diff --git a/example/all.eps b/docs/source/_static/examples/all.eps similarity index 100% rename from example/all.eps rename to docs/source/_static/examples/all.eps diff --git a/example/one_line.pbr322.toy.fa b/docs/source/_static/examples/one_line.pbr322.toy.fa similarity index 100% rename from example/one_line.pbr322.toy.fa rename to docs/source/_static/examples/one_line.pbr322.toy.fa diff --git a/example/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html b/docs/source/_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html similarity index 100% rename from example/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html rename to docs/source/_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html diff --git a/example/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html b/docs/source/_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html similarity index 100% rename from example/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html rename to docs/source/_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html diff --git a/example/pbr322.toy.compete.txt b/docs/source/_static/examples/pbr322.toy.compete.txt similarity index 100% rename from example/pbr322.toy.compete.txt rename to docs/source/_static/examples/pbr322.toy.compete.txt diff --git a/example/pbr322.toy.fa b/docs/source/_static/examples/pbr322.toy.fa similarity index 100% rename from example/pbr322.toy.fa rename to docs/source/_static/examples/pbr322.toy.fa diff --git a/docs/source/examples.rst b/docs/source/examples.rst new file mode 100644 index 0000000..8cf8e6a --- /dev/null +++ b/docs/source/examples.rst @@ -0,0 +1,39 @@ +Examples +======== + +Competition calculation +------------------------ + +Example of the output generated when the competition algorithm analyses the +``pbr322.toy.fa`` sequence. These results are described in the Bioinformatics +citation (see :doc:`citation`). + +Input file +~~~~~~~~~~ + +:download:`pbr322.toy.fa <_static/examples/pbr322.toy.fa>` + +Command +~~~~~~~ + +.. code-block:: bash + + sist -f pbr322.toy.fa -a A -o pbr322.toy.compete.txt -b -p -r + +Output files +~~~~~~~~~~~~ + +* :download:`one_line.pbr322.toy.fa <_static/examples/one_line.pbr322.toy.fa>`, + the sequence file format required by Inverted Repeat Finder (IRF) +* :download:`one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html <_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html>`, + an IRF output file +* :download:`one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html <_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html>`, + an IRF output file +* :download:`pbr322.toy.compete.txt <_static/examples/pbr322.toy.compete.txt>`, + the SIST output file + +Figure +~~~~~~ + +:download:`all.eps <_static/examples/all.eps>` represents graphically the +output shown in ``pbr322.toy.compete.txt``. diff --git a/docs/source/index.rst b/docs/source/index.rst index cb3047d..2ac4ff8 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -43,5 +43,6 @@ Run a competition calculation and write the result to a file: user-guide installation source-usage + examples development citation diff --git a/docs/source/source-usage.rst b/docs/source/source-usage.rst index aef52ef..ade056f 100644 --- a/docs/source/source-usage.rst +++ b/docs/source/source-usage.rst @@ -154,20 +154,5 @@ in the current working directory when these calculations are run. Example calculation ------------------- -The repository contains an example competition calculation based on -``pbr322.toy.fa``. - -The command is: - -.. code-block:: bash - - sist \ - -f pbr322.toy.fa \ - -a A \ - -o pbr322.toy.compete.txt \ - -b \ - -p \ - -r - -The example directory also contains IRF intermediate output and an EPS -representation of the competition result. +See :doc:`examples` for a full worked competition calculation, including +downloadable input/output files and an EPS representation of the result. diff --git a/example/README.txt b/example/README.txt deleted file mode 100644 index bd83ab1..0000000 --- a/example/README.txt +++ /dev/null @@ -1,15 +0,0 @@ -Example of output generated when the competion algorithm analyzes the pbr322.toy.fa sequence. These results are described in the Bioinformatics citation. - -To execute type the following on the command line: -sist -f pbr322.toy.fa -a A -o pbr322.toy.compete.txt -b -p -r - -Input files: -1. pbr322.toy.fa - -Output files: -1. one_line.pbr322.toy.fa : sequences file format required by Inverted Repeat Finder (IRF) -2. one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html: IRF output file -3. one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html: IRF output file -4. pbr322.toy.compete.txt : output file - -Figure all.eps represents graphically the output shown in pbr322.toy.compete.txt