| Previous changeset 38:9f71cd7b2554 (2026-02-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit cee1ce4bd7d82088b9bf62403bc175c13223e020 |
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modified:
macros.xml |
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added:
scripts/infer_stasis_clusters.py test-data/bstill-in1.json |
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removed:
scripts/hyphy_summary.py |
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| diff -r 9f71cd7b2554 -r 07774580b606 macros.xml --- a/macros.xml Wed Feb 25 20:58:10 2026 +0000 +++ b/macros.xml Wed Mar 11 11:17:55 2026 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.5.93</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">2.5.96</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">24.0</token> <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token> |
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| diff -r 9f71cd7b2554 -r 07774580b606 scripts/hyphy_summary.py --- a/scripts/hyphy_summary.py Wed Feb 25 20:58:10 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,679 +0,0 @@\n-import argparse\n-import json\n-import re\n-from collections import defaultdict\n-\n-import BioExt\n-from Bio import SeqIO\n-from Bio.Seq import Seq\n-from Bio.SeqRecord import SeqRecord\n-from BioExt.uds import _align_par\n-\n-\n-class HyPhySummary(object):\n-\n- def __init__(self, arguments, summary_json=None, annotation_json=None):\n- self.arguments = arguments\n- self.ref_map = ''\n- self.summary_json = {}\n- self.annotation_json = {}\n- self.include_in_annotation = {}\n- self.test_map = {}\n- self.site_reports = {}\n- self.labels = {}\n- self.ref_seq_map = []\n- self.cfel = {}\n- self.relax = {}\n- self.busted = {}\n- self.slac = {}\n- self.fel = {}\n- self.meme = {}\n- self.meme_full = {}\n- self.prime = {}\n- self.fade = {}\n- self.bgm = {}\n- self.ref_genes = [\n- ['genome', 'ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGG"..b" return generate_error(char_index)\n- current_node_annotation += current_char\n- except Exception as e:\n- return generate_error(char_index)\n- print(e)\n-\n- if (len(clade_stack) != 1):\n- return generate_error(len(nwk_str) - 1)\n-\n- if (len(current_node_name)):\n- tree_json['name'] = current_node_name\n-\n- return {\n- 'json': tree_json,\n- 'error': None\n- }\n-\n-\n-if __name__ == '__main__':\n- parser = argparse.ArgumentParser(description='Summarize selection analysis results.')\n- parser.add_argument('--combined', help='Combined reference and query alignment from TN-93', required=False, type=str)\n- parser.add_argument('--pvalue', help='p-value to use', required=False, type=float, default=0.05)\n- parser.add_argument('--gene', help='Name of the gene or sequence being analyzed', required=False, type=str)\n- parser.add_argument('--labels', help='JSON file with labels', required=False, type=str)\n- parser.add_argument('--annotation-output', help='Write a JSON file with site annotations', required=True, type=str)\n- parser.add_argument('--summary-output', help='Write a JSON file here segment annotations', required=True, type=str)\n- parser.add_argument('--annotation-inputs', help='Comma-separated list of site annotation files to merge', required=False, type=str)\n- parser.add_argument('--summary-inputs', help='Comma-separated list of segment annotation files to merge', required=False, type=str)\n- parser.add_argument('--default-tag', help='Default name for sequences that have no explicit label', required=False, type=str, default='Reference')\n- parser.add_argument('--name', help='The sequence ID to highlight', required=False, default='MN908947')\n- parser.add_argument('--mode', help='Operation mode, generate a summary or merge multiple summaries', type=str, choices=['summary', 'merge'], default='summary')\n- parser.add_argument('--relax', help='Path to RELAX.json file', required=False, type=str)\n- parser.add_argument('--busted', help='Path to BUSTED.json file', required=False, type=str)\n- parser.add_argument('--slac', help='Path to SLAC.json file', required=False, type=str)\n- parser.add_argument('--fel', help='Path to FEL.json file', required=False, type=str)\n- parser.add_argument('--cfel', help='Path to CFEL.json file', required=False, type=str)\n- parser.add_argument('--meme', help='Path to MEME.json