File: metastudent.1

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.\" ========================================================================
.\"
.IX Title "METASTUDENT 1"
.TH METASTUDENT 1 "2015-04-02" "'%s'" "'User Commands'"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
metastudent \- predictor of gene ontology terms from protein sequence
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
metastudent \-i \fI\s-1FASTA_FILE\s0\fR \-o \fI\s-1RESULT_FILE_PREFIX\s0\fR [\-\-debug] [\-\-keep\-temp] [\-\-silent] [\-\-output\-blast] [\-\-blast\-only] [\-\-all\-predictions] [\-\-ontologies=\fI\s-1MFO\s0 or \s-1BPO\s0 or \s-1CCO\s0 or \s-1MFO,BPO\s0 or ...\fR] [\-\-with\-images] [\-\-blast\-kickstart\-databases=\fI\s-1BLAST_RESULT_FILE\s0(S)\fR] [\-\-temp\-dir=\fI\s-1DIR\s0\fR] [\-\-config=\fI\s-1CONFIG_FILE\s0\fR]
!!! Make sure your fasta file contains at most 500 sequences !!!
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Metastudent predicts Gene Ontology (\s-1GO\s0) terms from the Molecular Function Ontology (\s-1MFO\s0), Biological Process Ontology (\s-1BPO\s0) and Cellular Component Ontology (\s-1CCO\s0)
for input protein sequences by homology-based inference from already annotated proteins.
.PP
Large (1 \s-1GB\s0 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
       \fImetastudentdata\fR (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 \fIsudo\fR\|(8).
.SS "Output format"
.IX Subsection "Output format"
For each selected ontology (see \fI\-\-ontologies\fR), one output file is produced (see \fI\-o\fR).
Each line in each file associates a protein with a \s-1GO\s0 term and a reliability for the association (0.0 to 1.0). The following format is used:
<\s-1PROTEIN ID\s0><\s-1TAB\s0><\s-1GO_TERM\s0><\s-1TAB\s0><\s-1RELIABILITY\s0>
.SH "REFERENCES"
.IX Header "REFERENCES"
.IP "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. \s-1BMC\s0 Bioinformatics, 14(Suppl 3), S7." 4
.IX Item "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."
.SH "OPTIONS"
.IX Header "OPTIONS"
.PD 0
.IP "\-i \s-1FASTA_FILE\s0" 4
.IX Item "-i FASTA_FILE"
.PD
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.
.IP "\-o \s-1RESULT_FILE_PREFIX\s0" 4
.IX Item "-o RESULT_FILE_PREFIX"
The file name prefix of the output files. \s-1GO\s0 terms are organized in ontologies. Metatstudent treats each ontology differently and outputs one result file for each. For example, if <\s-1RESULT_FILE\s0>=./myresult and \s-1MFO \s0(Molecular Function Ontology) and \s-1BPO \s0(Biological Process Ontology) ontologies are selected (see option \fB\-\-ontologies\fR), then metastudent creates two output files: \fI./myresult.MFO.txt\fR and \fI./myresult.BPO.txt\fR.
.IP "\-\-debug" 4
.IX Item "--debug"
Print extra debugging messages.
.IP "\-\-keep\-temp" 4
.IX Item "--keep-temp"
Whether to keep the temp directories after metastudent has finished (they can be useful when errors occur or in combination with \fB\-\-blast\-kickstart\-databases\fR).
.IP "\-\-silent" 4
.IX Item "--silent"
No progress messages (stdout), only errors (stderr).
.IP "\-\-output\-blast" 4
.IX Item "--output-blast"
Whether to output the result of the \s-1BLAST\s0 runs. Useful in combination with \fB\-\-blast\-kickstart\-databases\fR. Output file name format is \fI\s-1RESULT_FILE_PREFIX\s0\fR.<\s-1BLAST_OPTIONS\s0>.blast.
.IP "\-\-blast\-only" 4
.IX Item "--blast-only"
Whether to only output the result of the \s-1BLAST\s0 runs, and nothing else. See options \fI\-\-output\-blast\fR and \fI\-\-blast\-kickstart\-databases\fR.
.IP "\-\-all\-predictions" 4
.IX Item "--all-predictions"
Whether to output the prediction results of the individual predictors. File name format of the output file is <\s-1RESULT_FILE_PREFIX\s0>.<\s-1ONTOLOGY\s0>.<\s-1METHOD\s0>.txt.
