metastudent - Online in the Cloud

PROGRAM:

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.

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