NAME

       metastudent - predictor of gene ontology terms from protein sequence

SYNOPSIS

       metastudent -i FASTA_FILE -o RESULT_FILE_PREFIX [--debug] [--keep-temp] [--silent]
       [--output-blast] [--blast-only] [--all-predictions] [--ontologies=MFO or BPO or MFO,BPO]
       [--blast-kickstart-databases=BLAST_RESULT_FILE(S)] [--temp-dir=DIR] [--config=CONFIG_FILE]
       !!! Make sure your fasta file contains at most 500 sequences !!!

DESCRIPTION

       Metastudent predicts Gene Ontology (GO) terms from the Molecular Function Ontology (MFO)
       and Biological Process Ontology (BPO) for input protein sequences by homology-based
       inference from already annotated proteins.

       Large (1 GB in total) data files necessary for the operation of metastudent are downloaded
       automatically on the first use of the program.  The download is restartable.  You can also
       make an explicit call to
              metastudentdata (by default /usr/bin/metastudentdata) to download the data files.
       In case the data directory (by default /usr/share/metastudent-data) is not writable and
       you are not root, the operation is
              reattempted with sudo(8).

   Output format
       For each selected ontology (see --ontologies), one output file is produced (see -o).  Each
       line in each file associates a protein with a GO term and a reliability for the
       association (0.0 to 1.0). The following format is used: <PROTEIN
       ID><TAB><GO_TERM><TAB><RELIABILITY>

REFERENCES

       Hamp, T., Kassner, R., Seemayer, S., Vicedo, E., Schaefer, C., Achten, D., ... & Rost, B.
       (2013). Homology-based inference sets the bar high for protein function prediction. BMC
       Bioinformatics, 14(Suppl 3), S7.

OPTIONS

       -i FASTA_FILE
           The input fasta file. Please try to remove any special formattings (e.g. whitespaces)
           in the sequences before using them as input. Due to high memory usage, make sure your
           fasta file contains at most 500 sequences.

       -o RESULT_FILE_PREFIX
           The file name prefix of the output files. GO terms are organized in ontologies.
           Metatstudent treats each ontology differently and outputs one result file for each.
           For example, if <RESULT_FILE>=./myresult and MFO (Molecular Function Ontology) and BPO
           (Biological Process Ontology) ontologies are selected (see option --ontologies), then
           metastudent creates two output files: ./myresult.MFO.txt and ./myresult.BPO.txt.

       --debug
           Print extra debugging messages.

       --keep-temp
           Whether to keep the temp directories after metastudent has finished (they can be
           useful when errors occur or in combination with --blast-kickstart-databases).

       --silent
           No progress messages (stdout), only errors (stderr).

       --output-blast
           Whether to output the result of the BLAST runs. Useful in combination with
           --blast-kickstart-databases. Output file name format is
           RESULT_FILE_PREFIX.<BLAST_OPTIONS>.blast.

       --blast-only
           Whether to only output the result of the BLAST runs, and nothing else. See options
           --output-blast and --blast-kickstart-databases.

       --all-predictions
           Whether to output the prediction results of the individual predictors. File name
           format of the output file is <RESULT_FILE_PREFIX>.<ONTOLOGY>.<METHOD>.txt.

       --no-names
           Whether to exclude the actual GO term names as a column in the output prediction
           file(s).

       --with-images
           Whether to also generate an image that displays the predicted GO terms as a GO graph.
           This option can only be used with exactly one input sequence and only when connected
           to the internet.

       --ontologies=MFO or BPO or MFO,BPO
           A comma separated list of ontologies to create predictions for. Default is MFO,BPO. If
           used in combination with --blast-kickstart-databases, the number and order of the
           ontologies must correspond to the kickstart files.

       --blast-kickstart-databases=<BLAST_RESULT_FILES>
           Since running BLAST is usually the part that takes the longest in metastudent, this
           option allows you to re-use the output of a previous run. This is useful to test, for
           example, different parameters or when you have lost a prediction. The number of
           kickstart files must correspond to the number of ontologies (see option --ontologies).
           Separate the file paths with commas. For example:
           --blast-kickstart-databases=<RESULT_FILE_MFO>,<RESULT_FILE_BPO> (kickstart for both
           ontologies) or --blast-kickstart-databases=,<RESULT_FILE_BPO> (only kickstart BPO;
           note the comma).

       --temp-dir=DIR
           The parent temp directory to use instead of the one specified with tmpDir in the
           metastudent configuration file.

       --config=FILE
           The path to a custom metastudent configuration file; overrides all settings of the
           configuration files found in the FILES section of this man page.

FILES

       <package_data_dir>/metastudentrc.default
           The metastudent configuration file.

       <sysconfdir>/metastudentrc
           The metastudent configuration file, overrides
           <package_data_dir>/metastudentrc.default.

       <homedir>/.metastudentrc
           The metastudent configuration file, overrides <sysconfdir>/metastudentrc.

EXAMPLES

       The example test.fasta file can be found in <package_doc_dir>/examples (usually
       /usr/share/doc/metastudent/examples).

       Predict the GO terms for the sequences in test.fasta for both the MFO and the BPO
       ontology:
            metastudent -i test.fasta -o test.result

       Create the BLAST output to predict the MFO terms for sequences in test.fasta (not the
       actual predictions, yet; see next example).
            metastudent -i test.fasta -o test.result --blast-only --output-blast --ontologies=MFO

       Predict the MFO and BPO terms for sequences in test.fasta with a precomputed MFO BLAST
       output (see previous example; note the comma at the end).
            metastudent -i test.fasta -o test.result --ontologies=MFO,BPO --blast-kickstart-databases=test.result_eval0.001_iters3_srcexp.mfo.blast,

BUGS

       Please use this link to report bugs:

       <https://rostlab.org/bugzilla3/enter_bug.cgi?product=metastudent>

AUTHOR

       Tobias Hamp <hampt@rostlab.org>

'1s'                                        2013-12-23                             METASTUDENT(1)