"""Part one of the third step of the pipeline: refinement - extension.
-Extents the model by mapping missing genes to reactions via NCBI, KEGG,
+Extends the model by mapping missing genes to reactions via NCBI, KEGG,
MetaNetX and BiGG.
"""
@@ -1052,7 +1052,7 @@ Source code for specimen.hqtb.core.refinement.extension
bigg_metabolites:pd.DataFrame,
namespace:Literal['BiGG']='BiGG') -> dict[cobra.Metabolite,int]:
"""Based on a given KEGG equation and a model, get or
- create metabolite entires in/for the model.
+ create metabolite entries in/for the model.
Args:
- model (cobra.Model):
diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html
index c870bf8..bc228c2 100644
--- a/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html
+++ b/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/_modules/specimen/hqtb/core/validation.html b/docs/build/html/_modules/specimen/hqtb/core/validation.html
index 60358f6..b0da381 100644
--- a/docs/build/html/_modules/specimen/hqtb/core/validation.html
+++ b/docs/build/html/_modules/specimen/hqtb/core/validation.html
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/_modules/specimen/hqtb/workflow.html b/docs/build/html/_modules/specimen/hqtb/workflow.html
index 83f402c..48ee9d9 100644
--- a/docs/build/html/_modules/specimen/hqtb/workflow.html
+++ b/docs/build/html/_modules/specimen/hqtb/workflow.html
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/_modules/specimen/util/set_up.html b/docs/build/html/_modules/specimen/util/set_up.html
index 134e779..aa80413 100644
--- a/docs/build/html/_modules/specimen/util/set_up.html
+++ b/docs/build/html/_modules/specimen/util/set_up.html
@@ -18,7 +18,7 @@
-
+
@@ -225,7 +225,7 @@ Source code for specimen.util.set_up
The media config and the config for the cmpb / CarveMe + Modelpolisher based pipeline
can be downloaded using 'media' and 'cmpb' respectively
- For the htqb / high-quality template based pipeline:
+ For the hqtb / high-quality template based pipeline:
Depending on the knowledge of the user, either a 'hqtb-basic' or an 'hqtb-advanced' type
of configuration file can be downloaded (or 'hqtb-defaults' for developers).
@@ -234,7 +234,7 @@ Source code for specimen.util.set_up
- filename (str, optional):
Filename/filepath to save the downloaded config file under.
Defaults to 'my_basic_config.yaml'.
- - type (Literal['htqb-basic','htqb-advanced','htqb-defaults','media','cmpb'], optional):
+ - type (Literal['hqtb-basic','hqtb-advanced','hqtb-defaults','media','cmpb'], optional):
The type of file to download.
Can be 'hqtb-basic', 'hqtb-advanced' or 'hqtb-defaults' or 'media' or 'cmpb'.
Defaults to 'hqtb basic'.
@@ -247,19 +247,19 @@ Source code for specimen.util.set_up
match type:
# the 'beginner' version
case 'hqtb-basic':
- config_file = files('specimen.data.config').joinpath('htqb_basic_config_expl.yaml')
+ config_file = files('specimen.data.config').joinpath('hqtb_basic_config_expl.yaml')
with open(config_file, "r") as cfg_file, open(filename, 'w') as cfg_out:
for line in cfg_file:
cfg_out.write(line)
# for advanced users
case 'hqtb-advanced':
- config_file = files('specimen.data.config').joinpath('htqb_advanced_config_expl.yaml')
+ config_file = files('specimen.data.config').joinpath('hqtb_advanced_config_expl.yaml')
with open(config_file, "r") as cfg_file, open(filename, 'w') as cfg_out:
for line in cfg_file:
cfg_out.write(line)
# for developer: the config with all internal defaults
case 'hqtb-defaults':
- config_file = files('specimen.data.config').joinpath('htqb_config_default.yaml')
+ config_file = files('specimen.data.config').joinpath('hqtb_config_default.yaml')
with open(config_file, "r") as cfg_file, open(filename, 'w') as cfg_out:
for line in cfg_file:
cfg_out.write(line)
@@ -384,7 +384,7 @@ Source code for specimen.util.set_up
# load both files
match pipeline:
case 'hqtb':
- defaultc_path = files('specimen.data.config').joinpath('htqb_config_default.yaml')
+ defaultc_path = files('specimen.data.config').joinpath('hqtb_config_default.yaml')
case 'cmpb':
defaultc_path = files('specimen.data.config').joinpath('cmpb_config.yaml')
case _:
diff --git a/docs/build/html/_modules/specimen/util/util.html b/docs/build/html/_modules/specimen/util/util.html
index 0b81185..1c16c7f 100644
--- a/docs/build/html/_modules/specimen/util/util.html
+++ b/docs/build/html/_modules/specimen/util/util.html
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/_sources/pipeline_idea.rst.txt b/docs/build/html/_sources/pipeline_idea.rst.txt
index d93a94e..772be29 100644
--- a/docs/build/html/_sources/pipeline_idea.rst.txt
+++ b/docs/build/html/_sources/pipeline_idea.rst.txt
@@ -32,7 +32,7 @@ workflow in Figure :numref:`pgab_workflow` can be used.
