deploy: fb1556e

docs/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 68666ed7422b1e0bf84ee532afdab9b6
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_sources/index.rst.txt

@@ -0,0 +1,76 @@
+HogProf
+=====================
+
+  - HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient.
+  - Still under major development and may change.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   usage
+   troubleshooting
+   credits
+
+Installation
+------------
+
+To install My Project, run the following command:
+
+Using pip
+
+
+.. code-block:: bash
+   $ pip install hogprof
+ 
+Or from github 
+.. code-block:: bash
+$ git clone https://github.com/DessimozLab/HogProf.git
+$ pip install -r pipreqs.txt .
+
+Quickstart
+-----
+
+To use the library we need an OMA instance's HDF5 file containing HOG info and some accesory files.
+
+.. code-block:: bash
+   $ mkdir YourOmaDirectory
+   $ cd YourOmaDirectory
+   $ wget https://omabrowser.org/All/OmaServer.h5
+   $ wget https://omabrowser.org/All/oma-go.txt.gz
+
+Let's create a directory for the phylogenetic rpfiling database were going to make.
+
+
+.. code-block:: bash
+   $ mkdir YourDBDirectory
+
+Ok. We're ready! Now let's compile a database containing all HOGs and our desired taxonomic levels using default settings. Launch the lshbuilder.
+dbtypes available on the command line are : all , plants , archaea, bacteria , eukarya , protists , fungi , metazoa and vertebrates. These will use the NCBI taxonomy as a tree to annotate events in different gene family's histories.
+
+.. code-block:: bash
+   $python lshbuilder.py --outpath YourHogProfDirectory --dbtype all --OMA YourOmaDirectory/OmaServer.h5 --nthreads numberOfCPUcores          
+
+This should build a taxonomic tree for the genomes contained in the release and then calculate enhanced phylogenies for all HOGs in OMA.
+Once the database is completed it can be interogated using a profiler object. Construction and usage of this object should be done using a python script or notebook.
+
+
+.. code-block:: python
+   import HogProf
+   myproject.do_x()
+
+
+
+
+Troubleshooting
+---------------
+
+
+If you encounter any issues while using My Project, please file a bug report on our GitHub repository: https://github.com/user/repo/issues
+
+
+Credits
+-------
+
+My Project was created by John Doe.

docs/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}