diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..87be936 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: 2 + +build: + os: "ubuntu-22.04" + tools: + python: "3.10" + +python: + install: + - requirements: docs/requirements.txt + +sphinx: + configuration: docs/soure/conf.py diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..c0424a1 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,2 @@ +Sphinx==8.0.2 +sphinx-rtd-theme==2.0.0 diff --git a/docs/source/_static/annotcolor.png b/docs/source/_static/annotcolor.png new file mode 100644 index 0000000..fd67404 Binary files /dev/null and b/docs/source/_static/annotcolor.png differ diff --git a/docs/source/_static/clear.svg b/docs/source/_static/clear.svg new file mode 100644 index 0000000..0ba7218 --- /dev/null +++ b/docs/source/_static/clear.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/source/_static/exportdialog.png b/docs/source/_static/exportdialog.png new file mode 100644 index 0000000..de96966 Binary files /dev/null and b/docs/source/_static/exportdialog.png differ diff --git a/docs/source/_static/filterdialog.png b/docs/source/_static/filterdialog.png new file mode 100644 index 0000000..830ff90 Binary files /dev/null and b/docs/source/_static/filterdialog.png differ diff --git a/docs/source/_static/minus.svg b/docs/source/_static/minus.svg new file mode 100644 index 0000000..17483d6 --- /dev/null +++ b/docs/source/_static/minus.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/source/_static/plus.svg b/docs/source/_static/plus.svg new file mode 100644 index 0000000..66308ef --- /dev/null +++ b/docs/source/_static/plus.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/source/_static/primerresults.png b/docs/source/_static/primerresults.png new file mode 100644 index 0000000..b5d41ba Binary files /dev/null and b/docs/source/_static/primerresults.png differ diff --git a/docs/source/_static/primerseq.png b/docs/source/_static/primerseq.png new file mode 100644 index 0000000..c4ecaa6 Binary files /dev/null and b/docs/source/_static/primerseq.png differ diff --git a/docs/source/_static/primersetting.png b/docs/source/_static/primersetting.png new file mode 100644 index 0000000..ed851d2 Binary files /dev/null and b/docs/source/_static/primersetting.png differ diff --git a/docs/source/_static/update.svg b/docs/source/_static/update.svg new file mode 100644 index 0000000..d0d7154 --- /dev/null +++ b/docs/source/_static/update.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/source/index.rst b/docs/source/index.rst index a7aa805..39aa1a2 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -18,4 +18,6 @@ documentation for details. install window usage + others + output diff --git a/docs/source/others.rst b/docs/source/others.rst new file mode 100644 index 0000000..920b1fb --- /dev/null +++ b/docs/source/others.rst @@ -0,0 +1,120 @@ +Other Features +============== + +Mapping Analysis +---------------- + +The mapping analysis will locate the found repeats into gene features (CDS, UTR, intron, exon). Before mapping, you should import gtf or gff annotation files. + +Go to **Toolbar**, and then click |locate| to perform mapping analysis. After mapping, the repeats mapped in gene exon (pink), intron (green), CDS (purple), 3'UTR (blue), 5'UTR (yellow) will be marked as different colors in table. + + .. figure:: _static/annotcolor.png + +Design Primer +------------- + +Krait2 use `primer3 `_ to design primers. Before primer design, you can set corresponding parameters for primer3. The meaning of primer3 tags can be found in `primer3 manual `_. + + .. figure:: _static/primersetting.png + :width: 500 + :align: center + +First, you should select some repeats in table, and then click |primer| to design primers. If primer designed successfully, the primers will be displayed in Primer result table. + + .. figure:: _static/primerresults.png + :align: center + +The description of each column in primer result table: + +.. list-table:: + :header-rows: 1 + :align: center + + * - Column + - Description + * - ID + - unique identifier generated by Krait + * - locus + - repeat identifier which is composed of repeat type, input file id and repeat id + * - entry + - primer entry id, each locus may has multiple designed primers + * - product size + - product size + * - strand + - forward or reverse + * - Tm + - melting temperatures for forward and reverse primers + * - GC content + - GC content for forward and reverse primers + * - 3' End stability + - 3' end stability for forward and reverse primers + * - primer sequences + - primer sequences for forward and reverse primers + +Click the row in primer table, you can view the primer sequence location in input sequence file. The sequences enclosed by the dotted boxes are the positions of the primers. + + .. figure:: _static/primerseq.png + :align: center + + +Perform Statistics +------------------ + +After searching repeat, you can click |statistics| to perform statistics analysis. + +Motif Standardization +^^^^^^^^^^^^^^^^^^^^^ + +**Level 0** + +no standardization will be performed + +**Level 1** + +Similar motifs. For example, CA can be viewed as AC. ATGcan represent TGA and GAT + +**Level 2** + +Reverse complementary motifs, including Level 1. For example, CAT is a reverse complementary motif of ATG. ATG can represent TGA, +GAT, CAT, ATC and TCA + +**Level 3** + +Complementary motifs, including Level 1 and Level 2. For example, TAC is a complementary motif of ATG. ATG can represent TGA,GAT, +CAT, ATC, TCA, TAC, ACT and CTA + +**Level 4** + +Reverse motifs, including Level 1, Level 2 and Level 3. For example, GTA is a reverse motif of ATG. ATG can represent TGA,GAT, CAT, +ATC, TCA, TAC, ACT, CTA, GTA, TAG and AGT + + + +Filter Tables +------------- + +The repeats in current table can be filtered by setting different conditions according to each column. Go to **Toolbar** and click |filter| to open filter dialog. + + .. figure:: _static/filterdialog.png + :width: 500 + :align: center + +Click |plus| to add filter condition, click |minus| to remove current filter condition, click |clear| to clear all filter conditions, after setting filters, you can click |update| update table to do filter and update the rows in current table. + + +.. |locate| image:: _static/locating.svg + :width: 20 +.. |primer| image:: _static/primer.svg + :width: 20 +.. |statistics| image:: _static/statistics.svg + :width: 20 +.. |filter| image:: _static/filter.svg + :width: 20 +.. |plus| image:: _static/plus.svg + :width: 20 +.. |minus| image:: _static/minus.svg + :width: 20 +.. |clear| image:: _static/clear.svg + :width: 20 +.. |update| image:: _static/update.svg + :width: 20 \ No newline at end of file diff --git a/docs/source/output.rst b/docs/source/output.rst new file mode 100644 index 0000000..62143bd --- /dev/null +++ b/docs/source/output.rst @@ -0,0 +1,25 @@ +Export Results +============== + +Export Result Tables +-------------------- + +Krait2 supports exporting results to csv or tsv formatted file. + +Go to **File** menu, click **Export selected rows...** to export selected rows in current table into a file. + +Go to **File** menu, click **Export current table...** to export all rows in current table into a file. + +Go to **File** menu, click **Export all tables...** to open exporting dialog. You can export all tables for current input file or for all input files. You can also select csv or tsv as output format. + + .. figure:: _static/exportdialog.png + :width: 400 + :align: center + + +Export Statistics Report +------------------------ + +Krait2 allows users to export html formatted statistical report file. + +Go to **File** menu, click **Export statistics report...** to export html file. \ No newline at end of file diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 1c8f0d0..ff2fc56 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -207,6 +207,7 @@ The description of each column in GTRs table: * - motif - repeat unit of GTR + .. |ssr| image:: _static/ssr.svg :width: 20 .. |cssr| image:: _static/cssr.svg