How to compare and merge multiple files?
perl,shell,bioinformatics,bioperl
I think something like this should do what you want. We use a hash to gather the 'reference' file and turn it into a set of keys with an empty array. Then we iterate on the other files, extracting '3 values' as key, and the last value as an actual...
Processing FASTQ files based on mate pair length
perl,bioinformatics,bioperl,fastq,sequencing
As you have read, your problem is because of a spurious push that adds an integer value to the end of the @fh array. I presume you were aiming to extend the array to be long enough to add the new file handle. You can do that by assigning to...
Can't install Bioperl Module (properly?)
BioPerl uses many modules that you might not have installed. From BioPerl INSTALL file: Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a few failed tests may not affect your usage of BioPerl Most of the time you...
Install BioPerl with custom library path
perl,module,installation,bioperl
Being without root access is a common issue, that's why there is perlbrew. \curl -L http://install.perlbrew.pl | bash Then just install cpanminus for use with perlbrew: Installing to local perl (perlbrew). curl -L http://cpanmin.us | perl - App::cpanminus That should enable you to have a stable environment for installing all...
BioPerl/BioGraphics only prints one value instead of all
In this line my @SNPs = "408777 408900 409100 409480"; You're just creating an array with a single element of that whole string. Try my @SNPs = qw(408777 408900 409100 409480); ...
Converting PHYLIP text file to a PNG image
perl,tree,bioinformatics,scientific-computing,bioperl
This code produces SVG output on STDOUT (I'm not qualified to comment on whether the correct nodes are displayed): use v5.16; # sets strict and warnings use Bio::Phylo::Forest; use Bio::Phylo::Treedrawer; my $string = '(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);'; my $forest = Bio::Phylo::IO->parse( -format => 'newick', -string => $string )->first; my $treedrawer = Bio::Phylo::Treedrawer->new( -width...