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Questions tagged [bioperl]

BioPerl is a package of Perl tools for computational molecular biology.

BioPerl is a toolkit of Perl modules useful in building bioinformatics solutions in Perl. Addition auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in their repository.

References:

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Add tag to bioperl DB::SAM/BAM

I have a bam file and use bioperl (Bio::DB::Sam) to work with it. Now i wanted to ask if there is any possibility to add tags to alignments in this File? i use my $iterator = $bam->features(-iterator => 1, …
I3ilbo
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Failed installation of Bio::Grep on Windows subsystem for Linux

I have installed bioperl on WSL Ubuntu 18.04 with sudo apt-get install bioperl bioperl-run. I tried to install Bio::Grep with cpanm but it failed. From build.log file it seems that something fails during testing: # #…
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Unable to install Bio::SeqIO module on Ubuntu for Windows 10 from Microsoft Store

I used Ubuntu 18.04 LTS for Windows from Microsoft store and tried to install BioPerl module Bio::SeqIO with cpanm Bio::SeqIO. Perl version is v5.26.1. It seems that module installation failed: ! Installing the dependencies failed: Module…
zubenel
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Eponine.t failure as a test for Bio::Tools::Run::Alignment::Muscle

I am trying to install a Perl Module Bio::Tools::Run::Alignment::Muscle. I am using this docker image: FROM ubuntu:16.04 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections RUN apt-get update && apt-get install -y…
Cindy Almighty
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How to apply multithreading to Bio::SeqIO translate code (Bioperl)?

I am translating a fasta nucleotide file into protein sequences by this code use Bio::SeqIO; use Getopt::Long; my ($format,$outfile) = 'fasta'; GetOptions( 'f|format:s' => \$format, 'o|out|outfile:s' => \$outfile, ); my $oformat =…
BioDeveloper
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BIO-Perl Error when running the first program

I tried to run bio perl using Eclipse. The code I tried to execute is: use Bio::Seq; $seq_obj = BIO::Seq->new(-seq=> "atcgatgcatgcatgcatgc", -alphabet=> 'dna'); #print $seq_obj->seq; And I got the following error: Can't locate object method "new"…
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How to download gene expression data from NCBI gene database

In the NCBI gene database, I can add the expression tracks (circled in picture blow) through 'Tracks' button, but How I can download the expression data directly, not just look the picture?
YudongCai
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Bioperl testing error in Perl

Newbie here, I am trying to use Bioperl module in the perl environment. My configuration are Windows Vista/32 Active Perl 5.10.1 Bioperl 1.6.1 Padre and Per Studio 2010 IDE For the installation guideline I went through BioPerlWiki and used PPM…
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perl check for valid DNA sequence with regex

I want to write a subroutine that takes a FASTA file as an argument and prints out the sequence (without the header). The subroutine should check if the sequence contains any other letters than DNA bases (A, T, G, C). Here's my…
ic23oluk
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How to check whether an attribute of an object has a value?

I get an error such as "can't call method 'xxxx' on an undefined value" when attempting to check if an object has been created (by the perl module Bio::Perl). Is there a general way of checking if an attribute has a value or not? I would have liked…
keeg
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What is the equivalent function in Biopython for BioPerl's Bio::DB::Fasta?

I'm translating a Perl code to a Python code using BioPython. I got something like: my $db = Bio::DB::Fasta->new($path,$options) and I'm looking for a similar function in Biopython. Is there anything like this?
Thefirefilou
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Why won't Eclipse recognize $PERL5LIB?

I followed BioPerl manual: I cloned a fresh copy of bioperl-live under ~/src then added the following line to my ~/.profile (I'm using Ubuntu): export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB" However,BioPerl modules are not recognized in…
David B
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How do I install the latest BioPerl version when using perlbrew?

I'm using perlbrew and I would like to install the latest bioperl version. Should I use cpanm or git? If git - do I just install as usual (AKA git clone ... then make and build), or should I do anything special? UPDATE Specifically, I'm not sure I…
David B
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How to count sequences in a fasta file using Bioperl

Good evening, i have a bioperl code to count the number of sequences in a fasta file, but i am trying to modify the code to count sequences shorter than 20 and longer from 120 in any given fasta file. The code is below use strict; use…
Oluwole
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Can't run Clustalw through Bioperl

I m trying to run the script below. but I get the error: ------------- EXCEPTION ------------- MSG: Cannot find executable for clustalw. path="clustalw.exe" STACK Bio::Tools::Run::WrapperBase::executable C:/Perl64/site/lib/Bio/Tools/Run/…
Dimitri C
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