kandi X-RAY | prokka Summary
kandi X-RAY | prokka Summary
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.
Top functions reviewed by kandi - BETA
prokka Key Features
prokka Examples and Code Snippets
Trending Discussions on prokka
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
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...
ANSWERAnswered 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
I have multiple files named:
I want to use sed to print out:
I want to use the "printed" words in a command like this (prokka is a tool for genome annotation):...
ANSWERAnswered 2022-Jan-29 at 11:50
You can use string splitting with string manipulation:
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:...
ANSWERAnswered 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:
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:...
ANSWERAnswered 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:
The problem is:
A software called "RGI" will automatically append
.txt as suffix to the output file. So if my
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
How can I solve the problem? The following is a part of my code:...
ANSWERAnswered 2021-Aug-06 at 20:41
.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:
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:...
ANSWERAnswered 2021-Aug-03 at 10:58
The problem is with:
If I have a .txt file with 4 columns that looks like this:...
ANSWERAnswered 2020-Oct-30 at 21:30
OK, I created the 4 files with the template content as listed above; I also created a file called
control.txt that matches your
.txt file above.
Using the following shell script as a wrapper around
sed does what you're asking on my installation.
No vulnerabilities reported
Reuse Trending Solutions
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page