Tag: BioPerl

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Are you looking for your next opportunity in bioinformatics? Then you need a strong CV that showcases your relevant qualifications and experience in the field. In this guide, we’ll teach you how to create an impressive application that showcases your top achievements. You can also check out our bioinformatics CV…

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

Provided by: libbio-perl-run-perl_1.6.9-3_all NAME Bio::Installer::Clustalw – DESCRIPTION of Object SYNOPSIS Give standard usage here DESCRIPTION Describe the object here FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation…

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Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::DB::Flat::BDB::swiss – swissprot adaptor for Open-bio standard BDB-indexed flat file SYNOPSIS See Bio::DB::Flat. DESCRIPTION This module allows swissprot files to be stored in Berkeley DB flat files using the Open- Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use…

Prokka installation – compilation aborted 0 Hi, I installed Prokka using this code posted at github.com/tseemann/prokka sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl sudo cpan Bio::Perl git clone github.com/tseemann/prokka.git $HOME/prokka $HOME/prokka/bin/prokka –setupdb All the steps worked pretty well except the last line for database indexing $HOME/prokka/bin/prokka –setupdb I…

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Structure::StructureI – Abstract Interface for a Structure objects SYNOPSIS Give standard usage here DESCRIPTION Describe the interface here FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing…

Bio::Network::Interaction – describes a protein-protein interaction # Add an interaction with some attributes use Bio::Network::Interaction; my $interx = Bio::Network::Interaction->new(-weight => $score, -id => $id); $gr->add_interaction(-nodes => [($node1,$node2)], -interaction => $interx); # Retrieve an interaction using an identifier my $interaction = $gr->get_interaction_by_id($id); my $id = $interaction->primary_id; my $wt = $interaction->weight; my…

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::AlignIO::nexus – NEXUS format sequence input/output stream SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. use Bio::AlignIO; my $in = Bio::AlignIO->new(-format => ‘nexus’, -file => ‘aln.nexus’); while( my $aln = $in->next_aln ) { # do something with the alignment } DESCRIPTION…

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::PopGen::IO::phase – A parser for Phase format data SYNOPSIS # Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => ‘phase’, -file => ‘data.phase’); # Some IO might support reading in a population at a time my @population; while( my…

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Location::CoordinatePolicyI – Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print “Location of feature “, $feature->primary_tag(), ” employs a “, ref($location->coordinate_policy()),…

Provided by: libbio-perl-run-perl_1.7.1-3_all NAME Bio::Tools::Run::Phylo::Phylip::Base – Base object for Phylip modules SYNOPSIS # Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules DESCRIPTION This module is just a base object for Bioperl Phylip wrappers. IMPORTANT PHYLIP VERSION ISSUES By default…

binutils-2.31.1.tar.xz   59.00b   August 17 2018 binutils-2.32.tar.xz   57.00b   February 8 2019 at 19:01 bio-svgenes-0.3.3.gem   58.00b   August 30 2013 bio-svgenes-0.4.1.gem   58.00b   September 2 2015 biogrep-1.0.tar.gz   55.00b   September 2 2015 bioinfo-0.1.2.tar.gz   57.00b   September 2 2015 biom-format-1.1.2.tar.gz   61.00b   July 10 2013 biom-format-1.2.0.tar.gz   61.00b   October 15 2013 biom-format-2.1.3.tar.gz   61.00b   September 2 2015 biom-format-2.1.7.tar.gz   61.00b   November…

Bio-Graphics-2.39.tar.gz   1.09Mb   July 31 2014 Bio-SamTools-1.39.tar.gz   323.75Kb   August 29 2013 Bio-SamTools-1.41.tar.gz   330.81Kb   December 22 2014 BioPerl-1.6.901.tar.gz   11.72Mb   May 19 2011 BioPerl-DB-1.006900.tar.gz   481.25Kb   December 11 2010 BioPerl-Network-1.006900.tar.gz   2.10Mb   April 21 2011 BioPerl-Run-1.006900.tar.gz   13.87Mb   April 21 2011 Birth-gkrellm.tar.gz   25.48Kb   January 15 2002 Bit-Vector-6.4.tar.gz   128.85Kb   October 3 2004 Bit-Vector-7.2.tar.gz   134.59Kb   March 9 2012…

