since tags is a list, Pandas broadcasts all other fields to same size as tags and make a dataframe. You can do:

Source https://stackoverflow.com/questions/70190479

QUESTION

How to label xAxis with series data using Highcharts?

Asked 2021-Nov-19 at 09:33

I'm newbie to highchart and I've got a demo for polar chart using highcharts

...

ANSWER

Answered 2021-Nov-19 at 09:33

You can get the associated value through series data. Example:

Source https://stackoverflow.com/questions/70030181

QUESTION

Read Authors@R field from DESCRIPTION of R package as vector

Asked 2021-Oct-21 at 18:48

How can I read Authors@R field from DESCRIPTION file as vector?

...

ANSWER

Answered 2021-Oct-21 at 18:48

We may wrap with eval(parse as it returns a string

Source https://stackoverflow.com/questions/69667175

QUESTION

How to migrate 'current' mysql timestamp value to postgreSQL

Asked 2021-Oct-06 at 17:08

I have Mysql DB that contains table 'tariff' with field

...

ANSWER

Answered 2021-Oct-06 at 09:22

there are several errors in that code:

use timestamp instead of datetime
use current_timestamp instead of current_timestamp()
the interval value needs to be enclosed in single quotes

So you need to use:

Source https://stackoverflow.com/questions/69462971

QUESTION

how to split a column in dataframe into list of tuple

Asked 2021-Sep-28 at 14:31

I found some answers online, but I have no experience with regular expressions, which I believe is what is needed here and if there is another way it would be better.

I have a complexed column in my dataframe that needs to be split by either a ',' ';' '(' ')' ':'

Example string:

...

ANSWER

Answered 2021-Sep-28 at 14:31

By doing

Source https://stackoverflow.com/questions/69363585

QUESTION

Multiple inputs into new prompt & Powershell -run as and -nonewwindow issue

Asked 2021-Sep-20 at 20:03

Here is what I currently do, file 1:

...

ANSWER

Answered 2021-Sep-20 at 20:03

Can anyone help me solve the start cmd -nonewwindow -verb runas issue

Unfortunately, there is no solution: Windows fundamentally does not allow you to run an elevated process (run as admin, requested with -Verb RunAs) directly in a non-elevated process' console window - that is why Start-Process syntactically prevents combining -NoNewWindow with -Verb RunAs.

OR input multiple lines of code into a new elevated command prompt with only one file, please?

While there is a solution, it'll be hard to maintain:

You can pass the lines of your second batch file (the one you want to eliminate) to cmd /c on a single line, joined with &:

Note: To facilitate side effect-free experimentation, the original diskpart command was replaced with findstr -n ., which merely prints the lines received via stdin, preceded by their line number.

Source https://stackoverflow.com/questions/69243757

QUESTION

Multiple "if" condition for R-Shiny Calculator App

Asked 2021-Aug-08 at 09:23

I want to create an R-shiny application that calculates creatinine clearance. According to the formula below, the calculation necessitates many "if" conditions:

In addition, I'd like to show the results of the dose adjustment depending on the creatinine clearance data.

The following is the code I'm attempting to create. Still, I'm having difficulty displaying the final results table that includes the creatinine clearance calculations (based on gender and serum creatinine conditions) and how to show antibiotic dose adjustments based on creatinine clearance results.

...

ANSWER

Answered 2021-Aug-07 at 12:56

This might get you started. Please note that you may need to adjust somethings for the issues noted in my comments.

Source https://stackoverflow.com/questions/68689299

QUESTION

How to lowercase a variable expansion

Asked 2021-Aug-02 at 15:32

I have the following code and variables declared. How do I make sure that $shared_mailbox_alias becomes lowercase when expanded to the Mailbox creation cmdlet below? Since it's based on $Project_code which is typed in capital letters:

...

ANSWER

Answered 2021-Aug-02 at 15:32

Solved, thanks for the input, this is the syntax I used:

Source https://stackoverflow.com/questions/68612450

QUESTION

Expanding variables in Powershell, to Linux commands

Asked 2021-Aug-01 at 16:07

On the following Powershell script:

...

ANSWER

Answered 2021-Aug-01 at 13:23

I see that the below link has spaces between $Project_number & $Project_code

Source https://stackoverflow.com/questions/68610689

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install cre

Use HPC or server. Add bcbio to PATH and PYTHONPATH in .bash_profile:. bcbio installs many other useful tools (including java and R) and datasets through bioconda and cloudbiolinux. 1.2 Clone cre to ~/cre and add it to PATH. 1.3 (Optional) Install/update OMIM. By default CRE uses cre/data/omim.txt and cre/data/omim.inheritance.csv. Result - omim.txt with omim description of diseases related to ~ 4000 genes We use the improved OMIM inheritance table from https://www.cs.toronto.edu/~buske/cheo/.Download the second file with inheritance mappings. It references genes by gene name (symbol) rather than by Ensembl_id which is a requirement for CRE. Most gene names (symbols) could be mapped automatically with Ensembl biomart genes.R, but some genes (not many) might need manual curation to assign the correct ENSEMBL_ID. 1.4 (Optional) Install/update Orphanet: cd ~/cre/data; ~/cre/cre.orphanet.sh Orphanet provides descriptions for ~3600 genes:. By default CRE uses orphanet.txt 1.5 (Optional) Update Gnomad gene contraint scores: Rscript ~/cre/cre.gnomad_scores.R By default using ~/cre/data/gnomad_scores.csv. 1.6 (Optional) Imprinted genes. By default using ~/cre/data/imprinting.txt. 1.7 (Optional) Install HGMD pro database Install HGMD pro and dump information with ~/cre/cre.hgmd2csv.sql.
Installation manual
Installation and update examples
Goto https://omim.org/downloads/ and request the latest database.
In a couple of days you will receive: genemap2.txt, genemap.txt, mim2gene.txt, mimTitles.percent.txt, mimTitles.txt, morbidmap.txt.
Preprocess OMIM with cre.omim.sh: cd OMIM_DIR;~/cre/cre.omim.sh
By default it uses bcbio.templates.wes.yaml config with following features:.
Prepare input files: family_sample_1.fq.gz, family_sample_2.fq.gz, or family_sample.bam and place them into family/input folder.
There might be many samples in a family(project).
TEST: NIST Ashkenazim trio: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio (download OsloUniversityHospital exomes).
run cre.prepare_bcbio_run.sh [family].
4 callers, the order is important, because variant metrics in ensemble calling (like AD) are picked up from the first caller in the list (gatk)
ensemble calling
realignment and recalibration. There is no much gain in precision/sensitivity with RR, but to make bam files consistent with other projects it is on here. Actually, realignment helps samtools to call indels better.
no bed file. Let callers call every variant which has coverage, we will filter poorly covered variants later. Modern exome capture kits are so perfect, that we can discover a useful non-coding variant. No sense to filter them out during that stage.
effects: VEP. There is a holywar VEP/snpEff/Annovar. My choice is VEP. You will see later both Ensembl and Refseq in the report, so no reason for using Annovar.
effects_transcripts: all. We want all effects of a variant on all transcripts to be reported.
aligner: bwa. Even staring with bam files, bwa is used. Sometimes input bam files aligned against older reference, or different (chr) naming scheme. It is better to have a bam file consistent with calls made.
custom annotation cre.vcfanno.conf using data sources installed in bcbio.
creates gemini database with vcf2db

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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