.. _pgab_workflow:
-.. figure:: images/genome2draft.svg
+.. figure:: images/genome2draft.png
:alt: Workflow from genome sequence to a draft model
Workflow from genome sequence to a draft model
diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
index 30fee9d..f316efc 100644
--- a/docs/build/html/_static/basic.css
+++ b/docs/build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js
index d06a71d..4d67807 100644
--- a/docs/build/html/_static/doctools.js
+++ b/docs/build/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Base JavaScript utilities for all Sphinx HTML documentation.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js
index 250f566..367b8ed 100644
--- a/docs/build/html/_static/language_data.js
+++ b/docs/build/html/_static/language_data.js
@@ -5,7 +5,7 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -13,7 +13,7 @@
var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
/**
* Porter Stemmer
diff --git a/docs/build/html/_static/searchtools.js b/docs/build/html/_static/searchtools.js
index 7918c3f..92da3f8 100644
--- a/docs/build/html/_static/searchtools.js
+++ b/docs/build/html/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
.then((data) => {
if (data)
listItem.appendChild(
- Search.makeSearchSummary(data, searchTerms)
+ Search.makeSearchSummary(data, searchTerms, anchor)
);
// highlight search terms in the summary
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
@@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => {
);
else
Search.status.innerText = _(
- `Search finished, found ${resultCount} page(s) matching the search query.`
- );
+ "Search finished, found ${resultCount} page(s) matching the search query."
+ ).replace('${resultCount}', resultCount);
};
const _displayNextItem = (
results,
@@ -137,6 +137,22 @@ const _displayNextItem = (
// search finished, update title and status message
else _finishSearch(resultCount);
};
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+ const leftScore = a[4];
+ const rightScore = b[4];
+ if (leftScore === rightScore) {
+ // same score: sort alphabetically
+ const leftTitle = a[1].toLowerCase();
+ const rightTitle = b[1].toLowerCase();
+ if (leftTitle === rightTitle) return 0;
+ return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+ }
+ return leftScore > rightScore ? 1 : -1;
+};
/**
* Default splitQuery function. Can be overridden in ``sphinx.search`` with a
@@ -160,13 +176,26 @@ const Search = {
_queued_query: null,
_pulse_status: -1,
- htmlToText: (htmlString) => {
+ htmlToText: (htmlString, anchor) => {
const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
- htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+ for (const removalQuery of [".headerlinks", "script", "style"]) {
+ htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+ }
+ if (anchor) {
+ const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+ if (anchorContent) return anchorContent.textContent;
+
+ console.warn(
+ `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+ );
+ }
+
+ // if anchor not specified or not found, fall back to main content
const docContent = htmlElement.querySelector('[role="main"]');
- if (docContent !== undefined) return docContent.textContent;
+ if (docContent) return docContent.textContent;
+
console.warn(
- "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
+ "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
);
return "";
},
@@ -239,16 +268,7 @@ const Search = {
else Search.deferQuery(query);
},
- /**
- * execute search (requires search index to be loaded)
- */
- query: (query) => {
- const filenames = Search._index.filenames;
- const docNames = Search._index.docnames;
- const titles = Search._index.titles;
- const allTitles = Search._index.alltitles;
- const indexEntries = Search._index.indexentries;
-
+ _parseQuery: (query) => {
// stem the search terms and add them to the correct list
const stemmer = new Stemmer();
const searchTerms = new Set();
@@ -284,16 +304,32 @@ const Search = {
// console.info("required: ", [...searchTerms]);
// console.info("excluded: ", [...excludedTerms]);
- // array of [docname, title, anchor, descr, score, filename]
- let results = [];
+ return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+ },
+
+ /**
+ * execute search (requires search index to be loaded)
+ */
+ _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+ const filenames = Search._index.filenames;
+ const docNames = Search._index.docnames;
+ const titles = Search._index.titles;
+ const allTitles = Search._index.alltitles;
+ const indexEntries = Search._index.indexentries;
+
+ // Collect multiple result groups to be sorted separately and then ordered.