I’m using SCRMshaw to predict CRMs and I’m trying to use the enrichment bash script that comes with it. At first it had the problem of Can’t locate Bio/SeqIO.pm in @INC but this was fixed by exporting the path to a BioPerl installation in an Anaconda environment I made for…

prokka –setupdb issue 0 i wish to do gene annotation using prokka on my linux environment. but i am getting the following thing only instead of answer. i dont know where i made mistake. The command i used: prokka –outdir /home/prokkareport /home/annotation/finalized_contig_fasta the result :[20:43:37] This is prokka 1.14.5 [20:43:37]…

Provided by: libbio-perl-perl_1.7.2-3_all NAME Bio::PopGen::IO::prettybase – Extract individual allele data from PrettyBase format SYNOPSIS Do not use directly, use through the Bio::PopGen::IO driver DESCRIPTION This object will parse comma delimited PrettyBase output. PrettyBase is defined by the SeattleSNPs pga.gs.washington.edu/ This is expected to be tab delimited (you can vary with…

Links for bioperl Debian Resources: Maintainers: External Resources: The following binary packages are built from this source package: bioperl herramientas de Perl para biología molecular computacional libbio-perl-perl BioPerl core perl modules Other Packages Related to bioperl adep: debhelper-compat (= 13) Package not available adep: libmodule-build-perl framework for building and installing…

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::Factory::SequenceFactoryI – This interface allows for generic building of sequences in factories which create sequences (like SeqIO) SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my $seqbuilder = Bio::Seq::SeqFactory->new(‘-type’ => ‘Bio::PrimarySeq’); my $seq =…

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Primer::Pair – two primers on left and right side SYNOPSIS use Bio::Tools::Primer::Pair; my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp); # helper functions print “GC percentage different”,$pf->gc_difference(),”\n”; print “product length is “,$pf->product_length,”\n”; DESCRIPTION Primer Pairs represents one primer in a primer pair. This…

Provided by: libbio-perl-perl_1.7.7-2_all NAME Bio::Search::GenericStatistics – An object for statistics SYNOPSIS my $void = $obj->set_statistic(“statistic_name”,”statistic_value”); my $value = $obj->get_statistic(“statistic_name”); DESCRIPTION This is a basic container to hold the statistics returned from a program. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl…

bp_multi_hmmsearch.pl BioPerl wrappers: scripts Maintainer: Debian Med Packaging Team Section: science Install bp_multi_hmmsearch.pl Debian apt-get install bioperl-run Click to copy Ubuntu apt-get install bioperl-run Click to copy Kali Linux apt-get install bioperl-run Click to copy Raspbian apt-get install bioperl-run Click to copy Share Installing bp_multi_hmmsearch.pl command is simple. just copy…

BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 There is a newer version of BioPerl Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Accessing BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 To load the module for BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 please use this command…

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Name Last modified Size Description Parent Directory   –   bioperl-run_1.6.9-2.debian.tar.gz 2013-11-15 15:13 9.1K   bioperl-run_1.6.9-2.dsc 2013-11-15 15:13 1.6K   bioperl-run_1.6.9-2_all.deb 2013-11-15 15:33 41K   bioperl-run_1.6.9-3.debian.tar.xz 2015-07-03 08:23 8.7K   bioperl-run_1.6.9-3.dsc 2015-07-03 08:23 2.2K   bioperl-run_1.6.9-3_all.deb 2015-07-03 08:43 39K   bioperl-run_1.6.9.orig.tar.gz 2011-06-19 02:04 14M   bioperl-run_1.7.1-3.debian.tar.xz 2017-01-13 15:13 12K  …

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. SYNOPSIS use Bio::Map::OrderedPosition; # the first marker in the sequence my $position = Bio::Map::OrderedPosition->new(-order => 1, -positions…

Bio::SeqIO::fasta(3) fasta sequence input/output stream SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION This object can transform Bio::Seq objects to and from fasta flat file databases. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules….

