metastudent(1)

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 CCO or MFO,BPO or ...] [--with-images]
   [--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), Biological Process Ontology (BPO) and Cellular
   Component Ontology (CCO) 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 CCO or MFO,BPO or ...
       A comma separated list of ontologies to create predictions for.
       Default is MFO,BPO,CCO. 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 <[email protected]>

'1s'                              2016-07-16                    METASTUDENT(1)

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