Mercurial > repos > iuc > hyphy_summary
changeset 3:bd90215b7d15 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"
| author | iuc |
|---|---|
| date | Sat, 03 Jul 2021 08:53:45 +0000 |
| parents | d7c01f81739b |
| children | 11fc6218365d |
| files | hyphy_summary.xml scripts/hyphy_summary.py test-data/summary/ORF6-segment.json test-data/summary/merged-segment.json test-data/summary/merged-site.json test-data/summary/nsp7-segment.json test-data/summary/nsp8-segment.json test-data/summary/nsp8-site.json |
| diffstat | 8 files changed, 68668 insertions(+), 198 deletions(-) [+] |
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--- a/hyphy_summary.xml Fri Jun 18 15:37:03 2021 +0000 +++ b/hyphy_summary.xml Sat Jul 03 08:53:45 2021 +0000 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="hyphy_summary" version="1.1.0" name="HyPhy-Summary" profile="21.01"> +<tool id="hyphy_summary" version="1.2.0" name="HyPhy-Summary" profile="21.01"> <description>generate summary report of HyPhy analyses</description> <requirements> - <requirement type="package" version="0.19.7">python-bioext</requirement> + <requirement type="package" version="0.20.1">python-bioext</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/scripts/hyphy_summary.py' @@ -97,19 +97,19 @@ <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" /> </when> <when value="merge"> - <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Segment annotations to merge" /> - <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Site annotations to merge" /> + <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Summaries to merge" /> + <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Annotations to merge" /> </when> </conditional> </inputs> <outputs> - <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Segment annotations" /> - <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Site annotations" /> + <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Summary" /> + <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Annotation" /> </outputs> <tests> <test> <param name="mode" value="summary" /> - <param name="name" value="epi_isl_1009769" /> + <param name="name" value="REFERENCE" /> <param name="gene" value="nsp8" /> <param name="combined" value="summary/nsp8.combined.fas" /> <param name="fade" value="summary/nsp8.FADE.json" /> @@ -128,7 +128,7 @@ </test> <test> <param name="mode" value="summary" /> - <param name="name" value="epi_isl_1009769" /> + <param name="name" value="REFERENCE" /> <param name="gene" value="ORF6" /> <param name="combined" value="summary/ORF6.combined.fas" /> <param name="fade" value="summary/ORF6.FADE.json" /> @@ -140,7 +140,7 @@ </test> <test> <param name="mode" value="summary" /> - <param name="name" value="epi_isl_1009769" /> + <param name="name" value="REFERENCE" /> <param name="gene" value="nsp7" /> <param name="combined" value="summary/nsp7.combined.fas" /> <param name="fade" value="summary/nsp7.FADE.json" />
--- a/scripts/hyphy_summary.py Fri Jun 18 15:37:03 2021 +0000 +++ b/scripts/hyphy_summary.py Sat Jul 03 08:53:45 2021 +0000 @@ -107,7 +107,7 @@ if self.cfel is None: return node_tags = {} - _ = self._newick_parser(self.cfel['input']['trees']['0'], False, node_tags, self.cfel)['json'] + _ = newick_parser(self.cfel['input']['trees']['0'], False, node_tags, self.cfel, self.arguments, self.labels)['json'] if self.summary_json is not None: omegas = {} T = {} @@ -191,7 +191,7 @@ return defaultdict(int) compressed_subs = {} node_tags = {} - the_tree = self._newick_parser(self.slac['input']['trees']['0'], False, node_tags, self.slac)['json'] + the_tree = newick_parser(self.slac['input']['trees']['0'], False, node_tags, self.slac, self.arguments, self.labels) root_node = None if self.summary_json is not None: for branch, info in self.slac['branch attributes']['0'].items(): @@ -210,9 +210,9 @@ if gs[0] >= 0: self.labels[root_node] = self.slac['branch