Notes From Demo 2

Demo number two was about seeing the samifier and the predicted proteins implemented in Java. We had a chat too about how the web app was going.

We installed the java command line tools and here you can see their output when no parameters are given:

The samifier

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$ java -jar samifier.jar
usage: samifier -c <chromosomeDir> -g <genomeFile> -m <mappingFile> -o
       <outputFile> -r <searchResultsFile>
 -c <chromosomeDir>       Directory containing the chromosome files in
                          FASTA format for the given genome
 -g <genomeFile>          Genome file in gff format
 -m <mappingFile>         File mapping protein identifier to ordered locus
                          name
 -o <outputFile>          Filename to write the SAM format file to
 -r <searchResultsFile>   Mascot search results file in txt format

and the protein generator

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$ java -jar protein_generator.jar
usage: protein_generator -d <Database Name> -f <Genome File> [-g <Glimmer
       File>] [-i <Split Interval>] -o <Output File> [-t <Translation
       Table File>]
 -d <Database Name>            Database name
 -f <Genome File>              Genome file in FASTA format
 -g <Glimmer File>             Glimmer txt file. Can't be used with the -i
                               option.
 -i <Split Interval>           Size of the intervals into which the genome
                               will be split. Can't be used with the -g
                               option.
 -o <Output File>              Filename to write the FASTA format file to
 -t <Translation Table File>   File containing a mapping of codons to
                               amino acids, in the format used by NCBI.

although the option -i is still pending, it is meant to be for virtual proteins for next sprint.

The samifier code is in here and the protein generator here.

We also demoed in the web application the new look & feel, based on the SBI website. It’s still work in progress as we need to define how the menus are going to change for this application. That will be a discussion for our next planning meeting. We also showed how to enter an input collection in the system, although there were also questions pending in terms of the metadata model.

For this sprint we want to focus in working with the samifier (reverse strand proteins, the mzIdentML format,) and the protein generator.