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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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Perl: array goes empty after passing it to a function?

I'm working on a project that's scalating a lot, lately, and I'm re-writing code to make it more OOP and passing all redundant code into sub-routines. The script checks whether a gene exists in the database (through various means) or not. It may…
Leitouran
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Can't locate Bio/SeqIO.pm in @INC

Hi I am trying to install VelvetOptimizer using docker. and it say Can't locate Bio/SeqIO.pm in @INC. It requires the following to be installed: Velvet >= 0.7.51 ,Perl >= 5.8, BioPerl >= 1.4 and i have installed them Please find the…
nad87563
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Using command line argument as a file name in perl

The following perl script takes an argument from the command line and use that as the output file name. my $str = $ARGV[0]; my $out_handler= Bio::SeqIO->new( -file => $str, -format => 'Fasta' ); It is similar to this example. while I run…
mahmood
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Perl Bio::DB::Sam crashes during call to get_features_by_id()

I am using Bio::DB::Sam in a Centos7 environment, using version 0.1.17 of samtools. I am using this procedure to perform my installation: wget http://sourceforge.net/projects/samtools/files/samtools/0.1.17/samtools-0.1.17.tar.bz2 tar xjf…
phonybone
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hash of arrays to create unique ids

I want to create unique IDs for file with gene transcripts. Each row consists of transcript_id and intron coordinated in the format: chromosome:start_coord-end_coord:strand. My file looks like this: CUFF.59321 …
Olha Kholod
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Remove Perl modules from CPAN on Mac

As far as I know it is required to run CPAN with sudo on Mac sudo perl -MCPAN -e shell to install new modules. Theoretically, a module can be removed by deleting it from the Perl folders. My question is: Where are Perl modules put when installed…
Martin Preusse
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CPAN error (Segmentation fault 11)

I wanted to get some advice on an error I am getting on my mac whenever I try to launch CPAN. I'm trying to install BioPerl on my machine, but whenever I try to launch cpan or execute the following: perl -MCPAN -e shell I get an error Segmentation…
Matt
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Bio::DB::Fasta, Can't call method "index_file" on an undefined value at script.pl line

I would like to reload a pre-index file in perl which has been previously indexed as following: ./first_script.pl hg19.fa use Bio::DB::Fasta; my $db = Bio::DB::Fasta->new($file_fasta); ... in an another script I would like to re-load the…
EpiMan
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Why is this script creating a corrupted PNG file on Windows?

I am trying to create a PNG file. The script below executes without returning any errors, the output file tester.png cannot be viewed (and the cmd window prints the attached the attached text). I am not sure why I cannot view the PNG file produced…
neemie
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BioPerl: extract CDS error

I am trying to extract CDS and corresponding amino acid sequences from GenBank file using BioPerl. The script is shown below: while (my $seq_object = $in->next_seq){ for my $feat_object ($seq_object->get_SeqFeatures) { if ($feat_object…
RonnB
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Extracting information from a .gtf to a new text file using PERL

I have the the below .gtf file, i need to extract only 4 variables (chromosome, start/stop codon and transcripst i.d. 1 Cufflinks transcript 11869 14412 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.2"; FPKM…
Sarah-Jane Lennon
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Perl Biomart timeout error

I'm using Biomart Perl API to download data from web serwer. Sometimes I get error message: Problems with the web server: 500 read timeout. Is it possible to somehow catch this error and try to download file again?
Lucas
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Installation of bioperl in Ubuntu 12.04LS

I am trying to install Bioperl package in Perl environment of version 5.20.0, But I am unable to get in to the stuffs. Idea and suggestion of websites varies and its going to be uneasy for me. Please suggest me the protocols for installing Bioperl…
Rajkishore90
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Install BioPerl with custom library path

I tried to install a new version of BioPerl on my PC without root and get errors concerning too old versions of required modules. So I installed them into a custom directory. Is there a possibility to set up a library parameter next to…
pyr0
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BioPerl/BioGraphics only prints one value instead of all

I am trying to plot SNPs onto a gene (or below). The code I have is the following: #!/usr/bin/perl use strict; use warnings; use Bio::Graphics; use Bio::SeqFeature::Generic; my @SNPs = "408777 408900 409100 409480"; my $gene_name = "GSTd10"; my…
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