marcelm / marcelm/cutadapt

UMI '--rename' regex/utility

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feature-request
Dominant language
Python
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Merged PRs (30d)
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Description

Hi cutadapt devs,

I want to use cutadapt --rename to extract the meaningful portion of the UMI to the read name, but process the read to cut the entirety of the UMI. If this is currently possible can you let me know how I might change the below to achieve this? If it's not possible, can you add this as a feature in a future version? TIA!

A simple example is where I want to cut the first 7bp from R1 but only add the first 6bp to the read name;

cutadapt -u 7 --rename='{id} {comment} $(echo {cut_prefix} | cut -c1-6)'

What I'm hoping to get is;
1:2101:13928:1000 1:N:0:GTCGCCTT+AAA/ACTAATT NTTTAT

But what is returned is;
1:2101:13928:1000 1:N:0:GTCGCCTT+AAA/ACTAATT $(echo NTTTATT | cut -c1-6)

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the cutadapt --rename option and how it expands {cut_prefix}, using the command and expected output in the issue as the behavioral example. Determine whether the rename utility can support selecting only part of the trimmed UMI, then add coverage for cutting 7 bases while naming only the first 6; done means the output matches the requested read name.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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