On 08/11/13 01:31 PM, JC Grenier wrote: > Yes, I have those programs. I'll erase everything and redo it completely. How > much time is it suppose to take?
I would say around 1 hour including downloads. > > > 2013/11/8 Sébastien Boisvert <sebastien.boisver...@ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>> > > On 08/11/13 11:41 AM, JC Grenier wrote: > > Hi there, > > > Hi, > > > I got a couple of question for you today. If I want to get the > information about the Biological Abundance and the GeneOntology Terms in the > same analysis, how should I proceed? If I'm putting two search terms in the > command line, would it be alright and detect automatically where to look for > each analysis step? > > Ex : > mpiexec -n 48 Ray -k 31 -p Sample.filtered.R1.fq.gz > Sample.filtered.R2.fq.gz -s Sample.filtered.single.fq.gz -o RAY_k31_c100 > -search ~/NCBI-taxonomy/NCBI-Finished-__Bacterial-Genomes -with-taxonomy > ~/NCBI-taxonomy/Genome-to-__Taxon.tsv ~/NCBI-taxonomy/TreeOfLife-__Edges.tsv > ~/NCBI-taxonomy/Taxon-Names.__tsv -search ~/GeneOntology/EMBL_CDS___Sequences > -gene-ontology ~/GeneOntology/OntologyTerms.__txt > ~/GeneOntology/Annotations.txt > > > I believe this will work quite well. > > Basically, the -search commands will add colors to the kmers of the graph. > If your headers for your NCBI genomes have "gi" numbers, then this will > create a separate namespace and > -with-taxonomy will pick them up to perform a LCA (Last Common Ancestor) > in the taxonomic tree for each kmer. > > see > https://github.com/sebhtml/__ray/blob/master/Documentation/__Taxonomy.txt > <https://github.com/sebhtml/ray/blob/master/Documentation/Taxonomy.txt> > > > Another question, I tried to redo the same files as on your 2012 > Paper (as found on GitHub) using all your scripts you provide there: > > > https://github.com/sebhtml/__Paper-Replication-2012/tree/__master/Build-Input-Files-for-__Gene-Ontology > > <https://github.com/sebhtml/Paper-Replication-2012/tree/master/Build-Input-Files-for-Gene-Ontology> > > And I'm not able to get this completed. The script Rebuild-Fasta.py > apparently does nothing at the end of the day. It's creating > EMBL_CDS_Sequences folder, but the only file in it is empty and the rest of > the procedure is not producing the right things. > > > I tested that and it worked: > > > git clone https://github.com/sebhtml/__Paper-Replication-2012.git > <https://github.com/sebhtml/Paper-Replication-2012.git> > cd Paper-Replication-2012 > cd Build-Input-Files-for-Gene-__Ontology > ./Main.sh > > > And I got this: > > Generating parts. > Thank you for your kind patience ! > > To use these builds with Ray Ontologies (via the Ray binary), add these > options: > > -search \ > > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences > \ > -gene-ontology \ > > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/OntologyTerms.__txt > \ > > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/Annotations.txt > \ > > > 2.8G > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/Annotations.txt > 28M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/OntologyTerms.__txt > > > [boiseb01@ls30 ~]$ du -sh > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/*|head > 97M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__0.fasta > 87M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__100.fasta > 81M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__101.fasta > 82M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__102.fasta > 123M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__103.fasta > 110M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__104.fasta > 108M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__105.fasta > 89M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__106.fasta > 88M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__107.fasta > 82M > /home/boiseb01/test-paper-__replication/Paper-Replication-__2012/Build-Input-Files-for-__Gene-Ontology/EMBL_CDS___Sequences/000-Sequences.Part.__108.fasta > > > > Do you have wget and gzip ? > > Can you help me with this or indicate a way to get the proper files > to launch the gene-ontology search? > > Thanks a lot. > -- > Jean-Christophe Grenier, M.Sc. > > ------------------------------__----------- > /Bio-informaticien/ > /Laboratoire de Philip Awadalla/ > /Laboratoire de Luis Barreiro/ > /CHU Sainte-Justine/ > //3175, Côte Sainte-Catherine, local B-607 > ///Tél : 514-345-4931 <tel:514-345-4931> poste 5199/ > ------------------------------__----------- > > > > > > -- > Jean-Christophe Grenier, M.Sc. > > ----------------------------------------- > /Bio-informaticien/ > /Laboratoire de Philip Awadalla/ > /Laboratoire de Luis Barreiro/ > /CHU Sainte-Justine/ > //3175, Côte Sainte-Catherine, local B-607 > ///Tél : 514-345-4931 poste 5199/ > ----------------------------------------- ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. 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