+ // Each is an array of [docname, title, anchor, descr, score, filename].
+ const normalResults = [];
+ const nonMainIndexResults = [];
+
_removeChildren(document.getElementById("search-progress"));
- const queryLower = query.toLowerCase();
+ const queryLower = query.toLowerCase().trim();
for (const [title, foundTitles] of Object.entries(allTitles)) {
- if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
+ if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
for (const [file, id] of foundTitles) {
let score = Math.round(100 * queryLower.length / title.length)
- results.push([
+ normalResults.push([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
@@ -308,46 +344,47 @@ const Search = {
// search for explicit entries in index directives
for (const [entry, foundEntries] of Object.entries(indexEntries)) {
if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
- for (const [file, id] of foundEntries) {
- let score = Math.round(100 * queryLower.length / entry.length)
- results.push([
+ for (const [file, id, isMain] of foundEntries) {
+ const score = Math.round(100 * queryLower.length / entry.length);
+ const result = [
docNames[file],
titles[file],
id ? "#" + id : "",
null,
score,
filenames[file],
- ]);
+ ];
+ if (isMain) {
+ normalResults.push(result);
+ } else {
+ nonMainIndexResults.push(result);
+ }
}
}
}
// lookup as object
objectTerms.forEach((term) =>
- results.push(...Search.performObjectSearch(term, objectTerms))
+ normalResults.push(...Search.performObjectSearch(term, objectTerms))
);
// lookup as search terms in fulltext
- results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+ normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
// let the scorer override scores with a custom scoring function
- if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
-
- // now sort the results by score (in opposite order of appearance, since the
- // display function below uses pop() to retrieve items) and then
- // alphabetically
- results.sort((a, b) => {
- const leftScore = a[4];
- const rightScore = b[4];
- if (leftScore === rightScore) {
- // same score: sort alphabetically
- const leftTitle = a[1].toLowerCase();
- const rightTitle = b[1].toLowerCase();
- if (leftTitle === rightTitle) return 0;
- return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
- }
- return leftScore > rightScore ? 1 : -1;
- });
+ if (Scorer.score) {
+ normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+ nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+ }
+
+ // Sort each group of results by score and then alphabetically by name.
+ normalResults.sort(_orderResultsByScoreThenName);
+ nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+ // Combine the result groups in (reverse) order.
+ // Non-main index entries are typically arbitrary cross-references,
+ // so display them after other results.
+ let results = [...nonMainIndexResults, ...normalResults];
// remove duplicate search results
// note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
@@ -361,7 +398,12 @@ const Search = {
return acc;
}, []);
- results = results.reverse();
+ return results.reverse();
+ },
+
+ query: (query) => {
+ const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+ const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
// for debugging
//Search.lastresults = results.slice(); // a copy
@@ -466,14 +508,18 @@ const Search = {
// add support for partial matches
if (word.length > 2) {
const escapedWord = _escapeRegExp(word);
- Object.keys(terms).forEach((term) => {
- if (term.match(escapedWord) && !terms[word])
- arr.push({ files: terms[term], score: Scorer.partialTerm });
- });
- Object.keys(titleTerms).forEach((term) => {
- if (term.match(escapedWord) && !titleTerms[word])
- arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
- });
+ if (!terms.hasOwnProperty(word)) {
+ Object.keys(terms).forEach((term) => {
+ if (term.match(escapedWord))
+ arr.push({ files: terms[term], score: Scorer.partialTerm });
+ });
+ }
+ if (!titleTerms.hasOwnProperty(word)) {
+ Object.keys(titleTerms).forEach((term) => {
+ if (term.match(escapedWord))
+ arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+ });
+ }
}
// no match but word was a required one
@@ -496,9 +542,8 @@ const Search = {
// create the mapping
files.forEach((file) => {
- if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
- fileMap.get(file).push(word);
- else fileMap.set(file, [word]);
+ if (!fileMap.has(file)) fileMap.set(file, [word]);
+ else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
});
});
@@ -549,8 +594,8 @@ const Search = {
* search summary for a given text. keywords is a list
* of stemmed words.
