[Biopython-dev] [Biopython (old issues only) - Bug #3060] (Migrated) Add ungap method to the SeqRecord?

[redmine at redmine.open-bio.org]

Issue #3060 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated
URL set to https://github.com/biopython/biopython/issues/1017

Moved to GitHub as https://github.com/biopython/biopython/issues/1017

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Bug #3060: Add ungap method to the SeqRecord?
https://redmine.open-bio.org/issues/3060#change-15387

* Author: Peter Cock
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.54b
* URL: https://github.com/biopython/biopython/issues/1017
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Biopython 1.53 added an ungap method to the Seq object.

This is a possible enhancement request to add a matching ungap method to the SeqRecord object, where the per-letter-annotation and features should be adjusted to match.

My motivating example is to take an ACE file loaded with SeqIO, remove the gaps, and output the contigs as FASTQ or QUAL files. This requires the per-letter-annotation to be sliced to match the ungapped sequence.

Likewise any features fully contained within ungapped regions should be retained and their co-ordinates shifted. I'm not sure if we should do anything about features spanning a gap - the simple option which I have implemented is they are lost. This is done via the existing SeqRecord slicing and addition code.

Patch to follow...

See also Bug 3054 for adding upper and lower methods to the SeqRecord, and the broader discussion on Bug 2351 about strings, Seq and SeqRecord objects.

---Files--------------------------------
seqrecord_ungap.patch (4.74 KB)


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