From e9b27ae7b8c3f7cb7a4f0e6a9926b0019ecc5fe0 Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Wed, 6 Mar 2024 20:03:23 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20=20@=205c0db?= =?UTF-8?q?77d0e9b09e8dc679aedfdc41f20fc7dea28=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- _sources/advanced/index.rst.txt | 90 ++++++++++++++++++++++++-------- advanced/index.html | 51 ++++++++++++++++-- index.html | 2 + objects.inv | Bin 487 -> 515 bytes searchindex.js | 2 +- 5 files changed, 116 insertions(+), 29 deletions(-) diff --git a/_sources/advanced/index.rst.txt b/_sources/advanced/index.rst.txt index b39d4d1..ec02b7c 100644 --- a/_sources/advanced/index.rst.txt +++ b/_sources/advanced/index.rst.txt @@ -10,6 +10,8 @@ This section describes the various features and options of ClipKIT. - Log_ - Complementary_ - Codon_ +- Gaps_ +- `Gap Characters`_ - `Sequence Type`_ - `All options`_ @@ -138,6 +140,44 @@ codon will be trimmed. To conduct codon-based trimming, use the -co/\\-\\-codon | +.. _Gaps: + +Gaps +---- + +Positions with gappyness greater than threshold will be trimmed. +Must be between 0 and 1. (Default: 0.9). This argument is ignored +when using the kpi and kpic mdoes of trimming as well as an +iteration of trimming that uses smart-gap. + +To specify a gaps threshold, use the -g/\\-\\-gaps argument. + +.. code-block:: shell + + clipkit --gaps 0.4 + + # or + + clipkit --g 0.4 + +| + +.. _`Gap Characters`: + +Gap Characters +-------------- + +Specifies gap characters used in the input file. For example, +"NnXx-?" would specify that "N", "n", "X", "x", "-", and "?" are +gap characters. Note, the first gap character cannot be "-" because +the parser will interpret the gaps list as a new argument. + +.. code-block:: shell + + clipkit -gc NnXx-? + +| + .. _`Sequence Type`: Sequence Type @@ -171,29 +211,33 @@ All options --------------------- -+-----------------------------+-------------------------------------------------------------------+ -| Option | Usage and meaning | -+=============================+===================================================================+ -| -h/\\-\\-help | Print help message | -+-----------------------------+-------------------------------------------------------------------+ -| -v/\\-\\-version | Print software version | -+-----------------------------+-------------------------------------------------------------------+ -| -m/\\-\\-mode | Specify trimming mode (default: smart-gap) | -+-----------------------------+-------------------------------------------------------------------+ -| -o/\\-\\-output | Specify output file name | -+-----------------------------+-------------------------------------------------------------------+ -| -g/\\-\\-gaps | Specify gappyness threshold (between 0 and 1). *Default: 0.9* | -+-----------------------------+-------------------------------------------------------------------+ -| -co/\\-\\-codon | Codon codon-based trimming. *Default: off* | -+-----------------------------+-------------------------------------------------------------------+ -| -if/\\-\\-input_file_format | Specify input file format*. *Default: auto-detect* | -+-----------------------------+-------------------------------------------------------------------+ -| -of/\\-\\-output_file_format| Specify output file format*. *Default: input file type* | -+-----------------------------+-------------------------------------------------------------------+ -| -l/\\-\\-log | Create a log file. *Default: off* | -+-----------------------------+-------------------------------------------------------------------+ -| -c/\\-\\-complementary | Create a complementary alignment file. *Default: off* | -+-----------------------------+-------------------------------------------------------------------+ ++-----------------------------+-----------------------------------------------------------------------+ +| Option | Usage and meaning | ++=============================+=======================================================================+ +| -h/\\-\\-help | Print help message | ++-----------------------------+-----------------------------------------------------------------------+ +| -v/\\-\\-version | Print software version | ++-----------------------------+-----------------------------------------------------------------------+ +| -m/\\-\\-mode | Specify trimming mode (default: smart-gap) | ++-----------------------------+-----------------------------------------------------------------------+ +| -o/\\-\\-output | Specify output file name | ++-----------------------------+-----------------------------------------------------------------------+ +| -g/\\-\\-gaps | Specify gappyness threshold (between 0 and 1). *Default: 0.9* | ++-----------------------------+-----------------------------------------------------------------------+ +| -gc/\\-\\-gap_characters | Specifies gap characters used in input file (AAs: Xx-?*; NTs: XxNn-?* | ++-----------------------------+-----------------------------------------------------------------------+ +| -co/\\-\\-codon | Codon codon-based trimming. *Default: off* | ++-----------------------------+-----------------------------------------------------------------------+ +| -s/\\-\\-sequence | Specifies sequence type of input file. *Default: auto-detect* | ++-----------------------------+-----------------------------------------------------------------------+ +| -if/\\-\\-input_file_format | Specify input file format*. *Default: auto-detect* | ++-----------------------------+-----------------------------------------------------------------------+ +| -of/\\-\\-output_file_format| Specify output file format*. *Default: input file type* | ++-----------------------------+-----------------------------------------------------------------------+ +| -l/\\-\\-log | Create a log file. *Default: off* | ++-----------------------------+-----------------------------------------------------------------------+ +| -c/\\-\\-complementary | Create a complementary alignment file. *Default: off* | ++-----------------------------+-----------------------------------------------------------------------+ \*Acceptable file formats include: diff --git a/advanced/index.html b/advanced/index.html index dd7133b..fd80062 100644 --- a/advanced/index.html +++ b/advanced/index.html @@ -94,6 +94,8 @@
  • Log
  • Complementary
  • Codon
    • +
  • Gaps
    • +
  • Gap Characters
  • Sequence Type
  • All options
    • @@ -174,6 +176,8 @@