*/
- makeSearchSummary: (htmlText, keywords) => {
- const text = Search.htmlToText(htmlText);
+ makeSearchSummary: (htmlText, keywords, anchor) => {
+ const text = Search.htmlToText(htmlText, anchor);
if (text === "") return null;
const textLower = text.toLowerCase();
diff --git a/docs/build/html/cmpb/about-pipeline.html b/docs/build/html/cmpb/about-pipeline.html
index 825a824..0ebcc24 100644
--- a/docs/build/html/cmpb/about-pipeline.html
+++ b/docs/build/html/cmpb/about-pipeline.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/cmpb/cmpb-config.html b/docs/build/html/cmpb/cmpb-config.html
index 8e01ed3..907f0cf 100644
--- a/docs/build/html/cmpb/cmpb-config.html
+++ b/docs/build/html/cmpb/cmpb-config.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/cmpb/run-pipeline.html b/docs/build/html/cmpb/run-pipeline.html
index b81da49..348ef76 100644
--- a/docs/build/html/cmpb/run-pipeline.html
+++ b/docs/build/html/cmpb/run-pipeline.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/dev-notes.html b/docs/build/html/dev-notes.html
index e8df9f0..38d5c44 100644
--- a/docs/build/html/dev-notes.html
+++ b/docs/build/html/dev-notes.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 3596f2c..1769ec6 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/help.html b/docs/build/html/help.html
index 92c0113..81cd7b9 100644
--- a/docs/build/html/help.html
+++ b/docs/build/html/help.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/about-pipeline.html b/docs/build/html/hqtb/about-pipeline.html
index 60613b3..2f3aec5 100644
--- a/docs/build/html/hqtb/about-pipeline.html
+++ b/docs/build/html/hqtb/about-pipeline.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/hqtb-config.html b/docs/build/html/hqtb/hqtb-config.html
index d4feef5..21fc6a1 100644
--- a/docs/build/html/hqtb/hqtb-config.html
+++ b/docs/build/html/hqtb/hqtb-config.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/run-pipeline.html b/docs/build/html/hqtb/run-pipeline.html
index 9d8e091..c2b91ca 100644
--- a/docs/build/html/hqtb/run-pipeline.html
+++ b/docs/build/html/hqtb/run-pipeline.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/analysis.html b/docs/build/html/hqtb/step-desc/analysis.html
index b78ce06..4db7210 100644
--- a/docs/build/html/hqtb/step-desc/analysis.html
+++ b/docs/build/html/hqtb/step-desc/analysis.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/bidirect_blast.html b/docs/build/html/hqtb/step-desc/bidirect_blast.html
index d92079c..1295af1 100644
--- a/docs/build/html/hqtb/step-desc/bidirect_blast.html
+++ b/docs/build/html/hqtb/step-desc/bidirect_blast.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/gen_draft.html b/docs/build/html/hqtb/step-desc/gen_draft.html
index 7cad26c..52d7167 100644
--- a/docs/build/html/hqtb/step-desc/gen_draft.html
+++ b/docs/build/html/hqtb/step-desc/gen_draft.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/refine-parts/annot.html b/docs/build/html/hqtb/step-desc/refine-parts/annot.html
index 96945ee..3d0bcd9 100644
--- a/docs/build/html/hqtb/step-desc/refine-parts/annot.html
+++ b/docs/build/html/hqtb/step-desc/refine-parts/annot.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/refine-parts/cleanup.html b/docs/build/html/hqtb/step-desc/refine-parts/cleanup.html
index 97ba1fc..d09f5b0 100644
--- a/docs/build/html/hqtb/step-desc/refine-parts/cleanup.html
+++ b/docs/build/html/hqtb/step-desc/refine-parts/cleanup.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/refine-parts/extension.html b/docs/build/html/hqtb/step-desc/refine-parts/extension.html
index 56a3097..a7462a5 100644
--- a/docs/build/html/hqtb/step-desc/refine-parts/extension.html
+++ b/docs/build/html/hqtb/step-desc/refine-parts/extension.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/refine-parts/smooth.html b/docs/build/html/hqtb/step-desc/refine-parts/smooth.html
index 596cdc9..437609a 100644
--- a/docs/build/html/hqtb/step-desc/refine-parts/smooth.html
+++ b/docs/build/html/hqtb/step-desc/refine-parts/smooth.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/refinement.html b/docs/build/html/hqtb/step-desc/refinement.html
index 7f95084..69dce11 100644
--- a/docs/build/html/hqtb/step-desc/refinement.html
