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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bioperl remove a node from newick tree

I'm trying to remove a node from a newick tree using bioperl. The tree file contains this data : (((A:5,B:5)90:2,C:4)25:3,D:10); Below is the code: use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; use strict; use warnings; my $input = new…
AWRAM
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Bioperl and Samtools

How can I run 'mpileup' using Bioperl ? When trying to run mpileup using Bio::Tools::Run::Samtools , I am getting 'mpileup' is not registered. What am I doing wrong? Any pointers towards the right direction are appreciated... thank you guys.....
yathrakaaran
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Trying to custom-sort a phylogenetic tree in BioPerl results in "undefined value" or "unblessed reference" error

I have a phylogenetic tree I am loading in BioPerl. I want to use a custom sort function ("$depth_sort" below) to order the nodes vertically when printing out the tree. However the documented method used below writes out the tree in the same order…
CAS
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Fetch attribute values from GFF3 database wiith bioperl

I already created a GFF3 DB with BioPerl Store Object (BIO:DB:SeqFeature:Store) I created the GFF3 file by myself from a Blastx result and created a series of my own tags as attributes. Now I would fetch this values from the database that BioPerl…
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How to safely uninstall bioperl that was installed via CPAN?

I installed BioPerl via CPAN. Several tests got failed and I force installed it. I now want to install it via ubuntu software centre. Can anyone describe how to remove BioPerl that was installed via CPAN using method given here.
Chirag
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Perl replace the top-level numbers only from a tree

I'm new to this website. Here's a problem that troubled me for >2 hr. I have a string (phylogenetic tree in newick format), which looks like: ((A:14,B:43):22,C:76,(D:54,(E:87,F:28):17):35); The tree may have multiple levels, indicated by…
Qiyun Zhu
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Selectively joining elements of an array into fewer elements of a new array

I'm having some trouble manipulating an array of DNA sequence data that is in .fasta format. What I would specifically like to do is take a file that has a few thousand sequences and adjoin sequence data for each sequence in the file onto a single…
amrezans
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wrapper script and GetOpts::Long perl

I have been trying to make GetOpts :: Long work for my code but it just doesn't respond. I have a wrapper script with about 8 scripts and 2 commands. I have been trying to GetOpts :: Long submit arguments into the separate codes, but it doesnt…
J_Dow
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How to display all the characters in only once using Perl

I tried the below code #!usr/local/bin/perl open(f1, "/home/httpd/cgi-bin/LDU/list1.txt"); while ( $line = ) { $line =~ m/(?:=")\w+/g; print "$line"; } I need the output to be displayed as follows acinetobacter_baumannii_26016_2 …
stackcareer
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BIOPERL. Bio::Graphics with GFF file

I need to obtain something like this: However, I cannot know how to continue... now I have this: In other words... I cannot know how to add tags and the corresponding transcripts, CDS, etc. My code right now is the following…
user2886545
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Downloading sequence file with perl

I am trying to download the sequence file from the gene bank database using perl but it shows error. I don't have any guide to correct my program. Can any one help me with this? The error is in line 6 (use Bio::DB::GenBank;) File accnumber.txt is…
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I want to replace a sequence name in fasta file with another name

I have one fasta file and one text file fasta file contains sequences in fasta format and text file contains name of genes now I want to replace name of the sequences in fasta file after '>' sign with the gene names in text file I am new to perl…
user2181315
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Cannot install Bioperl Moduals

Building BioPerl Reading skip patterns from 'INSTALL.SKIP'. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' Do not have write permissions on '/usr/local/bin' 6.…
Away
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Double restriction enzyme digest in Bioperl

I am trying to analyze several thousand sequences for double restriction enzyme cuts. For this example, let's say these two enzymes are EcoRI and MspI. I am using Bioperl modules for this (see the code below) and can make it work for single enzymes.…
berge2015
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How can I print the first result of a search sequence for each iteration?

How can I print the first occurrence of a protein sequence? For this query I get four results and I want only the first. use Bio::DB::GenBank; use Bio::DB::Query::GenBank; $query = "LEGK"; $query_obj = Bio::DB::Query::GenBank->new( -db …
MTG
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