---
name: "bp_unflatten_seq"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_unflatten_seq"
---

# bp\_unflatten\_seq(1p)

unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy

## NAME

bp\_unflatten\_seq - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy

## SYNOPSIS

```
  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.

See Bio::SeqFeature::Tools::Unflattener

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.

This is most easily illustrated with the default output format, **asciitree**

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)

By default, the GenBank types will be mapped to SO types

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

- \-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

- \-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)

- \-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)

- \-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

## 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.

```
  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>
```