Bio::G...r::useq(3pm)

🦋 Bio::G...r::useq(3pm) — the USeq data loader, bestie edition 🦋

okay so bestie, you found the manual page for Bio::Graphics::Browser2::DataLoader::useq and honestly? it's giving "niche but iconic." let's get into it 💅

---

✨ NAME ✨

Bio::Graphics::Browser2::DataLoader::useq — it's the data loader for the USeq archive. that's the whole job. she loads. she serves. periodt.

---

🌸 DESCRIPTION 🌸

so this little cutie is a data loader for the USeq archive, and you'll know you're dealing with one because the file extension is .useq. if you wanna know the actual ins and outs of the file format, the link is right here:

http://useq.sourceforge.net/useqArchiveFormat.html

and lowkey, here's the TL;DR so you're not lost: this format can store either genomic intervals — with or without text and/or scores — or quantitative scores along a chromosome, which is what we call point data. two moods, one file type, we love range 🫶

now, the tea: there is currently no native BioPerl adaptor for the USeq archive. none. zero. so when you upload the file, it gets converted into either UCSC BigBed or BigWig format, depending on what's inside it. and if you've got stranded point data? oh she's fancy — that may get converted into two BigWig files, one for the Plus strand and one for the Minus strand. plus, configuration files are generated as appropriate for the converted files. she comes prepared, no cap ✨

---

🎀 SETUP 🎀

to actually process the USeq archive, the USeq package has to be installed in a globally accessible path. here's the link, note that it's missing its closing paren in the original and we're keeping it exactly as it is, iykyk:

http://useq.sourceforge.net

this location gets searched upon initiation. and the common paths she searches include these, in this exact order:

1. /usr
2. /usr/local
3. /opt
4. /opt/gbrowse
5. /data
6. /data/opt
7. /Applications

next up: the USeq App USeq2UCSCBig (a jar file) is what does the actual converting of the USeq archive. but she's high maintenance, bestie — this app requires three binary executables:

• java
• bedToBigBed
• wigToBigWig

those last two are UCSC utilities. all three get searched for in the environment $PATH variable. the UCSC utilities live here if you need them:

http://hgdownload.cse.ucsc.edu/admin/exe/

and the USeq Apps requires Java 1.6+. that's a plus sign, not a vibe, she needs the version.

⚠️ real talk: failure to find the paths for all three will result in failure to process the .useq file. all three. not two. not "two and a half." all of them. don't skip this part, it's the whole plot 😭

---

💖 AUTHOR 💖

this absolute legend wrote it:

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

and the legal bit, keeping it fully intact: this package is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. slay, permissive licensing, we stan 🌈

---

and that's the whole page, bestie!! this was written up as perl v5.40.0, dated 2024-10-20, and it's the manual page for Bio::G...r::useq(3pm). go forth and load those archives, you've got this 💜✨👑