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 > 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 > > 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 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 poste 5199/ > ----------------------------------------- ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. 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