c1f3643c3e308c7819a375ee5ea4170a45c679e5 hiram Wed Jun 26 14:51:38 2024 -0700 clean up cruft refs #32897 diff --git src/hg/hubApi/genomePriority.py src/hg/hubApi/genomePriority.py index 65e4830..fe7245a 100755 --- src/hg/hubApi/genomePriority.py +++ src/hg/hubApi/genomePriority.py @@ -1,495 +1,464 @@ #!/cluster/software/bin/python3 import subprocess import locale import sys import re import os import csv import requests from io import StringIO # special top priorities topPriorities = { 'hg38': 1, 'mm39': 2, 'hs1': 3, } ### key will be dbDb name, value will be priority number allPriorities = {} priorityCounter = len(topPriorities) + 1 #################################################################### def set_utf8_encoding(): """ Set UTF-8 encoding for stdin, stdout, and stderr in Python. """ if sys.stdout.encoding != 'utf-8': sys.stdout = open(sys.stdout.fileno(), mode='w', encoding='utf-8', buffering=1) if sys.stderr.encoding != 'utf-8': sys.stderr = open(sys.stderr.fileno(), mode='w', encoding='utf-8', buffering=1) #################################################################### def dbDbData(): # Run the MySQL command and capture the output as bytes result = subprocess.run( ["hgsql", "-hgenome-centdb", "-N", "-e", "SELECT name,scientificName,organism,taxId,sourceName,description FROM dbDb WHERE active=1;", "hgcentral"], stdout=subprocess.PIPE, stderr=subprocess.PIPE ) if result.returncode != 0: print(f"Error executing MySQL command: {result.stderr.decode('utf-8')}") exit(1) # Decode the output from bytes to string using utf-8 return result.stdout.decode('latin-1') #################################################################### ### given a URL to hgdownload file: /hubs/UCSC_GI.assemblyHubList.txt def readGenArkData(url): # Initialize a list to hold the dictionaries dataList = [] response = requests.get(url) response.raise_for_status() fileContent = response.text fileIo = StringIO(fileContent) reader = csv.reader(fileIo, delimiter='\t') for row in reader: if row and row[0].startswith('#'): continue dataDict = { "gcAccession": row[0], "asmName": row[1], "scientificName": row[2], "commonName": row[3], "taxId": row[4], "clade": row[5], } utf8Encoded= {k: v.encode('utf-8', 'ignore').decode('utf-8') if isinstance(v, str) else v for k, v in dataDict.items()} # Append the dictionary to the list dataList.append(utf8Encoded) # reset the list so that accessions such as GCF_000001405.40 # come before GCF_000001405.39 dataList.reverse() return dataList #################################################################### def dbDbCladeList(filePath): returnList = {} with open(filePath, 'r') as file: reader = csv.reader(file, delimiter='\t') for row in reader: if len(row) < 1: continue if row[0].startswith('#'): continue returnList[row[0]] = row[1] return returnList #################################################################### def readOrderTsv(clade): returnList = {} homeDir = os.environ.get('HOME') filePath = homeDir + "/kent/src/hg/makeDb/doc/" + clade + "AsmHub/" + clade + ".orderList.tsv" with open(filePath, 'r') as file: reader = csv.reader(file, delimiter='\t') for row in reader: returnList[row[0]] = row[1] return returnList #################################################################### # Define a key function for sorting by the first word, case insensitive def getFirstWordCaseInsensitive(row): firstWord = row.split('\t')[0] # Extract the first word return firstWord.lower() # Convert to lowercase for case-insensitive sorting #################################################################### def processDbDbData(data): # Initialize a list to hold the dictionaries dataList = [] # Split the data into lines (rows) rows = data.strip().split('\n') # reverse the rows so that names such as hg19 come before hg18 sortedRows = sorted(rows, key=getFirstWordCaseInsensitive, reverse=True) for row in sortedRows: # Split each row into columns columns = row.split('\t') # corresponds with