attributes']['0'][root_node]['codon'][0][i] try: - self._traverse_tree_in_order(the_tree, self.slac['branch attributes']['0'], i, None, root_node) + traverse_tree_in_order(the_tree, self.labels, self.slac['branch attributes']['0'], i, None, root_node) except Exception: - raise + pass compressed_subs[gs[0]] = self.labels for k in set([k[0] for k in node_tags.values()]): if len(k): @@ -433,195 +433,201 @@ gene_name = 'N/A' return (genomic_site_coord, gene_name, gene_site) - def _traverse_tree_in_order(self, node, slac_data, i, parent_tag, root): - node_tag = None - if node is None: - return - try: - nn = root if node['name'] == 'root' else node['name'] - except Exception: - raise - if nn in slac_data: - node_tag = slac_data[nn]['codon'][0][i] - if (parent_tag != node_tag): - self.labels[nn] = node_tag - self.labels[node['name']] = node_tag - if 'children' in node: - for c in node['children']: - if c is not None: - if 'name' in c: - self._traverse_tree_in_order(c, slac_data, i, node_tag, root) - - def _match_node_names(self, qry_node, ref_node, mapping): - if 'children' in qry_node and 'children' in ref_node: - mapping[ref_node['name']] = qry_node['name'] - if len(qry_node['children']) != len(ref_node['children']): - raise Exception('Internal topology mismatch') - for i, n in enumerate(ref_node['children']): - self._match_node_names(qry_node['children'][i], n, mapping) - elif 'children' in qry_node: - raise Exception('Topology mismatch') - elif 'children' in ref_node: - raise Exception('Topology mismatch') - else: - if qry_node['name'] != ref_node['name']: - raise Exception('Leaf name mismatch') - def _get_incoming_labels(self): json_data = self._load_json(self.arguments.labels) self.incoming_labels = json_data - def _newick_parser(self, nwk_str, bootstrap_values, track_tags, json_map): - clade_stack = [] - automaton_state = 0 - current_node_name = '' - current_node_attribute = '' - current_node_annotation = '' - quote_delimiter = None - name_quotes = {"'": 1, '"': 1} - def add_new_tree_level(): - new_level = {'name': None} - the_parent = clade_stack[len(clade_stack) - 1] - if ('children' not in the_parent): - the_parent['children'] = [] - clade_stack.append(new_level) - the_parent['children'].append(clade_stack[len(clade_stack) - 1]) - clade_stack[len(clade_stack) - 1]['original_child_order'] = len(the_parent['children']) +def traverse_tree_in_order(node, labels, slac_data, i, parent_tag, root): + node_tag = None + if 'name' not in node: + nn = root + else: + nn = root if node["name"] == 'root' else node["name"] + if nn in slac_data: + node_tag = slac_data[nn]["codon"][0][i] + if (parent_tag != node_tag): + labels[nn] = node_tag + labels[node["name"]] = node_tag + if "children" in node: + for c in node["children"]: + traverse_tree_in_order(c, labels, slac_data, i, node_tag, root) + + +def newick_parser(nwk_str, bootstrap_values, track_tags, json_map, import_settings, tags): + clade_stack = [] + automaton_state = 0 + current_node_name = "" + current_node_attribute = "" + current_node_annotation = "" + quote_delimiter = None + name_quotes = { + "'": 1, + '"': 1 + } - def finish_node_definition(): - nonlocal current_node_name - nonlocal current_node_annotation - nonlocal current_node_attribute - this_node = clade_stack.pop() - if (bootstrap_values and 'children' in this_node): - this_node['bootstrap_values'] = current_node_name - else: - this_node['name'] = current_node_name - this_node['attribute'] = current_node_attribute - this_node['annotation'] = current_node_annotation - try: - if 'children' not in this_node: - node_tag = self.arguments.default_tag - if json_map: - tn = json_map['branch attributes']['0'][this_node['name']] - else: - tn = this_node - nn = tn['original name'] if 'original name' in tn else tn['name'] - for k, v in self.incoming_labels.items(): - if nn.find(k) >= 0: - node_tag = v - break + def add_new_tree_level(): + new_level = { + "name": None + } + the_parent = clade_stack[len(clade_stack) - 1] + if "children" not in the_parent: + the_parent["children"] = [] + + clade_stack.append(new_level) + the_parent["children"].append(clade_stack[len(clade_stack) - 1]) + clade_stack[len(clade_stack) - 1]["original_child_order"] = len(the_parent["children"]) + + def finish_node_definition(): + nonlocal current_node_name + nonlocal current_node_annotation + nonlocal current_node_attribute + + this_node = clade_stack.pop() + if (bootstrap_values and "children" in this_node): + this_node["bootstrap_values"] = current_node_name + else: + this_node["name"] = current_node_name + + this_node["attribute"] = current_node_attribute + this_node["annotation"] = current_node_annotation + + try: + + if 'children' not in this_node: + node_tag = import_settings.default_tag + if json_map: + tn = json_map["branch attributes"]["0"][this_node["name"]] else: - counts = {} - node_tag = '' - for n in this_node['children']: - counts[n['tag']] = 1 + (counts[n['tag']] if n['tag'] in counts else 0) - if len(counts) == 1: - node_tag = list(counts.keys())[0] - this_node['tag'] = node_tag - except Exception: - raise - if track_tags is not None: - track_tags[this_node['name']] = [this_node['tag'], 'children' in this_node] - current_node_name = '' - current_node_attribute = '' - current_node_annotation = '' + tn = this_node + nn = tn["original name"] if "original name" in tn else tn["name"] + for k, v in tags.items(): + if nn.find(k) >= 0: + node_tag = v + break + else: + counts = {} + node_tag = "" + for n in this_node['children']: + counts[n["tag"]] = 1 + (counts[n["tag"]] if n["tag"] in counts else 0) + if len(counts) == 1: + node_tag = list(counts.keys())[0] + + this_node["tag"] = node_tag + except Exception as e: + pass + print(e) + + if track_tags is not None: + track_tags[this_node["name"]] = [this_node["tag"], 'children' in this_node] + + current_node_name = "" + current_node_attribute = "" + current_node_annotation = "" + + def generate_error(location): + return { + 'json': None, + 'error': + "Unexpected '%s' in '%s[ERROR HERE]%s'" % (nwk_str[location], nwk_str[location - 20:location + 1], nwk_str[location + 1:location + 20]) + } + + tree_json = { + "name": "root" + } + + clade_stack.append(tree_json) - def generate_error(location): - unexpected = nwk_str[location] - before = nwk_str[location - 20:location + 1] - after = nwk_str[location + 1:location + 20] - return { - 'json': None, - 'error': 'Unexpected %s in %s [ERROR HERE] %s' % (unexpected, before, after) - } - tree_json = {'name': 'root'} - clade_stack.append(tree_json) - space = re.compile(r'\s') - for char_index in range(len(nwk_str)): - try: - current_char = nwk_str[char_index] - if automaton_state == 0: - # look for the first opening parenthesis - if (current_char == '('): + space = re.compile(r"\s") + + for char_index in range(len(nwk_str)): + try: + current_char = nwk_str[char_index] + if automaton_state == 0: + # look for the first opening parenthesis + if (current_char == "("): + add_new_tree_level() + automaton_state = 1 + elif automaton_state == 1 or automaton_state == 3: + # case 1: // name + # case 3: { // branch length + # reading name + if (current_char == ":"): + automaton_state = 3 + elif current_char == "," or current_char == ")": + try: + finish_node_definition() + automaton_state = 1 + if (current_char == ","): + add_new_tree_level() + except Exception as e: + return generate_error(char_index) + print(e) + + elif (current_char == "("): + if len(current_node_name) > 0: + return generate_error(char_index) + else: add_new_tree_level() - automaton_state = 1 - elif automaton_state == 1 or automaton_state == 3: - # case 1: // name - # case 3: { // branch length - # reading name - if (current_char == ':'): - automaton_state = 3 - elif current_char == ',' or current_char == ')': - try: - finish_node_definition() - automaton_state = 1 - if (current_char == ','): - add_new_tree_level() - except Exception: - return generate_error(char_index) - elif (current_char == '('): - if len(current_node_name) > 0: + + elif (current_char in name_quotes): + if automaton_state == 1 and len(current_node_name) == 0 and len(current_node_attribute) == 0 and len(current_node_annotation) == 0: + automaton_state = 2 + quote_delimiter = current_char + continue + return generate_error(char_index) + else: + if (current_char == "["): + if len(current_node_annotation): return generate_error(char_index) else: - add_new_tree_level() - elif (current_char in name_quotes): - if automaton_state == 1 and len(current_node_name) == 0 and len(current_node_attribute) == 0 and len(current_node_annotation) == 0: - automaton_state = 2 - quote_delimiter = current_char - continue - return generate_error(char_index) + automaton_state = 4 else: - if (current_char == '['): - if len(current_node_annotation): - return generate_error(char_index) - else: - automaton_state = 4 + if (automaton_state == 3): + current_node_attribute += current_char else: - if (automaton_state == 3): - current_node_attribute += current_char - else: - if (space.search(current_char)): - continue - if (current_char == ';'): - char_index = len(nwk_str) - break - current_node_name += current_char - elif automaton_state == 2: - # inside a quoted expression - if (current_char == quote_delimiter): - if (char_index < len(nwk_str - 1)): - if (nwk_str[char_index + 1] == quote_delimiter): - char_index += 1 - current_node_name += quote_delimiter + if (space.search(current_char)): continue - quote_delimiter = 0 - automaton_state = 1 + if (current_char == ""): + char_index = len(nwk_str) + break + current_node_name += current_char + elif automaton_state == 2: + # inside a quoted expression + if (current_char == quote_delimiter): + if (char_index < len(nwk_str - 1)): + if (nwk_str[char_index + 1] == quote_delimiter): + char_index += 1 + current_node_name += quote_delimiter continue - else: - current_node_name += current_char - elif automaton_state == 4: - # inside a comment / attribute - if (current_char == ']'): - automaton_state = 3 - else: - if (current_char == '['): - return generate_error(char_index) - current_node_annotation += current_char - except Exception: - return generate_error(char_index) - if (len(clade_stack) != 1): - return generate_error(len(nwk_str) - 1) + quote_delimiter = 0 + automaton_state = 1 + continue + else: + current_node_name += current_char + elif automaton_state == 4: + # inside a comment / attribute + if (current_char == "]"): + automaton_state = 3 + else: + if (current_char == "["): + return generate_error(char_index) + current_node_annotation += current_char + except Exception as e: + return generate_error(char_index) + print(e) - if (len(current_node_name)): - tree_json['name'] = current_node_name + if (len(clade_stack) != 1): + return generate_error(len(nwk_str) - 1) - return { - 'json': tree_json, - 'error': None - } + if (len(current_node_name)): + tree_json['name'] = current_node_name + + return { + 'json': tree_json, + 'error': None + } if __name__ == '__main__':
--- a/test-data/summary/ORF6-segment.json Fri Jun 18 15:37:03 2021 +0000 +++ b/test-data/summary/ORF6-segment.json Sat Jul 03 08:53:45 2021 +0000 @@ -1,7 +1,1135 @@ { "ORF6": { - "map": [], + "map": [ + 27201, + 27204, + 27207, + 27210, + 27213, + 27216, + 27219, + 27222, + 27225, + 27228, + 27231, + 27234, + 27237, + 27240, + 27243, + 27246, + 27249, + 27252, + 27255, + 27258, + 27261, + 27264, + 27267, + 27270, + 27273, + 27276, + 27279, + 27282, + 27285, + 27288, + 27291, + 27294, + 27297, + 27300, + 27303, + 27306, + 27309, + 27312, + 27315, + 27318, + 27321, + 27324, + 27327, + 27330, + 27333, + 27336, + 27339, + 27342, + 27345, + 27348, + 27351, + 27354, + 27357, + 27360, + 27363, + 27366, + 27369, + 27372, + 27375, + 27378, + 27381 + ], "tree": 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