spot7.org logo
Home PHP C# C++ Android Java Javascript Python IOS SQL HTML Categories

extract gene-id + function annotation from .gff


You can use use Bio::FeatureIO for that. Below an example for your data:

use strict;
use warnings;
use Bio::FeatureIO;

# read infile "my.gff"
my $in  = Bio::FeatureIO->new(-file =>
"my.gff" , -format => 'GFF');

# write to outfile "out.txt"
open(my $fh, '>', 'out.txt') or die $!;
print $fh "Gene-ID	functionannotation
";

while ( my $feature = $in->next_feature() ) {
        my ($func) =
$feature->annotation()->get_Annotations('func_annotation');
        print $fh $feature->seq_id . "	" .
$func->value . "
" if $func;
}

File out.txt:

Gene-ID functionannotation
Niben044Scf00000988 MYB transcription factor
[Solanum lycopersicum]

Categories : Perl

Related to : extract gene-id + function annotation from .gff
Closure annotation for variadic function
"f5" is the expected pattern. /** * @param {...*} var_args * @return {number} */ function f5(var_args) { return arguments.length; } An alternative is: /** @type {function(...*):number} */ function f5() { return arguments.length; }

Categories : Javascript
Function to extract data frames from a list does not provide any output
The funtion seems to append column names of different datasets in the list with names of the list. If that is the case, use envir=.GlobalEnv in the assign extractDF<- function(x) { dfname<-names(x) n<-length(x) for (i in 1:n) { nam <- dfname[i] assign (nam, data.frame(x[i]), envir=.GlobalEnv) } } extractDF(SubPop) Now, check the df1 and df2. The colnames are chang

Categories : R
@Created annotation in Java
There is no @Created in Java nor in CDI. This is a custom qualifier that you create to indicate which implementation to use when injecting the element. If you read further in the example, there's an explanation about what @Created means: We would like other parts of the application to be aware of the fact that a new booking has been created, therefore we use the CDI to fire an event. We do so

Categories : Java
Will Slf4j annotation work in Grails?
All Grails artefacts (controllers, domain classes, taglibs, services, etc.) have a static logger field (named log) added to them automatically. Classes in src/groovy also have a logger field named log added to them automatically, but in this case, the logger is non-static. Therefore, the only time you'll need to explicitly add a logger is if you want to log something statically from a src/groovy

Categories : Grails
The annotation @EnableSpringDataWebSupport does not work with WebMvcConfigurationSupport?
It looks like configuration classes that extend WebMvcConfigurationSupport directly suffer from SPR-10565. The solution, at least for me, is to extend from DelegatingWebMvcConfiguration instead. If you're overriding individual callbacks in your configuration class you'll likely want to call the superclass' implementation of the callback as well to ensure it's all handled correctly.

Categories : Spring
Recently Add
unable to connect selenium webDriver through perl bindings
SSL error calling Perl web service via https using LWP
SOAP::Lite always faults in debug mode
perl referencing a hash outside of the scope that populated it (histogram)
Perl script to print out all the lines containing a keyword and the line below it
PERL Unicode Escape string pass from command line argument wrong output
Perl process crashes after handling signal
Marpa: Can I explicitly disallow keywords as identifiers?
Perl: Import text, containing ÅÄÖ, from file
error using perl - Proc::ProcessTable. works in cmd line, not in .pl file
DBIx::Class chaining resultsets with same table in prefetch
Time as input, print timetable in Perl
compare values of different tables perl
Automatically increasing ID generation using PERL
Syntax Error, first line after dostuff
Delete files in a folder using Perl
Perl '-d' operator is not detecting a directory
Perl appending text to new line
write_timeout in IO::Socket::Timeout
Using ForkManager and Perl properly?
Is a cyclic dependency solved with require?
Posting metric to google analytics from perl script
How can I check if a user enters my page the first time?
Sorting arrays of intervals in perl?
Perl: How to get the link target of a soundcloud feed mp3
Uninitialized value in concatenation
Perl code - pipe "|" in `open()` statement
perl command line backticks with matrix
Perl OO - Creating a list of objects
extract gene-id + function annotation from .gff
© Copyright 2017 spot7.org Publishing Limited. All rights reserved.