file', required=False, type=str)\n- parser.add_argument('--meme-full', help='Path to MEME-full.json file', dest='meme_full', required=False, type=str)\n- parser.add_argument('--prime', help='Path to PRIME.json file', required=False, type=str)\n- parser.add_argument('--fade', help='Path to FADE.json file', required=False, type=str)\n- parser.add_argument('--bgm', help='Path to BGM.json file', required=False, type=str)\n- arguments = parser.parse_args()\n- if arguments.mode == 'summary':\n- analyzer = HyPhySummary(arguments)\n- annotation_json, summary_json = analyzer.summary()\n- if annotation_json is not None:\n- with open(arguments.annotation_output, 'w') as fh:\n- json.dump(annotation_json, fh, indent=1)\n- if summary_json is not None:\n- with open(arguments.summary_output, 'w') as fh:\n- json.dump(summary_json, fh, indent=1)\n- else:\n- summary = {}\n- annotation = {}\n- for filename in arguments.annotation_inputs.split(','):\n- with open(filename, 'r') as fh:\n- annotation.update(json.load(fh))\n- for filename in arguments.summary_inputs.split(','):\n- with open(filename, 'r') as fh:\n- summary.update(json.load(fh))\n- with open(arguments.annotation_output, 'w') as fh:\n- json.dump(annotation, fh, indent=1)\n- with open(arguments.summary_output, 'w') as fh:\n- json.dump(summary, fh, indent=1)\n- exit(0)\n" |
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| diff -r 9f71cd7b2554 -r 07774580b606 scripts/infer_stasis_clusters.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/infer_stasis_clusters.py Wed Mar 11 11:17:55 2026 +0000 |
| [ |
| @@ -0,0 +1,171 @@ +#!/usr/bin/env python3 +""" +B-STILL Stasis Cluster Inference Tool +==================================== +Identifies regional footprints of extreme purifying selection (stasis) in B-STILL +JSON results using a FWER-controlled Hypergeometric Scan Statistic. + +Usage: + python3 infer_stasis_clusters.py input.json --ebf 10 --permutations 10000 --output results.json +""" + +import argparse +import json +import sys +import time + +import numpy as np +from scipy.stats import hypergeom + + +def get_sf_optimized(n, d, L, K, cache): + """Retrieves or computes Hypergeometric Survival Function value.""" + key = (n, d) + if key not in cache: + cache[key] = hypergeom.sf(n - 1, L, K, d) + return cache[key] + + +def scan_intervals(indices, L, K, max_size, sf_cache, threshold=None): + """ + Scans all possible intervals [i, j] anchored by stasis events. + Returns the minimum p-value if threshold is None, else returns all significant segments. + """ + best_p = 1.0 + segments = [] + num_events = len(indices) + + for n in range(3, min(max_size + 1, num_events + 1)): + for i in range(num_events - n + 1): + d = indices[i + n - 1] - indices[i] + 1 + p = get_sf_optimized(n, d, L, K, sf_cache) + + if threshold is None: + if p < best_p: + best_p = p + else: + if p <= threshold: + segments.append({ + "start": int(indices[i] + 1), + "end": int(indices[i + n - 1] + 1), + "p_value": p, + "k": n, + "d": int(d) + }) + + return best_p if threshold is None else segments + + +def merge_segments(segments, merge_dist=15): + """Merges overlapping or nearby significant segments.""" + if not segments: + return [] + segments.sort(key=lambda x: x['start']) + + merged = [] + curr = segments[0] + for next_s in segments[1:]: + if next_s['start'] <= curr['end'] + merge_dist: + curr['end'] = max(curr['end'], next_s['end']) + curr['p_value'] = min(curr['p_value'], next_s['p_value']) + curr['d'] = curr['end'] - curr['start'] + 1 + else: + merged.append(curr) + curr = next_s + merged.append(curr) + return merged + + +def main(): + parser = argparse.ArgumentParser(description="Infer stasis clusters from B-STILL JSON.") + parser.add_argument("input", help="Path to B-STILL JSON result file") + parser.add_argument("--ebf", type=float, default=10.0, help="EBF threshold for defining stasis sites (default: 10.0)") + parser.add_argument("--permutations", type=int, default=10000, help="Number of permutations for FWER control (default: 10000)") + parser.add_argument("--alpha", type=float, default=0.05, help="Family-wise error rate threshold (default: 0.05)") + parser.add_argument("--max-cluster", type=int, default=30, help="Maximum number of stasis sites per interval scan (default: 30)") + parser.add_argument("--merge", type=int, default=15, help="Distance in codons to merge adjacent clusters (default: 