    Advanced UsageLog

  • Complementary

  • Codon

    • +

  • Gaps

    • +

  • Gap Characters

  • Sequence Type

  • All options

    • @@ -289,8 +293,39 @@

    Output

    +
    +

    Gaps

    +

    Positions with gappyness greater than threshold will be trimmed. +Must be between 0 and 1. (Default: 0.9). This argument is ignored +when using the kpi and kpic mdoes of trimming as well as an +iteration of trimming that uses smart-gap.

    +

    To specify a gaps threshold, use the -g/--gaps argument.

    +
        clipkit <input> --gaps 0.4
+
+# or
+
+    clipkit <input> --g 0.4
+
    +
    +
    +

    +
    +
    +
    +

    Gap Characters

    +

    Specifies gap characters used in the input file. For example, +“NnXx-?” would specify that “N”, “n”, “X”, “x”, “-“, and “?” are +gap characters. Note, the first gap character cannot be “-” because +the parser will interpret the gaps list as a new argument.

    +
    clipkit <input> -gc NnXx-?
+
    +
    +
    +

    +
    +
    -

    Sequence Type

    +

    Sequence Type

    Specifies the type of sequences in the input file. The default is auto-detection of sequence type. Valid options include aa or nt for amino acids and nucleotides. This argument @@ -311,11 +346,11 @@

    Output

    -

    All options

    +

    All options

    --++ @@ -338,9 +373,15 @@

    Output

    - + + + + + + + diff --git a/index.html b/index.html index a12cacf..2a56d0d 100644 --- a/index.html +++ b/index.html @@ -253,6 +253,8 @@

    Quick StartLog
  • Complementary
  • Codon
    • +
  • Gaps
    • +
  • Gap Characters
  • Sequence Type
  • All options
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    Option

    -g/--gaps

    Specify gappyness threshold (between 0 and 1). Default: 0.9

    -co/--codon

    -gc/--gap_characters

    Specifies gap characters used in input file (AAs: Xx-?*; NTs: XxNn-?*

    -co/--codon

    Codon codon-based trimming. Default: off

    -s/--sequence

    Specifies sequence type of input file. Default: auto-detect

    -if/--input_file_format

    Specify input file format*. Default: auto-detect