Hello (cruel) world!
I'll be posting a bit or two on Perl and Biology for the masses, including my attempts at refactoring bits of BioPerl.
pyrimidine
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I blog about Perl (and biology).
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Do actual biologists use BioPerl? Where have you found it easier than writing a one-off script from scratch?
All depends on what your particular need is. If I just want the number of sequences in a large file or want to simply split up sequences for repeated analyses, I could just write simple one-off scripts.
However, if I intend on parsing FASTQ data and having it map to the proper quality code, or want to analyze some data (sequences, features, alignments) in more detail, or pipeline several analyses, I would rather use well-tested code vs rolling my own. Just to note, both use cases are things that have popped up on our mail list (I'm a BioPerl core dev), and we have directed some users to better resources than BioPerl in the past.
Speaking as a sometimes biologist, my experience of Bioperl has been that it is often slow, overly complex, and/or incomplete. Worse, the documentation and interface are utter garbage. Let's say I want to deal with a FASTA file. A straightforward CPAN search leads me to this:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/SeqIO/fasta.pm
Give me a break. FASTA is a simple format, and should be easy to handle. I'll just do '$/="\n>"' and forget about the module...
Speaking as a sometimes biologist, my experience of Bioperl has been that it is often slow, overly complex, and/or incomplete. Worse, the documentation and interface are utter garbage. Let's say I want to deal with a FASTA file. A straightforward CPAN search leads me to this:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/SeqIO/fasta.pm
Give me a break. FASTA is a simple format, and should be easy to handle. I'll just do '$/="\n>"' and forget about the module...