BP_UNFLATTEN_SEQ(1)

💅 NAME

okay bestie, welcome to BP_UNFLATTEN_SEQ(1) from User Contributed Perl Documentation ✨ this is all about bp_unflatten_seq, the main-character script that unflattens a genbank or genbank-style feature file into a nested SeqFeature hierarchy. periodt 💖

---

🧚 SYNOPSIS

run it like this, bestie:

bp_unflatten_seq.PLS -e 3 -gff ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

bp_unflatten_seq.PLS --detail ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

bp_unflatten_seq.PLS -i foo.embl --from embl --to chadoxml -o out.chado.xml

bp_unflatten_seq.PLS --notypemap --detail --to asciitree -ethresh 2 AE003644_Adh-genomic.gb

---

✨ DESCRIPTION

This script will unflatten a genbank or genbank-style file of SeqFeatures into a nested hierarchy. slay 💅

peep Bio::SeqFeature::Tools::Unflattener for the tool behind the magic.

In a GenBank/EMBL representation, features are 'flat' — for example, there is no link between an mRNA and a CDS, other than implicit links (eg via tags or via splice site coordinates) which may be hard to code for. it’s giving chaos, honestly 😭

This is most easily illustrated with the default output format, asciitree. look at this glow-up:

An unflattened genbank feature set may look like this (AB077698):

  Seq: AB077698
    databank_entry                                   1..2701[+]
    gene
      mRNA
        CDS hCHCR-G                                  80..1144[+]
        exon                                         80..1144[+]
      five_prime_UTR                                 1..79[+]
      located_sequence_feature                       137..196[+]
      located_sequence_feature                       239..292[+]
      located_sequence_feature                       617..676[+]
      located_sequence_feature                       725..778[+]
      three_prime_UTR                                1145..2659[+]
      polyA_site                                     1606..1606[+]
      polyA_site                                     2660..2660[+]

Or like this (portion of AE003734):

  gene
    mRNA CG3320-RA
      CDS CG3320-PA                                53126..54971[-]
      exon                                         52204..53323[-]
      exon                                         53404..53631[-]
      exon                                         53688..53735[-]
      exon                                         53798..53918[-]
      exon                                         54949..55287[-]
    mRNA CG3320-RB
      CDS CG3320-PB                                53383..54971[-]
      exon                                         52204..53631[-]
      exon                                         53688..53735[-]
      exon                                         53798..53918[-]
      exon                                         54949..55287[-]

The unflattening will also 'normalize' the containment hierarchy (in the sense of standardising it — e.g. making sure there is always a transcript record, even if genbank just specifies CDS and gene). it’s literally making sure nobody gets left out 🫶

By default, the GenBank types will be mapped to SO types. iconic behavior.

See Bio::SeqFeature::Tools::TypeMapper.

---

🎀 COMMAND LINE ARGUMENTS

• -i|input FILE — input file (can also be specified as last argument).
• -from FORMAT — input format (defaults to genbank).

probably doesn't make so much sense to use this for non-flat formats; ie other than embl/genbank. ngl, it’s a bit niche.

• -to FORMAT — output format (defaults to asciitree).

should really be a format that is nested SeqFeature aware; I think this is only asciitree, chadoxml and gff3. the way that list is short and specific 💅

• -gff — with export to GFF3 format (pre-3 GFFs make no sense with unflattened sequences, as they have no set way of representing feature graphs). lowkey important, bestie.
• -o|output FILE — outfile defaults to STDOUT.
• -detail — show extra detail on features (asciitree mode only).
• -e|ethresh INT — sets the error threshold on unflattening.

by default this script will throw a wobbly if it encounters weird stuff in the genbank file — raise the error threshold to signal these to be ignored (and reported on STDERR). dramatic? yes. useful? also yes 🫶

• -nomagic — suppress use_magic in unflattening (see Bio::SeqFeature::Tools::Unflattener).
• -notypemap — suppress type mapping (see Bio::SeqFeature::Tools::TypeMapper).

---

🌸 TODO

Bio::SeqFeature::Tools::Unflattener allows fine-grained control over the unflattening process — need to add more options to allow this control at the command line. bestie, the potential is highkey there ✨

---

🫶 FEEDBACK

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. fr fr, they want to hear from you 💖

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

https://github.com/bioperl/bioperl-live/issues

---

👑 AUTHOR

Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>

---

okay that’s the whole vibe, bestie 💖 this page is from perl v5.42.3, dated 2021-02-03, and the manual is BP_UNFLATTEN_SEQ(1) — go unflatten something and slay ✨🦋