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• How can I save BioPerl sequence nested features in genbank or embl format?

  - by Ryan Thompson

  In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

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• Bioperl, equivalent of IO::ScalarArray for array of Seq objects?

  - by Ryan Thompson

  In perl, we have IO::ScalarArray for treating the elements of an array like the lines of a file. In BioPerl, we have Bio::SeqIO, which can produce a filehandle that reads and writes Bio::Seq objects instead of strings representing lines of text. I would like to do a combination of the two: I would like to obtain a handle that reads successive Bio::Seq objects from an array of such objects. Is there any way to do this? Would it be trivial for me to implement a module that does this? My reason for wanting this is that I would like to be able to write a subroutine that accepts either a Bio::SeqIO handle or an array of Bio::Seq objects, and I'd like to avoid writing separate loops based on what kind of input I get. Perhaps the following would be better than writing my own IO module? sub process_sequences { my $input = $_[0]; # read either from array of Bio::Seq or from Bio::SeqIO my $nextseq; if (ref $input eq 'ARRAY') { my $pos = 0 $nextseq = sub { return $input->[$pos++] if $pos < @$input}; } } else { $nextseq = sub { $input->getline(); } } while (my $seq = $nextseq->()) { do_cool_stuff_with($seq) } }

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• Where do I find Nmake for Windows XP

  - by Shrujan

  Regarding BioPerl installation in Windows XP, I have installed Active Perl in Windows XP, and by using Perl Package Manager I have installed the BioPerl Repositories too. But I am not able to run the BioPerl yet. While running the BioPerl program in emacs it is showing the following error: make -k 'make' is not recognized as internal or external command, operable program or batch file I have tried to install Nmake for Windows but this error is showing. No webpage was found for the web address: http://download.microsoft.com/download/vc15/patch/1.52/w95/en-us/nmake15.exe How could this be resolved?

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• Language Niches and Niche Libraries

  - by Roman A. Taycher

  "Everyone Knows" ... ... that c is widely used for low level programs in large part because operating system/device apis are usually in c. ... that Java is widely used for enterprise applications in large part because of enterprise libraries and ide support. ... that ruby is widely used for webapps thanks in large part because of rails and its library ecosytem But lets go into to details what are the specific niches and subniches. Especially with respect to libraries. Where might you embed lua for application scripting versus python. Where would you use Java vs C#. Which languages do different scientists use? Also which languages have libraries for these subniches? Things like bioperl/scipy/Incanter. Please no flamewars about how nice each language or environment is. This is where they used. Also no complaints about marketing/PHBs. (Manually migrated) I asked this question again after it was closed on stackoverflow.com

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