prokka | : zap : : aquarius : Rapid prokaryotic genome annotation | Genomics library

by tseemann Perl Version: v1.14.5 License: No License

X-Ray Key Features Code Snippets Community Discussions(7)Vulnerabilities Install Support

kandi X-RAY | prokka Summary

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

Whole genome annotation is the process of identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information. Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.

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Quality

Security

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Support

prokka has a low active ecosystem.

It has 666 star(s) with 207 fork(s). There are 43 watchers for this library.

It had no major release in the last 12 months.

There are 186 open issues and 417 have been closed. On average issues are closed in 98 days. There are 25 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of prokka is v1.14.5

Quality

prokka has no bugs reported.

Security

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

License

prokka does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

prokka releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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prokka Key Features

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prokka Examples and Code Snippets

No Code Snippets are available at this moment for prokka.

Community Discussions

Trending Discussions on prokka

How to automate consecutive bash command line writing for multiple files

Using sed to extract the middle of a line/filename

Snakemake How to design downstream rules on empty output files?

How to modify a tsv-file column with Python

RGI output filename does not match snakefile output filename

error "positional argument follows keyword argument" in snakefile

Substitute several words in all files in a folder based on a .txt file

QUESTION

How to automate consecutive bash command line writing for multiple files

Asked 2022-Mar-19 at 21:57

Basically I need help for writing a script to repeat a command line times the number of elements from a list table, and every element value is used for replacing it three times in the main command line, besides every repeat is separated by " && " to form a consecutive string I can print out as text. I got a plain text file with 442 file names (without extension), let's say as a column without header, and every name or value I must replace it three times in the main command line, and repeat the command line replacing it with the next value times number of values: For instance

Here's the main command line I want to repeate using file or value SL5Y and print out

prokka --prefix SL5Y --cpus 6 --outdir SL5Y --rfam --addgenes --addmrna --cdsrnaolap SL5Y.fna

And here's the table

SL5Y

SL6Y

SO5Y

So what I basically need is a consecutive command line that looks as follows, but for 442 files, replacing every table value three times inside the repeat corresponding to that value; separated by ' && '

prokka --prefix SL5Y --cpus 6 --outdir SL5Y --rfam --addgenes --addmrna --cdsrnaolap SL5Y.fna && prokka --prefix SL6Y --cpus 6 --outdir SL6Y --rfam --addgenes --addmrna --cdsrnaolap SL6Y.fna && prokka --prefix SO5Y --cpus 6 --outdir SO5Y --rfam --addgenes --addmrna --cdsrnaolap SO5Y.fna

...

ANSWER

Answered 2022-Mar-19 at 19:27

I think you can use Python to do what you are trying to do, assuming the file names (without extensions) are contained in a file named 'list_of_file_names_without_extension.txt':

Source https://stackoverflow.com/questions/71541117

QUESTION

Using sed to extract the middle of a line/filename

Asked 2022-Jan-29 at 14:06

I have multiple files named:

Genus_species_strain.fasta

I want to use sed to print out:

Genus

species

strain

I want to use the "printed" words in a command like this (prokka is a tool for genome annotation):

...

ANSWER

Answered 2022-Jan-29 at 11:50

You can use string splitting with string manipulation:

Source https://stackoverflow.com/questions/70904757

QUESTION

Snakemake How to design downstream rules on empty output files?

Asked 2021-Aug-27 at 16:00

I am wondering how to deal with empty output files in downstream rules. An assembly of a short read fastq data with SHOVILL can fail and produce a 0-byte contigs.fa

If genome annotation with PROKKA is run on a 0-byte file it returns an error:

...

ANSWER

Answered 2021-Aug-27 at 16:00

I can think of two approaches, neither is perfect.

The first is basically what you did: use bash to work around. However, I would suggest the -s file test operator. This way, you still get notified of a genuine error from prokka:

Source https://stackoverflow.com/questions/68911209

QUESTION

How to modify a tsv-file column with Python

Asked 2021-Aug-21 at 16:29

I have a GFF3 file (mainly a TSV file with 9 columns) and I'm trying to make some changes in the first column of my file in order to overwrite the modification to the file itself.

The GFF3 file looks like this:

...

ANSWER

Answered 2021-Aug-21 at 16:25

You can use re.sub with pattern that starts with ^ (start of the string) + use lambda function in re.sub. For example:

Source https://stackoverflow.com/questions/68874736

QUESTION

RGI output filename does not match snakefile output filename

Asked 2021-Aug-07 at 02:12

The problem is:

A software called "RGI" will automatically append .txt as suffix to the output file. So if my sampleID is 7. Then the actual RGI output file will be 7.txt, which is different from the output file (7) defind in the snakefile rule. And snakemake will report errors like Job Missing files after 20 seconds. However, RGI still appends .txt as suffix even if you have preset a suffix (and the actual output file will look like 7.txt.txt).

How can I solve the problem? The following is a part of my code:

...

ANSWER

Answered 2021-Aug-06 at 20:41

Strip the .txt prefix from the output filename before passing it to rgi. I do this here using bash string manipulation but you can do it in other ways:

Source https://stackoverflow.com/questions/68683046

QUESTION

error "positional argument follows keyword argument" in snakefile

Asked 2021-Aug-03 at 10:58

When I run snakemake -np it says: SyntaxError in line 22 of /home/snakefile: positional argument follows keyword argument

It seems that it's a problem in the input section of rule prokka because other parts workded fine.

Belowe is my snakefile:

...

ANSWER

Answered 2021-Aug-03 at 10:58

The problem is with:

Source https://stackoverflow.com/questions/68630134