Filter codon - Githubissues

lokeshbio commented 1 year ago

This pull request contains a filtering step of ASVs if they contain STOP codons:TAA or TAG and also if the ASVs are of length that is a multiple of 3 as well.

PR checklist

[x] This comment contains a description of changes (with reason).
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lokeshbio commented 1 year ago

Hi @d4straub ,

Now I have made this feature very general, where people can use orf_start and orf_end to specify the start and end of the open reading frames in their amplicons! This would mean that it is not only 0,1,2 as we have discussed before but they can be even more specific to ask to look for stop codons in a specific length range in an amplicon! I thought this was even more generalizable than just 0,1,2. Hope this is fine! Please let me know if there is something you have in mind.

Cheers Lokesh

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit ac5b5c4

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

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lokeshbio commented 1 year ago

I haven't updated the PR yet! Will remove those in the next commit :)

On Thu, 11 May 2023, 16:28 Daniel Straub, @.***> wrote:

@.**** commented on this pull request.

On bin/filt_coi_stats.r https://github.com/nf-core/ampliseq/pull/575#discussion_r1191257202:

Do you really need bin/filt_coi_stats.r https://github.com/nf-core/ampliseq/pull/575/files/f1cd436a1b381e010a84ce8c11394355d7c61556#diff-fd246515d13c55f6fa931b4c7c83c1bd5872669a7e8c0bfd41c3b5b359e76cbb and bin/filt_codon_stats.r https://github.com/nf-core/ampliseq/pull/575/files/f1cd436a1b381e010a84ce8c11394355d7c61556#diff-832efbde6bd8bcaa52a74b5c8bfbc92e43eeeb87fd54d724a31d4a7cef0f1ac3 ?

— Reply to this email directly, view it on GitHub https://github.com/nf-core/ampliseq/pull/575#discussion_r1191257202, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGVCT34Y5FK45WGUPJRJ3GDXFTZRLANCNFSM6AAAAAAXPDMDX4 . You are receiving this because you authored the thread.Message ID: @.***>

lokeshbio commented 1 year ago

Hi @d4straub , Let me know if these changes look fine to you! I think I resolved all your comments! I made a little change from the last PR that --filter_codons will take the defaults as follows: --orf_start 1 --orf_end (end-of-the-ASV) --stop_codons "TAA,TAG". But of course one can use these three options to change to whatever they are interested in!

I thought this was more of a simple/detailed solution.

lokeshbio commented 1 year ago

 ./lib/WorkflowAmpliseq.groovy:
    110: Trailing whitespace

I do not understand why this error message occurs! ther eis no trailing whitespace in line 110!

d4straub commented 1 year ago

Now there isnt any more ;)

d4straub commented 1 year ago

The history of this PR is rather convoluted, I have no idea how you manage to do that weird changes. Anyway, good to go.

lokeshbio commented 1 year ago

It is werid that it says it has no conflicts with base branch! eventhough the PR was to the dev branch

lokeshbio commented 1 year ago

@d4straub , would you mind merging this PR? seems like I do not have write permissions! BTW, the test data for novaseq that I gave you long time ago, should also be fine as a test dataset for this PR as well! If the novaseq test data is still the same as the one I sent you.

d4straub commented 1 year ago

Done, thanks!

BTW, the test data for novaseq that I gave you long time ago, should also be fine as a test dataset for this PR as well!

I'll have a look, thanks!

nf-core / ampliseq

Filter codon #575

PR checklist

`nf-core lint` overall result: Passed :white_check_mark: :warning:

@.**** commented on this pull request.

nf-core / ampliseq

Filter codon #575

PR checklist

nf-core lint overall result: Passed :white_check_mark: :warning:

@.**** commented on this pull request.

`nf-core lint` overall result: Passed :white_check_mark: :warning: