METASTUDENT(1)

💖 METASTUDENT(1) 💖

okay so bestie, welcome to metastudent — she lives in section 1 of the User Commands manual, and she is literally a whole vibe. let me tell you everything about her, no cap. 🫶

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✨ NAME ✨

metastudent — predictor of gene ontology terms from protein sequence. it's giving fortune teller but for proteins 🔮✨

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🌸 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 !!!

🚨 bestie. Make sure your fasta file contains at most 500 sequences. that's not a suggestion, that's a boundary. respect it or she will simply pass away (out of memory). 💀

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👑 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. basically she looks at proteins that already know who they are and is like "yeah you're that too, periodt" 💅

Large (1 GB in total) data files necessary for the operation of metastudent are downloaded automatically on the first use of the program. and the download is restartable — so if your wifi decides to be a hater, you just pick right back up. iconic. 🦋

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).

so yeah, she will literally ask for the sudo powers herself. main character energy honestly. ✨

🌈 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>

three columns, tab separated, cute and clean. 🎀

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📚 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.

(the citation, bestie — always cite your sources, that's academic slay 💜)

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💅 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. she's yapping but it's useful yapping. 🙈
• --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). she goes quiet but she still tells you when something's wrong. 🎀
• --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. so no wifi = no picture, sorry bestie 😭
• --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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🗂️ FILES 🗂️

the config file chain, from least to most powerful (she reads them in order and the later ones win, iykyk):

• <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.

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🌟 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,

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💀 BUGS 💀

Please use this link to report bugs:

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

found something cursed? tell the devs, don't suffer in silence bestie 🫶

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🧚 AUTHOR 🧚

Tobias Hamp <hampt@rostlab.org>

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and that's the whole page, babe — this is metastudent, manual section '3s', dated 2022-01-20. go predict some GO terms and slay the day. mwah 💋✨