This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Biojava: The Key Named Program Is Not Set In This Remoteqblastoutputproperties Object

Hello. I'm trying to test this example from the Biojava legacy cookbook, but it gives me the following error: The key named PROGRAM is not set in this RemoteQBlastOutputProperties object. Any help on this please?

biojava
• 2,363 views • link
updated by Biostar Biostar • written by Peter • Peter

1 answer

It seems to be a known problem:

http://permalink.gmane.org/gmane.comp.java.bio.general/4048

I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Yes, I also found this, but there seems to be no solution.

• 10 views • link
written by Peter • Peter

Log in to answer this question.

More posts like this
  • TCGAbiolinks MSI data
    written by Elizabeth • Elizabeth
    Hi! I am trying to use this code to access Microsatellita data: query <- GDCquery(project = "TCGA-COAD", data.category = "Other", legacy = TRUE, access = …
  • MAGeCK "An error occurs while trying to compute p values. Quit.."
    written by fionamh • fionamh
    Hello, I'm getting the following error message when running mageck test in --paired mode "An error occurs while trying to compute p values. Quit.." Up …
  • difference between imports in biojava
    written by Moses Moses
    I'm using biojava classes and modules over Eclipse IDE. While going over the cookbook provided by the wiki page I reached the following point: http://biojava.org/wiki/BioJava:CookBook:PDB:read3.0 …
  • Where To Download Refseq Mrna Sequence Data?
    written by newDNASeqer newDNASeqer
    <p>I'm following this tutorial to create indicies of genome and transcripts at <a href='http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial'>http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial</a>, but could not find the RefSeq from <a href='http://physiology.med.cornell.edu/faculty/elemento/lab/files/refGene.txt.07Jun2010.fa'>http://physiology.med.cornell.edu/faculty/elemento/lab/files/refGene.txt.07Jun2010.fa</a> (the file …
  • Secondary Structure Of A Protein In Biojava
    written by potassiumiodide0990 potassiumiodide0990
    <p>Is there any biojava method which i can implement to predict the secondary structure of a protein for a given amino acid sequence?</p> <p>I came …
  • T-Test In R On Microarray Data
    written by Diana Diana
    <p>Hello everyone,</p> <p>I'm trying to do a simple t-test on my microarray sample in R. My sample looks like this:</p> <pre><code>gene_id gene sample_1 value_1 sample_2 …
  • Bio.Iupac Problem In Biopython
    written by Saifalharthi • Saifalharthi
    <p>i was testing this simple code</p> <pre><code> from Bio.Alphabet import IUPAC from Bio import Seq my_prot=Seq("AGTACACTGGT",IUPAC.protein) </code></pre> <p>and it gives me this error</p> <p>TypeError: 'module' …
  • Biojava And Blast+
    written by Peter • Peter
    <p>Dear all, </p> <p>i´m currently trying to parse several blast output files in order to show the results in my software. Since i have to …
  • Mounting A File System On Amazon Web Services
    written by Peter • Peter
    <p>Hi,</p> <p>I'm trying to use an Amazon Web Server linux instance to do some bioinformatics work. I believe I have setup an attached storage area …
  • Biojava Versus Biojavax
    written by Andrea_Bio • Andrea_Bio
    <p>Hi</p> <p>I'm new to BioJava so please forgive my ignorance.</p> <p>I believe BioJavaX is an extension to BioJava and that it is part of the …