+++ b/docs/build/html/hqtb/step-desc/refinement.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/hqtb/step-desc/validation.html b/docs/build/html/hqtb/step-desc/validation.html
index ef4f1ca..0c017ac 100644
--- a/docs/build/html/hqtb/step-desc/validation.html
+++ b/docs/build/html/hqtb/step-desc/validation.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index 5dda506..cca9701 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/installation.html b/docs/build/html/installation.html
index 150caaa..b47daa5 100644
--- a/docs/build/html/installation.html
+++ b/docs/build/html/installation.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/modules/classes.html b/docs/build/html/modules/classes.html
index e691b67..eee375c 100644
--- a/docs/build/html/modules/classes.html
+++ b/docs/build/html/modules/classes.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/modules/cmd.html b/docs/build/html/modules/cmd.html
index bc797eb..db80915 100644
--- a/docs/build/html/modules/cmd.html
+++ b/docs/build/html/modules/cmd.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/modules/cmpb.html b/docs/build/html/modules/cmpb.html
index 309e2fd..e888067 100644
--- a/docs/build/html/modules/cmpb.html
+++ b/docs/build/html/modules/cmpb.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/modules/core.html b/docs/build/html/modules/core.html
index 5c623e0..ad8469e 100644
--- a/docs/build/html/modules/core.html
+++ b/docs/build/html/modules/core.html
@@ -19,7 +19,7 @@
-
+
@@ -335,7 +335,7 @@ specimen.hqtb.core.refinement subpackage
-specimen.hqtb.core.refinement.cleanup.run(model: str, dir: str, biocyc_db: str | None = None, check_dupl_reac: bool = False, check_dupl_meta: bool = 'default', remove_unused_meta: bool = False, remove_dupl_reac: bool = False, remove_dupl_meta: bool = False, universal: str | None = None, media_path: str | None = None, namespace: Literal['BiGG'] = 'BiGG', growth_threshold: float = 0.05, iterations: int = 3, chunk_size: int = 10000, memote: bool = False)[source]
+specimen.hqtb.core.refinement.cleanup.run(model: str, dir: str, biocyc_db: str = None, check_dupl_reac: bool = False, check_dupl_meta: bool = 'default', remove_unused_meta: bool = False, remove_dupl_reac: bool = False, remove_dupl_meta: bool = False, universal: str = None, media_path: str = None, namespace: Literal['BiGG'] = 'BiGG', growth_threshold: float = 0.05, iterations: int = 3, chunk_size: int = 10000, memote: bool = False)[source]
Perform the second refinement step, cleanup, on a model.
The second refinement step resolves the following issues:
@@ -496,7 +496,7 @@ specimen.hqtb.core.refinement subpackage
specimen.hqtb.core.refinement.extension submodule
Part one of the third step of the pipeline: refinement - extension.
-Extents the model by mapping missing genes to reactions via NCBI, KEGG,
+
Extends the model by mapping missing genes to reactions via NCBI, KEGG,
MetaNetX and BiGG.
-
@@ -792,7 +792,7 @@
specimen.hqtb.core.refinement subpackage
specimen.hqtb.core.refinement.extension.get_metabolites_kegg(model: Model, equation: str, chem_xref: DataFrame, chem_prop: DataFrame, bigg_metabolites: DataFrame, namespace: Literal['BiGG'] = 'BiGG') dict[Metabolite, int][source]
Based on a given KEGG equation and a model, get or
-create metabolite entires in/for the model.
+create metabolite entries in/for the model.
- Args:
@@ -886,7 +886,7 @@ specimen.hqtb.core.refinement subpackage
-
-specimen.hqtb.core.refinement.extension.get_ncbi_info(table: DataFrame, ncbi_map_file: str | None = None) DataFrame[source]
+specimen.hqtb.core.refinement.extension.get_ncbi_info(table: DataFrame, ncbi_map_file: str = None) DataFrame[source]
Retrieve information from NCBI via mapping to precomputed files.
If no mapping exists, try via Entrez - implemented, but does not work well
@@ -1051,7 +1051,7 @@ specimen.hqtb.core.refinement subpackage
-
-specimen.hqtb.core.refinement.extension.map_to_KEGG(gene_table: DataFrame, working_dir: str, manual_dir: str, genome_summary: str | None = None) Path[source]
+specimen.hqtb.core.refinement.extension.map_to_KEGG(gene_table: DataFrame, working_dir: str, manual_dir: str, genome_summary: str = None) Path[source]
Map entries of the table from get_ncbi_info() to KEGG.
