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Keywords {🔍}

action, trim, adapter, lowercase, marcelm, peterjc, mask, cutadapt, commented, echo, llllllllaaaaaaxxxxxxxxxxxggggggrrrrrrr, output, discarduntrimmed, trimupto, sign, request, issue, adapters, mariloubodde, adaptor, sequence, marker, leave, examplefasta, quiet, proposed, comment, mentioned, extra, notation, specification, easier, implement, contributor, author, actionretain, makes, documentation, navigation, search, pull, requests, actions, security, enhancement, actiontrimupto, closed, primer, retained, found,

Topics {✒️}

io/en/latest/guide f1c30cc marcelm closed marcelm edits owner possibly inexactly matched auto-close happened discard-untrimmed shotgun sequencing reads comment metadata assignees feature request adapter specification string discard sequence marcelm added search trim mask lowercase request amplified data amplicon targets cutadapt v2 extra notation action $action primer sequence action modes action mode action trimupto additional action action=retain action {trim action trim action mask adapter specification makes sense action lowercase case requires primer sequences emphasis mine feature included assigned labels labels projects projects milestone milestone relationships leave unchanged found adapters current pipeline suggested earlier github $ cutadapt cutadapt //cutadapt special marker lot easier

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• Already have an account?
• I was wondering if you are planning to implement this?

Schema {🗺️}

DiscussionForumPosting:
      context:https://schema.org
      headline:Enhancement request: trim but keep adaptor, --action=trimupto
      articleBody:I have a usecase in mind were rather than adapter or primer sequence which I want to match and remove, I have markers for a region of interest, and I want the (possibly inexactly matched) marker to be retained in the output. Currently there are four action modes (correct as of cutadapt v2.8): ``` $ cutadapt -h | grep "\-\-action" -A 4 --action {trim,mask,lowercase,none} What to do with found adapters. mask: replace with 'N' characters; lowercase: convert to lowercase; none: leave unchanged (useful with --discard-untrimmed). Default: trim ``` Would you consider a new action mode, suggested name ``trimupto`` (trim up to) or ``trimuntil``, as follows: ``` --action {trim,mask,lowercase,trimupto,none} What to do with found adapters. mask: replace with 'N' characters; lowercase: convert to lowercase; trimupto: trim up to but retaining the adapter; none: leave unchanged (useful with --discard-untrimmed). Default: trim ``` Left adapter example: ``` $ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -g AAAAAA -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done Using --action trim: >example XXXXXXXXXXXGGGGGGRRRRRRR Using --action mask: >example NNNNNNNNNNNNNNXXXXXXXXXXXGGGGGGRRRRRRR Using --action lowercase: >example llllllllaaaaaaXXXXXXXXXXXGGGGGGRRRRRRR Using --action none: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Proposed output: ``` Using --action trimupto: >example AAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Using left and right adapter: ``` $ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -g AAAAAA...GGGGGG -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done Using --action trim: >example XXXXXXXXXXX Using --action mask: >example NNNNNNNNNNNNNNXXXXXXXXXXXNNNNNNNNNNNNN Using --action lowercase: >example llllllllaaaaaaXXXXXXXXXXXggggggrrrrrrr Using --action none: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Proposed output: ``` Using --action trimupto: >example AAAAAAXXXXXXXXXXXGGGGGG ``` Right adapter example: ``` $ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -a GGGGGG -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done Using --action trim: >example LLLLLLLLAAAAAAXXXXXXXXXXX Using --action mask: >example LLLLLLLLAAAAAAXXXXXXXXXXXNNNNNNNNNNNNN Using --action lowercase: >example LLLLLLLLAAAAAAXXXXXXXXXXXggggggrrrrrrr Using --action none: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Proposed output: ``` Using --action trimupto: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGG ```
      author:
         url:https://github.com/peterjc
         type:Person
         name:peterjc
      datePublished:2020-02-28T12:21:33.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
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      url:https://github.com/443/cutadapt/issues/443
      context:https://schema.org
      headline:Enhancement request: trim but keep adaptor, --action=trimupto
      articleBody:I have a usecase in mind were rather than adapter or primer sequence which I want to match and remove, I have markers for a region of interest, and I want the (possibly inexactly matched) marker to be retained in the output. Currently there are four action modes (correct as of cutadapt v2.8): ``` $ cutadapt -h | grep "\-\-action" -A 4 --action {trim,mask,lowercase,none} What to do with found adapters. mask: replace with 'N' characters; lowercase: convert to lowercase; none: leave unchanged (useful with --discard-untrimmed). Default: trim ``` Would you consider a new action mode, suggested name ``trimupto`` (trim up to) or ``trimuntil``, as follows: ``` --action {trim,mask,lowercase,trimupto,none} What to do with found adapters. mask: replace with 'N' characters; lowercase: convert to lowercase; trimupto: trim up to but retaining the adapter; none: leave unchanged (useful with --discard-untrimmed). Default: trim ``` Left adapter example: ``` $ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -g AAAAAA -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done Using --action trim: >example XXXXXXXXXXXGGGGGGRRRRRRR Using --action mask: >example NNNNNNNNNNNNNNXXXXXXXXXXXGGGGGGRRRRRRR Using --action lowercase: >example llllllllaaaaaaXXXXXXXXXXXGGGGGGRRRRRRR Using --action none: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Proposed output: ``` Using --action trimupto: >example AAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Using left and right adapter: ``` $ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -g AAAAAA...GGGGGG -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done Using --action trim: >example XXXXXXXXXXX Using --action mask: >example NNNNNNNNNNNNNNXXXXXXXXXXXNNNNNNNNNNNNN Using --action lowercase: >example llllllllaaaaaaXXXXXXXXXXXggggggrrrrrrr Using --action none: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Proposed output: ``` Using --action trimupto: >example AAAAAAXXXXXXXXXXXGGGGGG ``` Right adapter example: ``` $ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -a GGGGGG -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done Using --action trim: >example LLLLLLLLAAAAAAXXXXXXXXXXX Using --action mask: >example LLLLLLLLAAAAAAXXXXXXXXXXXNNNNNNNNNNNNN Using --action lowercase: >example LLLLLLLLAAAAAAXXXXXXXXXXXggggggrrrrrrr Using --action none: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR ``` Proposed output: ``` Using --action trimupto: >example LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGG ```
      author:
         url:https://github.com/peterjc
         type:Person
         name:peterjc
      datePublished:2020-02-28T12:21:33.000Z
      interactionStatistic:
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         interactionType:https://schema.org/CommentAction
         userInteractionCount:7
      url:https://github.com/443/cutadapt/issues/443
Person:
      url:https://github.com/peterjc
      name:peterjc
      url:https://github.com/peterjc
      name:peterjc
InteractionCounter:
      interactionType:https://schema.org/CommentAction
      userInteractionCount:7
      interactionType:https://schema.org/CommentAction
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