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Seg – parse “seg” output SYNOPSIS use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => ‘seg.fasta’); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, ” is low complexity\n”; } } DESCRIPTION “seg” identifies low-complexity regions on a protein sequence. It is…

Cjfields Author Name: Jason Stajich (@hyphaltip) Original Redmine Issue: 3328, redmine.open-bio.org/issues/3328 Original Date: 2012-02-17 Original Assignee: Bioperl Guts I am Cheng-Ruei Lee, a graduate student in Duke Biology. I’m analyzing many DNA alignments of a plant species. I first used (Bio::PopGen::Utilities -> aln_to_population()) to read in the fasta format alignment,…

Bio::Search::HSP::WABAHSP(3) HSP object suitable for describing WABA alignments SYNOPSIS # use this object as you would a GenericHSP # a few other methods have been added including state DESCRIPTION This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA…

Bio::TreeIO::nhx(3) TreeIO implementation for parsing SYNOPSIS # do not use this module directlyuse Bio::TreeIO;my $treeio = Bio::TreeIO->new(-format => ‘nhx’, -file => ‘tree.dnd’);my $tree = $treeio->next_tree; DESCRIPTION This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format. FEEDBACK Mailing Lists User feedback is an integral part of the evolution…

Bio::AlignIO::selex(3) selex sequence input/output stream SYNOPSIS # Do not use this module directly. Use it via the L<Bio::AlignIO> class.use Bio::AlignIO;use strict;my $in = Bio::AlignIO->new(-format => ‘selex’,-file => ‘t/data/testaln.selex’);while( my $aln = $in->next_aln ) {} DESCRIPTION This object can transform Bio::Align::AlignI objects to and from selex flat file databases. FEEDBACK Support…

 The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl. . The recommended packages are needed to run some of the included binaries, for a detailed…

Bio::Tools::Phylo::Molphy(3) parser for Molphy output SYNOPSIS use Bio::Tools::Phylo::Molphy;my $parser = Bio::Tools::Phylo::Molphy->new(-file => ‘output.protml’);while( my $r = $parser->next_result ) {# r is a Bio::Tools::Phylo::Molphy::Result object# print the model nameprint $r->model, “n”;# get the substitution matrix# this is a hash of 3letter aa codes -> 3letter aa codes representing# substitution ratemy $smat…

vep -i examples/homo_sapiens_GRCh38.vcf –database Can’t locate Bio/PrimarySeqI.pm in @INC (you may need to install the Bio::PrimarySeqI module) (@INC contains: /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/modules /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0 /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2 /home/youssef/anaconda3/envs/ngs1/lib/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/5.26.2 .) at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. Compilation failed in require at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm…

Bio::MapIO::mapmaker(3) A Mapmaker Map reader SYNOPSIS # do not use this object directly it is accessed through the Bio::MapIO system use Bio::MapIO;my $mapio = Bio::MapIO->new(-format => “mapmaker”,-file => “mapfile.map”);while ( my $map = $mapio->next_map ) { # get each mapforeach my $marker ( $map->each_element ) {# loop through the markers…

Bio::Root::Version(3) provide global, distribution-level versioning SYNOPSIS package Bio::Tools::NiftyFeature;require Bio::Root::RootI;# later, in client code:package main;use Bio::Tools::NiftyFeature 3.14;## alternative usage: NiftyFeature defines own $VERSION:package Bio::Tools::NiftyFeature;my $VERSION = 9.8;# later in client code:package main;# ensure we’re using an up-to-date BioPerl distributionuse Bio::Perl 3.14;# NiftyFeature has its own versioning scheme:use Bio::Tools::NiftyFeature 9.8; DESCRIPTION This…

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

Try to be as detailed as possible. Why do you need it? What data does it use? What should the user experience? ABI file parser –> read .abi files into JSON. We have chromatogram files. Would be great to be able to view these in the browser. Some other .abi…