Get KEGG.reaction ID from locus tag, if available, otherwise try EC number.
Entries of the finalised table are saved depending whether they were assigned
@@ -1091,7 +1091,7 @@
specimen.hqtb.core.refinement subpackage
-
-specimen.hqtb.core.refinement.extension.map_to_KEGG_row(row: Series, loci_list: list[str] | None = None) Series[source]
+specimen.hqtb.core.refinement.extension.map_to_KEGG_row(row: Series, loci_list: list[str] = None) Series[source]
Map a single entry of the table in map_to_KEGG() to KEGG.
- Args:
@@ -1346,7 +1346,7 @@ specimen.hqtb.core submodules
-
-specimen.hqtb.core.analysis.run(model_path: str, dir: str, media_path: str | None = None, namespace: Literal['BiGG'] = 'BiGG', pc_model_path: str | None = None, pc_based_on: Literal['id'] = 'id', test_aa_auxotrophies: bool = True, pathway: bool = True)[source]
+specimen.hqtb.core.analysis.run(model_path: str, dir: str, media_path: str = None, namespace: Literal['BiGG'] = 'BiGG', pc_model_path: str = None, pc_based_on: Literal['id'] = 'id', test_aa_auxotrophies: bool = True, pathway: bool = True)[source]
SPECIMEN Step 5: Analyse the generated model.
- Args:
@@ -1563,7 +1563,7 @@ specimen.hqtb.core submodules
-
-specimen.hqtb.core.bidirectional_blast.run(template: str, input: str, dir: str, template_name: str | None = None, input_name: str | None = None, temp_header: str = 'protein_id', in_header: str = 'locus_tag', threads: int = 2, extra_info: list[str] = ['locus_tag', 'product', 'protein_id'], sensitivity: Literal['sensitive', 'more-sensitive', 'very-sensitive', 'ultra-sensitive'] = 'more-sensitive')[source]
+specimen.hqtb.core.bidirectional_blast.run(template: str, input: str, dir: str, template_name: str = None, input_name: str = None, temp_header: str = 'protein_id', in_header: str = 'locus_tag', threads: int = 2, extra_info: list[str] = ['locus_tag', 'product', 'protein_id'], sensitivity: Literal['sensitive', 'more-sensitive', 'very-sensitive', 'ultra-sensitive'] = 'more-sensitive')[source]
Run the bidirectional blast on a template and input genome (annotated).
- Args:
diff --git a/docs/build/html/modules/hqtb.html b/docs/build/html/modules/hqtb.html
index d9c45f1..6d9fda2 100644
--- a/docs/build/html/modules/hqtb.html
+++ b/docs/build/html/modules/hqtb.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/modules/util.html b/docs/build/html/modules/util.html
index 9b6c1e5..e3bc7d9 100644
--- a/docs/build/html/modules/util.html
+++ b/docs/build/html/modules/util.html
@@ -19,7 +19,7 @@
-
+
@@ -146,7 +146,7 @@ specimen.util submodules
-- type (Literal[‘htqb-basic’,’htqb-advanced’,’htqb-defaults’,’media’,’cmpb’], optional):
The type of file to download.
+
- type (Literal[‘hqtb-basic’,’hqtb-advanced’,’hqtb-defaults’,’media’,’cmpb’], optional):
The type of file to download.
Can be ‘hqtb-basic’, ‘hqtb-advanced’ or ‘hqtb-defaults’ or ‘media’ or ‘cmpb’.
Defaults to ‘hqtb basic’.