15)") + parser.add_argument("--output", help="Path to save results in JSON format") + + args = parser.parse_args() + + try: + with open(args.input, "r") as f: + data = json.load(f) + except Exception as e: + print("Error loading JSON: {0}".format(e)) + sys.exit(1) + + sites = data.get("MLE", {}).get("content", {}).get("0", []) + ebfs = [s[12] if (len(s) > 12 and isinstance(s[12], (int, float))) else 0 for s in sites] + L = len(ebfs) + + if L < 10: + print("Alignment too short for cluster analysis.") + sys.exit(0) + + stasis_indices = np.array([i for i, val in enumerate(ebfs) if val >= args.ebf]) + K = len(stasis_indices) + + print("--- B-STILL Cluster Inference ---") + print("Input: {0}".format(args.input)) + print("Gene Length (L): {0} codons".format(L)) + print("Stasis Sites (K): {0} (EBF >= {1})".format(K, args.ebf)) + + if K < 3: + print("Insufficient stasis sites to form clusters (minimum 3 required).") + sys.exit(0) + + print("Running {0} permutations for FWER control...".format(args.permutations)) + null_min_ps = [] + all_positions = np.arange(L) + sf_cache = {} + + start_time = time.time() + for i in range(args.permutations): + if i > 0 and i % 1000 == 0: + elapsed = time.time() - start_time + print(" Processed {0} permutations... ({1:.1f} per sec)".format(i, i / elapsed)) + shuffled = sorted(np.random.choice(all_positions, K, replace=False)) + min_p = scan_intervals(shuffled, L, K, args.max_cluster, sf_cache) + null_min_ps.append(min_p) + + crit_p = np.percentile(null_min_ps, args.alpha * 100) + print("Gene-specific Critical P-value (FWER {0}): {1:.2e}".format(args.alpha, crit_p)) + + print("Scanning observed sequence for significant clusters...") + raw_segments = scan_intervals(stasis_indices, L, K, args.max_cluster, sf_cache, threshold=crit_p) + + final_clusters = merge_segments(raw_segments, merge_dist=args.merge) + + for c in final_clusters: + c['k'] = sum(1 for idx in stasis_indices if c['start'] <= idx + 1 <= c['end']) + + print("\nFound {0} significant stasis clusters:".format(len(final_clusters))) + if final_clusters: + print("\nLegend:") + print(" k : Number of high-confidence stasis sites within the cluster") + print(" d : Total span of the cluster in codons") + print("\n{:<8} | {:<8} | {:<5} | {:<5} | {:<10}".format("Start", "End", "k", "d", "P-value")) + print("-" * 45) + for c in final_clusters: + print("{:<8} | {:<8} | {:<5} | {:<5} | {:.2e}".format(c['start'], c['end'], c['k'], c['d'], c['p_value'])) + + if args.output: + output_data = { + "input_file": args.input, + "parameters": vars(args), + "summary": { + "gene_length": L, + "total_stasis_sites": K, + "critical_p_value": float(crit_p), + "num_clusters": len(final_clusters) + }, + "clusters": final_clusters + } + with open(args.output, "w") as f: + json.dump(output_data, f, indent=4) + print("\nDetailed results saved to {0}".format(args.output)) + + +if __name__ == "__main__": + main() |
| b |
| diff -r 9f71cd7b2554 -r 07774580b606 test-data/bstill-in1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bstill-in1.json Wed Mar 11 11:17:55 2026 +0000 |
| [ |
| b'@@ -0,0 +1,1880 @@\n+{\n+ "MLE": {\n+ "content": {\n+ "0": [\n+ [\n+ 2.37190144157317,\n+ 0.1886402906758332,\n+ 0.003967400746549269,\n+ 0.03170401941783556,\n+ 0.1405070629863407,\n+ 0.2478544806315437,\n+ 0.155938987532467,\n+ 0,\n+ 0,\n+ 1.668673069222721,\n+ 0.9606238475229101,\n+ 1.774898950889347,\n+ 1.224638397608354\n+ ],\n+ [\n+ 1.562666730096422,\n+ 0.7176422560937019,\n+ 0,\n+ 9.089104346594827e-07,\n+ 0,\n+ 0.01450154962095004,\n+ 0.2139088787662019,\n+ 0,\n+ 0,\n+ 0,\n+ 2.666666171615278e-05,\n+ 0,\n+ 0.05468540563699053\n+ ],\n+ [\n+ 0.6841064654452979,\n+ 0.6942845364725866,\n+ 0,\n+ 0.05269358336084695,\n+ 0,\n+ 0.07725223791333098,\n+ 0.5503080822201034,\n+ 0,\n+ 0,\n+ 0,\n+ 1.631978457912503,\n+ 0,\n+ 0.311129391337898\n+ ],\n+ [\n+ 1.603530309019734,\n+ 0.7640979882187913,\n+ 0,\n+ 9.480689290490966e-08,\n+ 0,\n+ 0.0129282189776549,\n+ 0.2196957351152485,\n+ 0,\n+ 0,\n+ 0,\n+ 2.781551610416608e-06,\n+ 0,\n+ 0.0486746608276061\n+ ],\n+ [\n+ 0.7745431936738028,\n+ 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}\n+ },\n+ "_comment": "Trimmed HyPhy B-STILL output (first 120 codon sites, first 13 metrics, removed posterior/grid/etc) to keep infer_stasis_clusters test input under planemo\'s 1MB lint limit."\n+}\n' |