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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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Merge fields in a file

I have a file with 7 columns, a GFF file having chromosomal regions.I want to collapse the rows where REGION ="exon" to only one row in the file.The row has to be collapsed on the basis of regions being overlapping with each other. REGION START …
Rgeek
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extract overlapping regions

I have a file characterizing genomic regions that looks like this: chrom chromStart chromEnd PGB chr1 12874 28371 2 chr1 15765 21765 1 chr1 15795 28371 2 chr1 18759 24759 1 chr1 28370 34961 1 chr3 233278 …
user3222627
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Perl program not working

I have written a perl program to find the percentage GC content in the given DNA string.But the program is executing the error situation(else part of conditional statement) $dna = "AGTC"; $a = 0; $g = 0; $t = 0; $c = 0; for ($p = 0; p < length…
user2877617
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Parsing GenBank file: get locus tag vs product

Basically, a GenBank file consists on gene entries (announced by 'gene' followed by its corresponding 'CDS' entry (only one per gene) like the two I show here below. I would like to get locus_tag vs product in a tab-delimited two column file. 'gene'…
biotech
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Accessing Fasta file using Bio::DB::Fasta

I have been using the module use Bio::DB::Fasta to access fasta files (documentation here:https://metacpan.org/pod/Bio::DB::Fasta#OBJECT-METHODS). I find that this is much fasta than using Samtools for extracting positions from a fasta file.…
user19758
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how to replace the same number of file1 with same number from file2

i have a list of query and hits gi in one file (file1) . i have another file in which complete name of hits is there(file2), now i want to replace Hits gi from file1 to file2 that have the complete Hit name. i want that gi must be replace with the…
Sidra Rafi
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Bio Perl: code to split paired end data?

I am a beginner with bioinformatics and I have been working on a little Bio Perl code to split my paired end MiSeq data (currently in 1 fastq file) into 2 files, each file containing one end of the pair. The different ends of the paired end reads…
user2852013
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use Bio::seq not working in Perl

I installed CPAN and then successfully installed Bioperl. I cannot find Bio perl folder in /usr/bin However, the files are present at home/.cpan/build/BioPerl-1.61/Bio/ I am unable to use Bio::SeqIO on Komodo IDE: Komodo Edit 8 OS: Ubuntu…
Death Metal
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Bioperl push $seq->id to array

I'm fairly new to Perl and Bioperl, I am trying to write a script which will identify instances of identical sequences. To achieve this, I envision a script which takes 2 infiles, the first a multiple alignment in fasta format and the second an…
user2460253
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Access abstract from pubmed using Bio::DB::EUtilities

I am using Bio::DB::EUtilities to query the Pubmed DB with given PMIDs (Pubmed Id). use Bio::DB::EUtilities; use strict; use warnings; my @ids = (23298400); my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', …
Matthias Munz
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Perl API Error: Bareword "SQL_INTEGER" not allowed while "strict subs" in use

I am attempting to connect to the Ensembl API using the following Perl code: #!/bin/perl use Bio::EnsEMBL::Registry; use DBI qw(:sql_types); my $registry = 'Bio::EnsEMBL::Registry'; $registry->load_registry_from_db( …
user2639056
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How can I query Genbank and print the results to a fasta file?

I have been trying to write a code using BioPerl that will query Genbank for a specific protein and then print the results to a fasta file. So far the code I have works and I can print the results to the screen, but not to a file. I have done lots…
user2852013
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bioperl package Bio::Tree::Tree can't locate object method as_text

I'm trying to use as_text method from Bio::Tree::Tree I get this message: can't locate object method as_text via package Bio::Tree::Tree I'm using the example here Note that I tried other methods in the same package and they worked normally. my…
Mariya
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How to read reference line (start with RN,RT,RA,RC,RX,RP,RL) and print all

Hello Everyone, I had a problem regarding a Perl Module as I am using this module to retrieve some specific lines form a flat file that contains multiple sets of information as I had mentioned in code.(This is an example code of …
meghavarshney
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pull out sequence from genbank formt

This code was working properly but now it complains, does the genbank structure changed? #!/usr/bin/perl -w …
user1876128
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