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Use the central HaMSt oneSeq
(Currently only available for internal use!)
We provide a central installation of HaMStR-oneSeq that you can directly use with your data. To use this, you must however have all the dependencies ready on your computer. You can install these libraries/tools using the command
/path/to/central/h1s/setup1s -o /path/to/oneSeq/data --lib
The same as the standalone version, you still need a genome_dir(*) folder, where all of your taxa of interest should be found, a blast_dir(*) folder, where the blast DBs of taxa that should be included in the core sets are stored, as well as a weight_dir(*) folder, where the annotation of all taxa in genome_dir and blast_dir are present in case you want to use FAS with HaMStR-oneSeq. These data must also follow the format of HaMStR-oneSeq. The easiest way to create the data from your genome files is using our functions /path/to/central/h1s/addTaxon1s or /path/to/central/h1s/addTaxa1s using this instruction.
(*) Hint: If you find genome_dir, blast_dir and weight_dir sound not good, you can rename them to anything you want :-)
We prepare also the ready-to-use data for some taxa. Please make use of them before waisting time for creating them again.
The usage of the central version of HaMStR-oneSeq is not much different than the standalone version, you just need to specify these options to your own directories:
-hmmpath=/path/to/your/core_orthologs-searchpath=/path/to/your/genome_dir-blastpath=/path/to/your/blast_dir-weightpath=/path/to/your/weight_dir-outpath=/path/to/your/output_directory
Otherwise, HaMStR-oneSeq will use the default directories, which are defined by the pathconfig.txt file in the installed h1s/bin/ folder.
For example:
/path/to/central/h1s/h1s --seqFile /path/to/mySeq.fa --seqName test --refspec HUMAN@9606@3 --blastpath ./blast_dir/ --searchpath ./genome_dir/ --weightpath ./weight_dir/ --hmmpath ./core_orthologs/ --outpath ./
where blast_dir, genome_dir, weight_dir are found in the current directory ./. The core ortholog called test will be saved in the current directory under core_orthologs/test/ folder. The final HaMStR-oneSeq output will be generated within ./test/ folder.
To learn about all available options of HaMStR-oneSeq, please use this command:
/path/to/central/h1s/h1s -h