the SELECT statement # name,scientificName,organism,taxId,sourceName,description # Create a dictionary for each row dataDict = { "name": columns[0], "scientificName": columns[1], "organism": columns[2], "taxId": columns[3], "sourceName": columns[4], "description": columns[5], } utf8Encoded= {k: v.encode('utf-8', 'ignore').decode('utf-8') if isinstance(v, str) else v for k, v in dataDict.items()} # Append the dictionary to the list dataList.append(utf8Encoded) return dataList #################################################################### # Function to remove non-alphanumeric characters def removeNonAlphanumeric(s): # Ensure string type if isinstance(s, str): reSub = re.sub(r'[^a-zA-Z0-9_]', ' ', s).strip() return re.sub(r'\s+', ' ', reSub) else: return s # Return as-is for non-string types #################################################################### def eliminateDupWords(s): # Split the sentence into words words = s.split() # Initialize a set to keep track of unique words encountered seenWords = set() # List to store the words with duplicates removed resultWords = [] for word in words: # Convert word to lowercase for case-insensitive comparison lowerWord = word.lower() # Check if the lowercase version of the word has been seen before if lowerWord not in seenWords: # If not seen, add it to the result list and mark as seen resultWords.append(word) seenWords.add(lowerWord) # Join the words back into a single string return ' '.join(resultWords) #################################################################### def establishPriorities(dbDb, genArk): global topPriorities global allPriorities global priorityCounter totalItemCount = 0 - print(f"### setting priorities, {len(dbDb):4} dbDb genomes, {len(genArk):4} genArk genomes") + expectedTotal = len(dbDb) + len(genArk) + print(f"### expected total: {expectedTotal:4} = {len(dbDb):4} dbDb genomes + {len(genArk):4} genArk genomes") itemCount = 0 for name, priority in topPriorities.items(): allPriorities[name] = priority itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\ttopPriorities count: {itemCount:4}") primateList = readOrderTsv('primates') mammalList = readOrderTsv('mammals') versionScan = {} # key is dbDb name without number version extension, # value is highest version number seen for this bare # name highestVersion = {} # key is dbDb name without number version extension, # value is the full dbDb name for the highest version # of this dbDb name allDbDbNames = {} # key is the full dbDb name, value is its version itemCount = 0 # scanning the dbDb entries, figure out the highest version number # of each name for item in dbDb: dbDbName = item['name'] splitMatch = re.match("([a-zA-Z]+)(\d+)", dbDbName) if splitMatch: allDbDbNames[dbDbName] = splitMatch.group(2) itemCount += 1 if splitMatch.group(1) in versionScan: if splitMatch.group(2) > versionScan[splitMatch.group(1)]: versionScan[splitMatch.group(1)] = splitMatch.group(2) highestVersion[splitMatch.group(1)] = dbDbName else: versionScan[splitMatch.group(1)] = splitMatch.group(2) highestVersion[splitMatch.group(1)] = dbDbName else: print("### dbDb name does not split: ", dbDbName) allDbDbNames[dbDbName] = 0 itemCount += 1 dbDbLen = len(dbDb) itemCount = 0 # homo sapiens come before anything else for item in dbDb: dbDbName = item['name'] if dbDbName not in allPriorities: sciName = item['scientificName'] if sciName.lower() == "homo sapiens": allPriorities[dbDbName] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tdbDb homo sapiens count: {itemCount:3}") itemCount = 0 # and now the GenArk homo sapiens should be lined up here next, # GCF/RefSeq first for item in genArk: gcAccession = item['gcAccession'] if not gcAccession.startswith("GCF_"): continue if gcAccession not in allPriorities: sciName = item['scientificName'] if sciName.lower() == "homo sapiens": allPriorities[gcAccession] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCF homo sapiens count: {itemCount:4}") itemCount = 0 # and now the GenArk homo sapiens should be lined up here next, # GCA/GenBank second for item in genArk: gcAccession = item['gcAccession'] if not gcAccession.startswith("GCA_"): continue if gcAccession not in allPriorities: sciName = item['scientificName'] if sciName.lower() == "homo sapiens": allPriorities[gcAccession] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCA homo sapiens count: {itemCount:4}") itemCount = 0 # the primates, GCF/RefSeq first for asmId, commonName in primateList.items(): gcAcc = asmId.split('_')[0] + "_" + asmId.split('_')[1] if not gcAcc.startswith("GCF_"): continue if gcAcc not in allPriorities: allPriorities[gcAcc] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCF primates count: {itemCount:4}") itemCount = 0 # and the GCA/GenBank primates for asmId, commonName in primateList.items(): gcAcc = asmId.split('_')[0] + "_" + asmId.split('_')[1] if not gcAcc.startswith("GCA_"): continue if gcAcc not in allPriorities: allPriorities[gcAcc] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCA primates count: {itemCount:4}") itemCount = 0 # the highest versions of each unique dbDb name get the top priorities sortByValue = sorted(versionScan.items(), key=lambda x: x[1], reverse=True) for key in sortByValue: highVersion = highestVersion[key[0]] -# if key[0] not in allPriorities: if highVersion not in allPriorities: -# allPriorities[key[0]] = priorityCounter allPriorities[highVersion] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tdbDb highest versions count: {itemCount:4}") itemCount = 0 # the mammals, GCF/RefSeq first for asmId, commonName in mammalList.items(): gcAcc = asmId.split('_')[0] + "_" + asmId.split('_')[1] if not gcAcc.startswith("GCF_"): continue if gcAcc not in allPriorities: allPriorities[gcAcc] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCF mammals count: {itemCount:4}") itemCount = 0 # and the GCA/GenBank mammals for asmId, commonName in mammalList.items(): gcAcc = asmId.split('_')[0] + "_" + asmId.split('_')[1] if not gcAcc.startswith("GCA_"): continue if gcAcc not in allPriorities: allPriorities[gcAcc] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCA mammals count: {itemCount:4}") itemCount = 0 # GCF RefSeq from GenArk next priority for item in genArk: gcAccession = item['gcAccession'] if not gcAccession.startswith("GCF_"): continue if gcAccession not in allPriorities: allPriorities[gcAccession] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCF count: {itemCount:4}") itemCount = 0 # GCA GenBank from GenArk next priority for item in genArk: gcAccession = item['gcAccession'] if not gcAccession.startswith("GCA_"): continue if gcAccession not in allPriorities: allPriorities[gcAccession] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tgenArk GCA count: {itemCount:4}") itemCount = 0 # the rest of the names just get incrementing priorities for dbName in sorted(allDbDbNames): if dbName not in allPriorities: allPriorities[dbName] = priorityCounter priorityCounter += 1 itemCount += 1 totalItemCount += itemCount print(f"{totalItemCount:4} - total\tthe rest of dbDb count: {itemCount:4}") #################################################################### """ table load procedure: hgsql -e 'DROP TABLE IF EXISTS genomePriority;' hgcentraltest hgsql hgcentraltest < genomePriority.sql hgsql -e 'LOAD DATA LOCAL INFILE "genomePriority.tsv" INTO TABLE genomePriority;' hgcentraltest hgsql -e 'ALTER TABLE genomePriority ADD FULLTEXT INDEX gdIx (name, commonName, scientificName, description);' hgcentraltest """ #################################################################### #################################################################### def main(): global priorityCounter global allPriorities if len(sys.argv) != 2: print("genomePriority.py - prepare genomePriority.tsv file from") print(" dbDb.hgcentral and UCSC_GI.assemblyHubList.txt file.