Protein Functional Site Prediction Using Position-Specific Rules
One you have uncompressed your download, you can run it directly from the command line.
Run the supplied shell script. If you run this script with no arguments, you will be presented with the usage instructions:
$ ./pirsitepredict.sh
You will see the following usage instructions:
Welcome to PIRSitePredict usage: java -Xms512M -Xmx2048M -jar PIRSitePredictorCommander.jar [options] Available options: -A,--hmmalign <PATH/TO/HMMALIGN/COMMAND> Path to the HMMER 3 hmmalign command. -d,--pirsr-data-dir <PATH/TO/PIRSR/Data/DIR> Required, the directory where the PIR Site Rule data (Site Rule, Site HMM models and Rule template sequence) files are located. -e,--eval <E-VALUE> The e-value cutoff of matches to SRHMM models (default: 0.0001). -F,--force-overwrite Force overwrite output directory. -f,--formats <PREDICTION-OUTPUT-FORMATS> Comma separated list of output formats. Supported formats are TSV, GFF3, XML. -h,--help Show help. -i,--iprscan-xml <PATH/TO/IPRSCAN/XML/FILE> Required, the path to InterProScan XML file. -l,--log-file <PATH/TO/LOG/FILE> Path to log file. -o,--output-dir <PATH/TO/OUTPUT/DIR> Output directory. It will be created automatically if it does not exist. Default: 'outputDir' in the current directory. -O,--organism <TAXONOMY> The taxonomic classification is composed of the kingdom, optionally followed by the name of a sub-taxon, to further limit the application of the UniRule to any taxonomic level. Valid values for kingdom are: Eukaryota,Bacteria, Archaea, Viruses, Bacteriophage, Plastid and Mitochondrion. Default: Eukaryota. -S,--hmmsearch <PATH/TO/HMMSEARCH/COMMAND> Path to the HMMER 3 hmmsearch command.
The distribution of PIRSitePredict provides a InterProScan XML test file (example/example_interproscan.xml) and its corresponding predictions in TSV, XML and GFF4 formats:
$ ./pirsitepredict.sh -d data -i example/example_interproscan.xml -S PATH/TO/hmmsearch -A /PATH/To/hmmalign -o example_test -f TSV,XML,GFF3 -F
2015/06/01 14:40:14:264 Welcome to PIRSitePredictor! Command options: -d data -i example/example_interproscan.xml -S hmmer-3.1b2-macosx-intel/binaries/hmmsearch -A hmmer-3.1b2-macosx-intel/binaries/hmmalign -o example_test -f TSV,XML,GFF3 -F 2015/06/01 14:40:14:590 PIRSitePredictor (Get Rule Trigger Info) 2015/06/01 14:40:14:678 PIRSitePredictor (Get Rule Template Info) 2015/06/01 14:40:14:678 PIRSitePredictor (Extract match info from InterProScan XML) ... Prediction results in TSV format is at: example_test/prediction/pirsr_prediction.tsv Prediction results in XML format is at: example_test/prediction/pirsr_prediction.xml Prediction results in GFF3 format is at: example_test/prediction/pirsr_prediction.gff3
$ mkdir /your/localworkdir/ $ cd /your/localworkdir/ $ ls my_interproscan.xml
$ docker run -v /your/localworkdir:/workdir chenc/pirsitepredict -d data -i /workdir/my_interproscan.xml -f TSV,XML,GFF3 -F -o /workdir/my_output Unable to find image 'chenc/pirsitepredict:latest' locally latest: Pulling from chenc/pirsitepredict 7448db3b31eb: Downloading [==> ] 2.151 MB/52.47 MB c36604fa7939: Downloading [=============> ] 5.32 MB/19.19 MB 29e8ef0e3340: Downloading [===> ] 3.068 MB/43.16 MB a0c934d2565d: Waiting a360a17c9cab: Waiting cfcc996af805: Waiting 2cf014724202: Waiting 4bc402a00dfe: Waiting 4fdacf43b5a9: Waiting e4ea4f8f03ad: Waiting 24ed79da47ae: Waiting bf24c863f343: Waiting d569faef9da4: Waiting 5de61f4e1166: Waiting 1a34d3d388b3: Waiting .... 7448db3b31eb: Pull complete c36604fa7939: Pull complete 29e8ef0e3340: Pull complete a0c934d2565d: Pull complete a360a17c9cab: Pull complete cfcc996af805: Pull complete 2cf014724202: Pull complete 4bc402a00dfe: Pull complete 4fdacf43b5a9: Pull complete e4ea4f8f03ad: Pull complete 24ed79da47ae: Pull complete bf24c863f343: Pull complete d569faef9da4: Pull complete 5de61f4e1166: Pull complete 1a34d3d388b3: Pull complete Digest: sha256:92439d3ac975872eac49f2da61ebb054e6fe9b68ae64f29b9096a9ded3bce2cf Status: Downloaded newer image for chenc/pirsitepredict:latest 2018/03/15 02:34:39:736 Welcome to PIRSitePredict! Current working directory: / Command options: -S hmmer-3.1b2-linux-intel-x86_64/binaries/hmmsearch -A hmmer-3.1b2-linux-intel-x86_64/binaries/hmmalign -d data -i /workdir/my_interproscan.xml -f TSV,XML,GFF3 -F -o /workdir/my_output 2018/03/15 02:34:40:529 PIRSitePredict (Get Rule Trigger Info) 2018/03/15 02:34:40:874 PIRSitePredict (Get Rule Template Info) 2018/03/15 02:34:40:884 PIRSitePredict (Extract match info from InterProScan XML) ... 2018/03/15 02:35:01:238 Prediction results in TSV format is at: /workdir/my_output/prediction/pirsr_prediction.tsv 2018/03/15 02:35:01:336 Prediction results in XML format is at: /workdir/my_output/prediction/pirsr_prediction.xml 2018/03/15 02:35:01:404 Prediction results in GFF3 format is at: /workdir/my_output/prediction/pirsr_prediction.gff3 2018/03/15 02:35:01:404 Prediction is finished. Results are in: "/workdir/my_output/prediction"
Protein Functional Site Prediction Using Position-Specific Rules