PGAB: From genome sequence to draft model
-
+
+
Fig. 1 Workflow from genome sequence to a draft model
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 0168d64..3676542 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 1666ce5..98f442d 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index a538517..350f335 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["cmpb/about-pipeline", "cmpb/cmpb-config", "cmpb/run-pipeline", "dev-notes", "help", "hqtb/about-pipeline", "hqtb/hqtb-config", "hqtb/run-pipeline", "hqtb/step-desc/analysis", "hqtb/step-desc/bidirect_blast", "hqtb/step-desc/gen_draft", "hqtb/step-desc/refine-parts/annot", "hqtb/step-desc/refine-parts/cleanup", "hqtb/step-desc/refine-parts/extension", "hqtb/step-desc/refine-parts/smooth", "hqtb/step-desc/refinement", "hqtb/step-desc/validation", "index", "installation", "modules/classes", "modules/cmd", "modules/cmpb", "modules/core", "modules/hqtb", "modules/util", "overview-pipes", "pipeline_idea", "specimen"], "filenames": ["cmpb/about-pipeline.rst", "cmpb/cmpb-config.rst", "cmpb/run-pipeline.rst", "dev-notes.rst", "help.rst", "hqtb/about-pipeline.rst", "hqtb/hqtb-config.rst", "hqtb/run-pipeline.rst", "hqtb/step-desc/analysis.rst", "hqtb/step-desc/bidirect_blast.rst", "hqtb/step-desc/gen_draft.rst", "hqtb/step-desc/refine-parts/annot.rst", "hqtb/step-desc/refine-parts/cleanup.rst", "hqtb/step-desc/refine-parts/extension.rst", "hqtb/step-desc/refine-parts/smooth.rst", "hqtb/step-desc/refinement.rst", "hqtb/step-desc/validation.rst", "index.rst", "installation.rst", "modules/classes.rst", "modules/cmd.rst", "modules/cmpb.rst", "modules/core.rst", "modules/hqtb.rst", "modules/util.rst", "overview-pipes.rst", "pipeline_idea.rst", "specimen.rst"], "titles": ["About CMPB", "CMPB Configuration File", "Run the CMPB Pipeline", "Notes for Developers", "Help & FAQ", "About HQTB", "HQTB Configuration File", "Run the HTQB Pipeline", "5. Step 5: Analyse the Model", "1. Step 1: Bidirectional BLAST", "2. Step 2: Generate a Draft Model", "3.3. Step 3, Part 3: Further Annotate the Model", "3.2. Step 3, Part 2: Cleaning the Model", "3.1. Step 3, Part 1: Extending the Model", "3.4. Step 3, Part 4: Smoothing", "3. Step 3: Further Refine the Model", "4. Step 4: Model Validation", "Welcome to SPECIMEN!", "Installation", "specimen.classes package", "The specimen.cmd_access submodule", "specimen.cmpb package", "specimen.hqtb.core package", "specimen.hqtb package", "specimen.util package", "Overview of the Pipelines", "PGAB: From genome sequence to draft model", "Contents of SPECIMEN"], "terms": {"under": [0, 1, 10, 20, 22, 24, 25], "construct": [0, 7, 10, 20, 25], "The": [0, 1, 2, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27], "carvem": [0, 1, 2, 17, 21, 24, 26], "modelpolish": [0, 2, 17, 24], "base": [0, 1, 2, 3, 5, 6, 7, 9, 10, 16, 17, 19, 20, 22, 23, 24, 26], "below": [1, 3, 6, 8, 9, 10, 14, 16, 25, 27], "underli": [1, 6, 22], "default": [1, 6, 19, 20, 21, 22, 23, 24], "i": [1, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 20, 22, 24, 25, 26, 27], "list": [1, 5, 6, 7, 20, 22, 27], "specimen": [1, 2, 3, 5, 7, 18], "pipelin": [1, 3, 4, 6, 8, 9, 10, 11, 12, 15, 16, 20, 21, 22, 23, 24, 26], "explain": [1, 2, 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\ No newline at end of file
