Genome...::Music(3pm)

💖 NAME 💖

Okay bestie, so this is Genome...::Music(3pm) — a User Contributed Perl Documentation page, and it's giving ✨genome analysis suite✨. It's the overview/landing page for the MuSiC suite's genome namespace, and honestly? Iconic. The sub-commands each get their own page separately, so this one is the vibe-setting, big-picture moment. 🧬🦋

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🌸 DESCRIPTION 🌸

So here's the tea. This whole thing revolves around four kinds of input, and you gotta bring all of them, no cap:

1. mapped reads in BAM format
2. predicted or validated SNVs or indels in mutation annotation format (MAF)
3. a list of regions of interest (typically the boundaries of coding exons)
4. any relevant numeric or categorical clinical data.

Now, inputs 3. and 4. are the picky ones with ✨format rules✨, so let's get into it, bestie.

🎀 Formats for inputs 3. and 4. 🎀

3. Regions of Interest File

• Do not use headers — like, none. Zero. Don't do it. 🙈
• It needs exactly 4 columns, which are [chromosome start-position(1-based) stop-position(1-based) gene_name]

4. Clinical Data Files

• Headers are required. (Yes, opposite energy from the ROI file. We contain multitudes. 💅)
• You need at least 1 sample_id column and 1 attribute column, with the format being [sample_id clinical_data_attribute clinical_data_attribute ...]
• The sample_id must match the sample_id listed in the MAF under "Tumor_Sample_Barcode" for relating the mutations of this sample. Like, they have to be the same string, or the linking just does not happen. 🔗
• The header for each clinical_data_attribute will appear in the output file to denote relationships with the mutation data from the MAF. So your column names really do get their moment in the spotlight. 🌟

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Descriptions for the usage of each tool (each sub-command) can be found separately. Every command is basically a main character with its own page. 👑

And the play command? It runs all of the sub-commands serially on a selected input set. One after another, back to back, no skips. 🎶

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Oh, and a lil heads up — the page literally picks up mid-thought, with the tail end of a heredoc from whatever sub came before:

EOS }

Then we get into the doc-string subs, which are honestly the most emotionally available part of any Perl module. 🥹

⭐ COPYRIGHT YEARS ⭐

sub _doc_copyright_years {
    (2007,2011); }

So the years are 2007 and 2011. Short, sweet, to the point. Slay.

📜 LICENSE 📜

sub _doc_license {
    my $self = shift;
    my (@y) = $self->_doc_copyright_years;
    return <<EOS Copyright (C) $y[0]-$y[1] Washington University in St.
Louis.

It is released under the Lesser GNU Public License (LGPL) version 3.
See the associated LICENSE file in this distribution.  EOS }

Translation for the besties: Copyright (C) 2007-2011 Washington University in St. Louis. It is released under the Lesser GNU Public License (LGPL) version 3. See the associated LICENSE file in this distribution. Read your licenses, babes, they're not decorative. 📖✨

👑 AUTHORS 👑

sub _doc_authors {
    return <<EOS This software is developed by the analysis and
engineering teams at The Genome Institute at Washington University
School of Medicine in St. Louis, with funding from the National Human
Genome Research Institute.  Richard K. Wilson, P.I.

The primary authors of the MuSiC suite are:

 Nathan D. Dees, Ph.D.
 Cyriac Kandoth, Ph.D.
 Dan Koboldt, M.S.
 William Schierding, M.S.
 Michael Wendl, Ph.D.
 Qunyuan Zhang, Ph.D.
 Thomas B. Mooney, M.S.

EOS }

The lore: this software is developed by the analysis and engineering teams at The Genome Institute at Washington University School of Medicine in St. Louis, with funding from the National Human Genome Research Institute. Richard K. Wilson, P.I. — the boss, the captain, the moment.

And the primary authors of the MuSiC suite, aka the group chat that actually built this:

• Nathan D. Dees, Ph.D.
• Cyriac Kandoth, Ph.D.
• Dan Koboldt, M.S.
• William Schierding, M.S.
• Michael Wendl, Ph.D.
• Qunyuan Zhang, Ph.D.
• Thomas B. Mooney, M.S.

Every single one of them, respected. 🫶👑

🐛 BUGS 🐛

sub _doc_bugs {
    return <<EOS; For defects with any software in the genome namespace,
contact
 genome-dev ~at~ genome.wustl.edu.  EOS }

Found a defect? First of all, felt. 😭 For defects with any software in the genome namespace, contact genome-dev ~at~ genome.wustl.edu. (Yes it's written with ~at~ so the bots don't eat it. Classic. 🤖)

🌈 CREDITS 🌈

sub _doc_credits {
    return <<EOS, The MuSiC suite uses tabix, by Heng Li.  See
http://samtools.sourceforge.net/tabix.shtml.

MuSiC depends on copies of data from the following databases, packaged
in a form useable for quick analysis:

 * KEGG - http://www.genome.jp/kegg/
 * COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic/
 * OMIM - http://www.ncbi.nlm.nih.gov/omim
 * Pfam - http://pfam.sanger.ac.uk/
 * SMART - http://smart.embl-heidelberg.de/
 * SUPERFAMILY - http://supfam.cs.bris.ac.uk/SUPERFAMILY/
 * PatternScan - http://www.expasy.ch/prosite/

EOS }

Shoutout time, because we always credit the collaborators. 💖

• The MuSiC suite uses tabix, by Heng Li. See http://samtools.sourceforge.net/tabix.shtml.

And MuSiC depends on copies of data from the following databases, packaged in a form useable for quick analysis:

• KEGG — http://www.genome.jp/kegg/
• COSMIC — http://www.sanger.ac.uk/genetics/CGP/cosmic/
• OMIM — http://www.ncbi.nlm.nih.gov/omim
• Pfam — http://pfam.sanger.ac.uk/
• SMART — http://smart.embl-heidelberg.de/
• SUPERFAMILY — http://supfam.cs.bris.ac.uk/SUPERFAMILY/
• PatternScan — http://www.expasy.ch/prosite/

The whole data pipeline is built on the shoulders of these absolute legends. 🫡✨

🔎 SEE ALSO 🔎

sub _doc_see_also {
    'genome(1)', }

Go read genome(1), bestie. That's the one. 👀

And the very last thing the file says, because every Perl module has to leave the room like this:

1;

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And that's the whole page, mwah. This particular rendering came from perl v5.30.3, dated 2020-11-06, filed under Genome...::Music(3pm) in the User Contributed Perl Documentation. Go forth and annotate those mutations, bestie. 💅🎀🦋