Tag: BioPerl

Ubuntu Manpage: Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of

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…

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man Bio::SeqIO::fasta (3): fasta sequence input/output stream

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….

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Ubuntu Manpage: Bio::Tools::Seg – parse “seg” output

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…

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segregating sites calculation fails on gapped sequences #132

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,…

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HSP object suitable for describing WABA alignments

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…

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man Bio::TreeIO::nhx (3): TreeIO implementation for parsing

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…

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man Bio::AlignIO::selex (3): selex sequence input/output stream

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…

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bioperl : Impish (21.10) : Ubuntu

 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…

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man Bio::Tools::Phylo::Molphy (3): parser for Molphy output

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…

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linux – How to fix Perl from anaconda not installing bioperl? Bailing out the installation for BioPerl

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…

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man Bio::MapIO::mapmaker (3): A Mapmaker Map reader

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…

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man Bio::Root::Version (3): provide global, distribution-level versioning

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…

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Fail to install Ensembl VEP

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…

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biojs – Github Plus

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…

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BioPerl dependency check always succeeds

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,…

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awitney/bioperl-run – githubmemory

$Id$ 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…

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Biopython Seqio.Index() And Seqio.Index_Db() Very Slow For Large Sequence

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…

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main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 in stage

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…

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Rewriting perl code using bioperl

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 =…

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Any tools converting Genbank format to GFF3 format?

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…

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biopython extract sequence from fasta

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,…

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Tools To Calculate Average Coverage For A Bam File?

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…

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Line length limit on input FASTA file: 65,536 characters (limit imposed by bioperl)

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:…

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Accepted bioperl-run 1.7.3-7 (source) into unstable

—–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…

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Difficulty installing Bioperl for use with GUIDANCE

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…

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Can’t locate Bio/SeqIO.pm – path error?

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…

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Ubuntu Manpage: Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl

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…

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Bioperl SeqIO.pm cannot be found

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…

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