.IP "\-\-no\-names" 4
.IX Item "--no-names"
Whether to exclude the actual \s-1GO\s0 term names as a column in the output prediction file(s).
.IP "\-\-with\-images" 4
.IX Item "--with-images"
Whether to also generate an image that displays the predicted \s-1GO\s0 terms as a \s-1GO\s0 graph. This option can only be used with exactly one input sequence and only when connected to the internet.
.IP "\-\-ontologies=\fI\s-1MFO\s0 or \s-1BPO\s0 or \s-1CCO\s0 or \s-1MFO,BPO\s0 or ...\fR" 4
.IX Item "--ontologies=MFO or BPO or CCO or MFO,BPO or ..."
A comma separated list of ontologies to create predictions for. Default is \s-1MFO,BPO,CCO.\s0 If used in combination with \fB\-\-blast\-kickstart\-databases\fR, the number and order of the ontologies must correspond to the kickstart files.
.IP "\-\-blast\-kickstart\-databases=<\s-1BLAST_RESULT_FILES\s0>" 4
.IX Item "--blast-kickstart-databases=<BLAST_RESULT_FILES>"
Since running \s-1BLAST\s0 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 \fB\-\-ontologies\fR). Separate the file paths with commas. For example: \-\-blast\-kickstart\-databases=<\s-1RESULT_FILE_MFO\s0>,<\s-1RESULT_FILE_BPO\s0> (kickstart for both ontologies) or \-\-blast\-kickstart\-databases=,<\s-1RESULT_FILE_BPO\s0> (only kickstart \s-1BPO\s0; note the comma).
.IP "\-\-temp\-dir=DIR" 4
.IX Item "--temp-dir=DIR"
The parent temp directory to use instead of the one specified with tmpDir in the metastudent configuration file.
.IP "\-\-config=FILE" 4
.IX Item "--config=FILE"
The path to a custom metastudent configuration file; overrides all settings of the configuration files found in the \s-1FILES\s0 section of this man page.
.SH "FILES"
.IX Header "FILES"
.IP "\fI<package_data_dir>/metastudentrc.default\fR" 4
.IX Item "<package_data_dir>/metastudentrc.default"
The metastudent configuration file.
.IP "\fI<sysconfdir>/metastudentrc\fR" 4
.IX Item "<sysconfdir>/metastudentrc"
The metastudent configuration file, overrides \fI<package_data_dir>/metastudentrc.default\fR.
.IP "\fI<homedir>/.metastudentrc\fR" 4
.IX Item "<homedir>/.metastudentrc"
The metastudent configuration file, overrides \fI<sysconfdir>/metastudentrc\fR.
.SH "EXAMPLES"
.IX Header "EXAMPLES"
The example \fItest.fasta\fR file can be found in \fI<package_doc_dir>/examples\fR (usually \fI/usr/share/doc/metastudent/examples\fR).
.IP "Predict the \s-1GO\s0 terms for the sequences in test.fasta for both the \s-1MFO\s0 and the \s-1BPO\s0 ontology:" 4
.IX Item "Predict the GO terms for the sequences in test.fasta for both the MFO and the BPO ontology:"
.Vb 1
\& metastudent \-i test.fasta \-o test.result
.Ve
.IP "Create the \s-1BLAST\s0 output to predict the \s-1MFO\s0 terms for sequences in test.fasta (not the actual predictions, yet; see next example)." 4
.IX Item "Create the BLAST output to predict the MFO terms for sequences in test.fasta (not the actual predictions, yet; see next example)."
.Vb 1
\& metastudent \-i test.fasta \-o test.result \-\-blast\-only \-\-output\-blast \-\-ontologies=MFO
.Ve
.IP "Predict the \s-1MFO\s0 and \s-1BPO\s0 terms for sequences in test.fasta with a precomputed \s-1MFO BLAST\s0 output (see previous example; note the comma at the end)." 4
.IX Item "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)."
.Vb 1
\& metastudent \-i test.fasta \-o test.result \-\-ontologies=MFO,BPO \-\-blast\-kickstart\-databases=test.result_eval0.001_iters3_srcexp.mfo.blast,
.Ve
.SH "BUGS"
.IX Header "BUGS"
Please use this link to report bugs:
.PP
<https://rostlab.org/bugzilla3/enter_bug.cgi?product=metastudent>
.SH "AUTHOR"
.IX Header "AUTHOR"
Tobias Hamp <hampt@rostlab.org>