annotate spring_map.py @ 41:f316caf098a6 draft default tip

"planemo upload commit 685e1236afde7cf6bb0c9236de06998d2c211dd3"
author guerler
date Mon, 01 Mar 2021 15:02:36 +0000
parents 172398348efd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #! /usr/bin/env python3
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2 import argparse
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3 from os import mkdir, system
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4 from os.path import isfile, isdir
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5
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6 from spring_package.DBKit import DBKit
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7 from spring_package.Molecule import Molecule
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8 from spring_package.Utilities import getId, getChain, getName
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10
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11 def getPDB(line, pdbDatabase):
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12 pdb = getName(line)
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13 pdbChain = getChain(line)
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14 pdbFile = "temp/temp.pdb"
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15 pdbDatabaseId = "%s.pdb" % pdb
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16 pdbDatabase.createFile(pdbDatabaseId, pdbFile)
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17 return pdbFile, pdbChain
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19
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20 def getSequences(fileName):
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21 sequences = dict()
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22 with open(fileName) as file:
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23 for line in file:
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24 if line.startswith(">"):
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25 name = getId(line.split()[0][1:])
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26 nextLine = next(file)
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27 sequences[name] = nextLine
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28 return sequences
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31 def findMatch(identifier, templates, databaseFile, pdbDatabase, evalue=0.0):
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32 if identifier in templates:
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33 return identifier
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34 resultSub = identifier[:2]
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35 fastaFile = "temp/%s/%s.fasta" % (resultSub, identifier)
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36 resultFile = "%s.result" % fastaFile
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37 if not isfile(resultFile):
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38 resultDir = "temp/%s" % resultSub
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39 if not isdir(resultDir):
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40 mkdir(resultDir)
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41 pdbFile, pdbChain = getPDB(identifier, pdbDatabase)
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42 mol = Molecule(pdbFile)
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43 seq = mol.getSequence(pdbChain)
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44 with open(fastaFile, "w") as fasta:
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45 fasta.write(">%s\n" % identifier)
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46 fasta.write("%s" % seq)
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47 system("psiblast -query %s -db %s -out %s" % (fastaFile, databaseFile, resultFile))
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48 maxMatch = None
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49 try:
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50 with open(resultFile) as file:
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51 for i in range(38):
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52 line = next(file)
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53 columns = line.split()
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54 maxMatch = getId(columns[0])
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55 maxScore = float(columns[2])
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56 if maxScore > evalue:
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57 return None
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58 except Exception:
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59 return None
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60 return maxMatch
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63 def main(args):
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64 if not isdir("temp"):
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65 mkdir("temp")
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66 logFile = open(args.log, "w")
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67 templateSequenceFile = "temp/templates.fasta"
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68 pdbDatabase = DBKit(args.index, args.database)
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69 templates = set()
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70 with open(args.list) as file:
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71 for rawId in file:
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72 templateId = getId(rawId)
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73 templates.add(templateId)
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74 if not isfile(templateSequenceFile):
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75 templateSequences = open(templateSequenceFile, "w")
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76 with open(args.list) as file:
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77 for rawId in file:
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78 templateId = getId(rawId)
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79 pdbFile, pdbChain = getPDB(templateId, pdbDatabase)
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80 try:
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81 templateMol = Molecule(pdbFile)
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82 templateSeq = templateMol.getSequence(pdbChain)
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83 templateSequences.write(">%s\n" % templateId)
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84 templateSequences.write("%s\n" % templateSeq)
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85 except Exception:
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86 logFile.write("Warning: File not found [%s].\n" % templateId)
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87 templateSequences.close()
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88 system("makeblastdb -in %s -dbtype prot" % templateSequenceFile)
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89 else:
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90 logFile.write("Using existing sequences for templates [%s].\n" % templateSequenceFile)
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91 logFile.write("Found %s template entries from `%s`.\n" % (len(templates), args.list))
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92 logFile.flush()
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93
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94 crossReference = list()
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95 with open(args.cross) as file:
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96 for line in file:
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97 cols = line.split()
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98 if len(cols) != 2:
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99 raise Exception("Invalid line in crossreference [%s]." % line)
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100 crossReference.append(dict(core=cols[0], partner=cols[1]))
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101 logFile.write("Loaded crossreference with %d entries.\n" % len(crossReference))
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102 logFile.flush()
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103
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104 for refEntry in crossReference:
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105 coreId = refEntry["core"]
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106 logFile.write("Processing %s.\n" % coreId)
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107 coreMatch = findMatch(coreId, templates, templateSequenceFile, pdbDatabase, evalue=args.evalue)
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108 partnerId = refEntry["partner"]
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109 logFile.write("Processing %s.\n" % partnerId)
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110 partnerMatch = findMatch(partnerId, templates, templateSequenceFile, pdbDatabase, evalue=args.evalue)
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111 if partnerMatch is None or coreMatch is None:
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112 logFile.write("Warning: Failed alignment [%s, %s].\n" % (coreId, partnerId))
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113 else:
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114 logFile.write("Found matching entries [%s, %s].\n" % (coreMatch, partnerMatch))
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115 refEntry["coreMatch"] = coreMatch
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116 refEntry["partnerMatch"] = partnerMatch
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117 logFile.flush()
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118
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119 entryCount = 0
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120 with open(args.output, 'w') as output_file:
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121 for refEntry in crossReference:
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122 coreId = refEntry["core"]
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123 partnerId = refEntry["partner"]
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124 if "coreMatch" in refEntry and "partnerMatch" in refEntry:
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125 entry = "%s\t%s\t%s\t%s\n" % (refEntry["coreMatch"], refEntry["partnerMatch"], refEntry["core"], refEntry["partner"])
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126 output_file.write(entry)
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127 entryCount = entryCount + 1
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128 else:
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129 logFile.write("Warning: Skipping failed missing partner match [%s, %s].\n" % (coreId, partnerId))
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130 logFile.write("Found %s cross reference entries.\n" % entryCount)
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131 logFile.close()
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132
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133
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134 if __name__ == "__main__":
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135 parser = argparse.ArgumentParser(description='Maps binding partners to template library')
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136 parser.add_argument('-l', '--list', help='List of template entries `PDB_CHAIN`', required=True)
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137 parser.add_argument('-i', '--index', help='PDB Database Index file (ffindex)', required=True)
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138 parser.add_argument('-d', '--database', help='PDB Database files (ffdata)', required=True)
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139 parser.add_argument('-c', '--cross', help='Cross reference (unmapped)', required=True)
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140 parser.add_argument('-o', '--output', help='Cross reference', required=True)
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141 parser.add_argument('-g', '--log', help='Log File', required=True)
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142 parser.add_argument('-e', '--evalue', help='e-Value threshold', type=float, default=0.0)
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143 args = parser.parse_args()
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144 main(args)