In the dependency checking script, the bash builtin command -v is used for checking whether BioPerl is installed. However, this command will always succeed as long as Perl is installed, as it does not execute the command. Consider changing e.g., github.com/abhijeetsingh1704/AcetoScan/blob/70f0428e4fffbff6af17ce5a83b26ce24abd0f29/AcetoScan_MacOS/scripts/AcetoScan_software_check.sh#L48 into if ! perl -MBio::SeqIO -e ‘printf “%vdn”, $Bio::SeqIO::VERSION,…

$Id$ o Version This is bioperl-run version 1.5.2, a developer release. o Description bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common bioperl objects. See the Changes file for more information about what is contained in here. o…

Before switching to Biopython, I thought there are similar indexing features in biopython as in bioperl. However, the biopython SeqIO.index_db() and SeqIO.index() methods are so inefficient that it’s almost impossible to random access a segment of genomic sequence using biopython. I tested the performance of biopython and bioperl in retrieving…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: sunp…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/p5-BioPerl-1.007007_1.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building biology/p5-BioPerl build started at Fri Oct 29…

Code: #!/usr/bin/perl use strict; use warnings; die “Usage: $0 <fasta_file style=”box-sizing: border-box; color: rgb(102, 102, 102); font-family: ‘Open Sans’, sans-serif; font-size: 13px; font-style: italic; line-height: 20px; background-color: rgb(251, 251, 251);”><coord_file style=”box-sizing: border-box;”>n” unless @ARGV > 0; my ($fasta_file, $coord_file) = @ARGV; open FASTA, “<” . $fasta_file; my $seq_id; my $dna_string =…

Any tools converting Genbank format to GFF3 format? 4 Dear all, As my title describe, I am asking help to convert Genbank format to GFF format.  By GOOGLing, I found a perl script bp_genbank2gff3.pl), which has many bioperl dependencies.  Could anyone inform me other easy-to-use tools?  Any suggestions will be…

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

Tools To Calculate Average Coverage For A Bam File? 12 I would like to get the average coverage of all the captured bases in a bam file. What would be the best way to do this? What I am looking is a simple one number like 40X. Given that there…

Hello, I’m trying to run the following command: agat_sp_extract_sequences.pl -g JU2526_Y39G10AR.22.gff -f JU2526*_region.fa -p And it throws the following error: ————- EXCEPTION: Bio::Root::Exception ————- MSG: Each line of the file must be less than 65,536 characters. Line 2 is 67824 chars. STACK: Error::throw STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757 STACK:…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 14 Sep 2021 18:52:51 +0200 Source: bioperl-run Architecture: source Version: 1.7.3-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: bioperl-run (1.7.3-7) unstable; urgency=medium . * d/watch: fix broken link to github and adjust…

Difficulty installing Bioperl for use with GUIDANCE 0 Hi, I am trying to use the Guidance software to analyze a set of 427 sequences. I have the software downloaded and installed the modules indicated in the Guidance user guide (Perl/BioPerl/Ruby), but when I attempt to run Guidance with the following…

Can’t locate Bio/SeqIO.pm – path error? 0 Hi, I am trying to run snippy on my UBUNTU18 (inside a conda env that has this tool installed) but am getting an error: Can’t locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO.pm module) I checked the posts here, and…

Provided by: libbio-procedural-perl_1.7.4-2_all NAME Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl VERSION version 1.7.4 SYNOPSIS See Bio::Perl for examples. DESCRIPTION The code in this distribution focuses on simple low-dependency procedural interfaces to BioPerl that don’t require knowledge of BioPerl classes and methods. FEEDBACK Mailing lists User feedback is an…

Hello, I am trying to run this command line in the terminal from Mac OS, which is copied from a protocol: FEELnc_codpot.pl –i <unannotated_transcript.fa> -a <mRNA_sequence.fa> -g <reference_genome.fa> -m ’shuffle’ –o <unannotated_transcript> However, I get the following error: command not found, probably because I am not using perl, so I…