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"whether": [1, 7, 22], "which": [1, 16, 20, 22, 24, 25, 27], "while": [4, 7, 18], "whole": [1, 20], "wish": [4, 25], "witha": 4, "without": [3, 22, 26], "work": [3, 10, 12, 22], "workflow": [2, 7, 9, 10, 17, 22, 26, 27], "working_dir": 22, "wrapper": [5, 7, 20, 21, 22], "wrapper_pipelin": [7, 23], "write": [4, 24], "written": 4, "x": [3, 6], "xin": [9, 10], "xlsx": 1, "xref": 20, "yaml": [2, 7, 23, 24], "yara": [9, 10], "ye": 26, "yet": [3, 4, 22], "ylgn": [1, 19], "you": [3, 4, 7, 25], "your": [2, 3, 5, 7, 20, 22, 25, 26], "your_folder_nam": 7, "\u00e4": [7, 17], "\u00f6": [7, 17]}, "titles": ["About CMPB", "CMPB Configuration File", "Run the CMPB Pipeline", "Notes for Developers", "Help & FAQ", "About HQTB", "HQTB Configuration File", "Run the HTQB Pipeline", "5. Step 5: Analyse the Model", "1. Step 1: Bidirectional BLAST", "2. Step 2: Generate a Draft Model", "3.3. Step 3, Part 3: Further Annotate the Model", "3.2. Step 3, Part 2: Cleaning the Model", "3.1. Step 3, Part 1: Extending the Model", "3.4. Step 3, Part 4: Smoothing", "3. Step 3: Further Refine the Model", "4. Step 4: Model Validation", "Welcome to SPECIMEN!", "Installation", "specimen.classes package", "The specimen.cmd_access submodule", "specimen.cmpb package", "specimen.hqtb.core package", "specimen.hqtb package", "specimen.util package", "Overview of the Pipelines", "PGAB: From genome sequence to draft model", "Contents of SPECIMEN"], "titleterms": {"1": [9, 13], "2": [10, 12], "3": [11, 12, 13, 14, 15], "4": [14, 16], "5": 8, "The": 20, "about": [0, 5], "analys": 8, "analysi": 22, "annot": [11, 22], "avail": 17, "base": 25, "bidirect": 9, "bidirectional_blast": 22, "blast": 9, "bug": 4, "can": 4, "carvem": 25, "cite": 17, "class": 19, "clean": 12, "cleanup": 22, "cmd_access": 20, "cmpb": [0, 1, 2, 21, 25], "collect": [2, 7], "configur": [1, 6], "content": [17, 27], "core": 22, "current": 3, "data": [2, 7], "develop": 3, "document": 3, "draft": [10, 26], "extend": 13, "extens": 22, "faq": 4, "file": [1, 6], "from": 26, "further": [11, 15, 25], "gener": [10, 20], "generate_draft_model": 22, "genom": 26, "github": 18, "help": 4, "high": 25, "how": 17, "hqtb": [5, 6, 7, 22, 23, 25], "htqb": 7, "i": 4, "idea": 25, "inform": [3, 25], "instal": 18, "issu": 4, "known": 4, "model": [8, 10, 11, 12, 13, 15, 16, 26], "modelpolish": 25, "modul": 24, "more": 25, "namespac": 4, "note": 3, "option": 20, "organ": 4, "overview": [0, 5, 25], "packag": [19, 21, 22, 23, 24], "part": [11, 12, 13, 14], "pgab": 26, "pipelin": [0, 2, 5, 7, 17, 25], "pydant": 4, "qualiti": 25, "quickstart": [2, 7], "refin": [15, 20, 22], "report": 19, "run": [2, 7, 20], "sequenc": 26, "set_up": 24, "setup": 20, "smooth": [14, 22], "specimen": [4, 17, 19, 20, 21, 22, 23, 24, 27], "statu": 3, "step": [8, 9, 10, 11, 12, 13, 14, 15, 16], "submodul": [19, 20, 21, 22, 23, 24, 27], "subpackag": [22, 23, 27], "templat": 25, "us": 4, "util": 24, "valid": [16, 22], "via": 18, "welcom": 17, "which": 4, "work": 4, "workflow": [21, 23]}})
\ No newline at end of file
diff --git a/docs/build/html/specimen.html b/docs/build/html/specimen.html
index c724403..8d8a481 100644
--- a/docs/build/html/specimen.html
+++ b/docs/build/html/specimen.html
@@ -19,7 +19,7 @@
-
+
diff --git a/docs/source/images/genome2draft.png b/docs/source/images/genome2draft.png
new file mode 100644
index 0000000..5239b6b
Binary files /dev/null and b/docs/source/images/genome2draft.png differ
diff --git a/docs/source/images/genome2draft.svg b/docs/source/images/genome2draft.svg
deleted file mode 100644
index 8c07bb3..0000000
--- a/docs/source/images/genome2draft.svg
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-
-
\ No newline at end of file
diff --git a/docs/source/pipeline_idea.rst b/docs/source/pipeline_idea.rst
index d93a94e..772be29 100644
--- a/docs/source/pipeline_idea.rst
+++ b/docs/source/pipeline_idea.rst
@@ -32,7 +32,7 @@ workflow in Figure :numref:`pgab_workflow` can be used.
.. _pgab_workflow:
-.. figure:: images/genome2draft.svg
+.. figure:: images/genome2draft.png
:alt: Workflow from genome sequence to a draft model
Workflow from genome sequence to a draft model