xenial (1) metastudent.1.gz

Provided by: metastudent_2.0.1-1_all bug

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 <hampt@rostlab.org>

'1s'                                               2015-04-02                                     METASTUDENT(1)