\n") print("Usage: genomePriority.py dbDb.name.clade.tsv\n") print("the dbDb.name.clade.tsv file is a manually curated file to relate") print(" UCSC database names to GenArk clades, in source tree hubApi/") print("This script is going to read the dbDb.hgcentral table, and the file") print(" UCSC_GI.assemblyHubList.txt from hgdownload.") print("Writing an output file genomePriority.tsv to be loaded into") print(" genomePriority.hgcentral. See notes in this script for load procedure.") sys.exit(-1) dbDbNameCladeFile = sys.argv[1] # Ensure stdout and stderr use UTF-8 encoding set_utf8_encoding() # Get the dbDb.hgcentral table data rawData = dbDbData() dbDbItems = processDbDbData(rawData) # and the correspondence of dbDb names to GenArk clade categories dbDbClades = dbDbCladeList(dbDbNameCladeFile) # read the GenArk data from hgdownload into a list of dictionaries genArkUrl = "https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt" genArkItems = readGenArkData(genArkUrl) establishPriorities(dbDbItems, genArkItems) outFile = "genomePriority.tsv" fileOut = open(outFile, 'w') itemCount = 0 - # name,scientificName,organism,taxId,sourceName,description # Print the dbDb data for entry in dbDbItems: - # Encode each entry value to UTF-8 before printing dbDbName = entry['name'] if dbDbName in allPriorities: priority = allPriorities[dbDbName] else: print("no priority for ", dbDbName) clade = dbDbClades.get(entry['name'], "n/a") - indexString = entry['name'] - indexString += " " + removeNonAlphanumeric(entry['scientificName']) - indexString += " " + removeNonAlphanumeric(entry['organism']) - indexString += " " + removeNonAlphanumeric(entry['description']) - indexString += " " + removeNonAlphanumeric(entry['sourceName']) - indexString += " " + entry['taxId'] - noDups = eliminateDupWords(indexString) descr = f"{entry['sourceName']} {clade} {entry['taxId']} {entry['description']}\n" description = re.sub(r'\s+', ' ', descr).strip() -# outLine =f"{entry['name']}\t{priority}\t{entry['organism']}\t{entry['scientificName']}\t{entry['taxId']}\t{description}\t{noDups}\n" outLine =f"{entry['name']}\t{priority}\t{entry['organism']}\t{entry['scientificName']}\t{entry['taxId']}\t{description}\n" fileOut.write(outLine) itemCount += 1 itemCount = 0 # Print the GenArk data for entry in genArkItems: gcAccession = entry['gcAccession'] if gcAccession in allPriorities: priority = allPriorities[gcAccession] else: print("no priority for ", gcAccession) cleanName = removeNonAlphanumeric(entry['commonName']) clade = re.sub(r'\(L\)$', '', entry['clade']) - indexString = entry['gcAccession'] - indexString += " " + removeNonAlphanumeric(entry['scientificName']) - indexString += " " + cleanName - indexString += " " + clade - indexString += " " + removeNonAlphanumeric(entry['asmName']) - indexString += " " + entry['taxId'] - noDups = eliminateDupWords(indexString) -# print(priority, entry['gcAccession'], entry['scientificName'], entry['commonName'], entry['taxId'], entry['asmName'], "'" + noDups + "'") -# print(priority, entry['gcAccession'], entry['scientificName'], entry['commonName'], entry['taxId'], "'" + noDups + "'") -# outLine =f"{priority}\t{entry['gcAccession']}\t{entry['scientificName']}\t{entry['taxId']}\t{entry['commonName']}\t{noDups}\n" -# outLine = f"{entry['gcAccession']}\t{priority}\t{entry['commonName'].encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{entry['asmName']}\t{noDups}\n" descr = f"{entry['asmName']} {clade} {entry['taxId']}\n" description = re.sub(r'\s+', ' ', descr).strip() outLine = f"{entry['gcAccession']}\t{priority}\t{entry['commonName'].encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{description}\n" fileOut.write(outLine) itemCount += 1 fileOut.close() -# print(removeNonAlphanumeric(entry['asmName'])) -# print(removeNonAlphanumeric(entry['commonName'])) -# gcAccession,scientificName,commonName,taxId,asmName - - -# cleanString = {k: removeNonAlphanumeric(v) for k, v in entry.items()} -# print(cleanString) - - if __name__ == "__main__": main()