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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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How to fix Perl from anaconda not installing bioperl? `Bailing out the installation for BioPerl-1.007002.`

I am using conda to install several packages. I already installed Perl under conda and is the one working in this machine (running Ubuntu 18.04). Now I am trying to use a script that requires bioperl. I tried to update conda, install bioperl…
Andrés Parada
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How do I solve this BioPerl-related mystery?

I'm using Ubuntu 10.04 and Perl 5.10.1. The BioPerl package has some nice scripts, such as bp_genbank2gff3.pl which converts files from genbank format to GFF3 format. The problem: I get unexpected results when using bp_genbank2gff3.pl: the gene…
David B
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Unable to install bioperl on Mac OS X

I'm trying to get biotools working on my Mac so that I can run some Perl5 code that uses Bio::DB::Sam, but am stymied. Mac OS X 10.10.4 perl 5.18.2 upgraded CPAN as per INSTALL instructions 'brew install expat' tells me that expat-2.1.0_1 is…
Greg Wilson
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How to Retrive multiple sequences from a database in Bioperl?

I have installed Bioperl1.6 via ppm and have placed .pl file in cgi-bin folder of my localhost. When I run this via url http://localhost/cgi-bin/bio2.pl it says "Internal Server Error" While if run any of the bioperl file either in CGI or .pl it…
Akash
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How do I convert a perl program into an installable module?

I have a perl program that I want to convert into a bioperl module. How do I do that? Is there an up-to date tutorial? That's really all I need. Thank you.
eugheugh
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Perl uninitialized value error after parsing html

I'm using Bioperl to find GOterms for genes. I retrieve an html file, convert it to text, get rid of all extra spaces and newlines, and try to go through the resulting array. However, I keep getting errors for accessing uninitialized values in the…
eugheugh
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Which is the best option to plot two different tracks (Chromosomes, fragments, scaffolds...) with Bio::Graphics?

I am working with the BioPerl module Bio::Graphics to plot some genomic coordinates. I have regions from different scaffolds or tracks that have evolutionary conserved elements, the idea is to plot the correspondent fragment with its elements in the…
Cristian Velandia
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Parse MEDLINE file for GWAS mining

I'm trying to parse as a 0,1 table a MedLine file to perform some statistical downstream analysis: PCA, GWAS, etc. I formatted it using a Python module called Bio.Medline with some additional shell commands. Now, I don't know how to continue. I need…
biotech
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Bioperl library installation in mysql server

I installed Bioperl and works correctly. then installed Bio::Tools::Run::Phylo::Phyml and it works good from terminal. But when I call same script contains it from a browser to using CGI method, I get this error: Can't locate…
Al007
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Can't install Bioperl Module (properly?)

I am not able to install a BioPerl Module via cpanm. With sudo cpanm Bio::SeqIO The output says: --> Working on Bio::SeqIO Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz ... OK Configuring BioPerl-1.006922 ...…
user3401516
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Build.PL wont run in git repo

I am trying to run the bioperl-live package and I have git-cloned the following repo git clone https://github.com/bioperl/bioperl-live.git and cd'd into bio-perl live where it was installed. I have then tried to run: perl Build.PL to which I get…
brucezepplin
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Extracting DNA sequences from FASTA file with BioPerl with non-standard header

I'm trying to extract sequences from a database using the following code: use strict; use Bio::SearchIO; use Bio::DB::Fasta; my ($file, $id, $start, $end) = ("secondround_merged_expanded.fasta","C7136661:0-107",1,10); my $db =…
jasongallant
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Find the number of matching two characters in a string in Perl

Is there a method in Perl (not BioPerl) to find the number of each two consecutive letters. I.e., number of AA, AC, AG, AT, CC, CA, ... in a sequence like this: $sequence = 'AACGTACTGACGTACTGGTTGGTACGA' PS: We can make it manually by using the…
AWRAM
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How can I identify which ranges a given value falls in?

I have two data sets: 'Data 1' and 'Data 2'. Could you please help me to find, for each value of posi in 'Data 1', the ranges in 'Data 2' where posi lies between Star_posi and end_posi. Data 1 Num posi 1 2 2 14 3 …
Phan
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Find the postion of SNP in the gen list

I have SNP data and gen list data. I am looking for the position of SNP cotain in the gen list data when I compare with gen list. For example: The SNP data : Pos_start pos_end 14185 14185 .... ..... The gen list data:…
Phan
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