Mercurial > repos > guerler > springsuite

annotate spring_map.py @ 38:80a4b98121b6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 22cd6b0fa88ce0ddc4052beab306f5ba10754f12"
author guerler
date Wed, 25 Nov 2020 17:38:24 +0000
parents 0be0af9e695d
children 172398348efd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
37
0be0af9e695d "planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"
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1 #! /usr/bin/env python3
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2 import argparse
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3 import os
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4
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5 from spring_package.DBKit import createFile
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6 from spring_package.Molecule import Molecule
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7
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8
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9 def getId(line):
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10 line = line.strip()
38
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11 if len(line) != 6 or line[4:5] != "_":
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12 raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % line)
37
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13 return line[:4].upper() + line[4:6]
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14
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15
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16 def getPDB(line, args):
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17 pdb = line[:4].lower()
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18 pdbChain = line[5:6]
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19 pdbFile = "%s/temp.pdb" % args.temp
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20 pdbDatabaseId = "%s.pdb" % pdb
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21 createFile(pdbDatabaseId, args.index, args.database, pdbFile)
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22 return pdbFile, pdbChain
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23
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24
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25 def getSequences(fileName):
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26 sequences = dict()
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27 with open(fileName) as file:
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28 for line in file:
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29 if line.startswith(">"):
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30 name = getId(line.split()[0][1:])
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31 nextLine = next(file)
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32 sequences[name] = nextLine
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33 return sequences
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34
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35
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36 def getHomologue(queryFile, queryResultFile, databaseFile):
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37 if not os.path.isfile(queryResultFile):
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38 os.system("psiblast -query %s -db %s -out %s" % (queryFile,
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39 databaseFile, queryResultFile))
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40 maxMatch = None
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41 try:
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42 with open(queryResultFile) as file:
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43 for i in range(38):
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44 line = next(file)
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45 maxMatch = getId(line.split()[0])
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46 except Exception:
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47 return None
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48 return maxMatch
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49
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50
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51 def main(args):
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52 logFile = open(args.log, "w")
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53 temp = args.temp.rstrip("/")
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54 templates = set()
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55 os.system("mkdir -p %s" % temp)
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56 templateSequenceFile = "%s/templates.fasta" % temp
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57 if not os.path.isfile(templateSequenceFile):
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58 templateSequences = open(templateSequenceFile, "w")
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59 with open(args.list) as file:
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60 for rawId in file:
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61 templateId = getId(rawId)
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62 templates.add(templateId)
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63 pdbFile, pdbChain = getPDB(templateId, args)
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64 try:
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65 templateMol = Molecule(pdbFile)
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66 templateSeq = templateMol.getSequence(pdbChain)
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67 templateSequences.write(">%s\n" % templateId)
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68 templateSequences.write("%s\n" % templateSeq)
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69 except Exception:
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70 logFile.write("Warning: File not found [%s].\n" % pdbFile)
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71 templateSequences.close()
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72 os.system("makeblastdb -in %s -dbtype prot" % templateSequenceFile)
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73 else:
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74 logFile.write("Using existing sequences for templates [%s].\n" % templateSequenceFile)
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75 logFile.write("Found %s template entries from `%s`.\n" % (len(templates), args.list))
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76 logFile.flush()
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77
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78 crossReference = list()
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79 with open(args.cross) as file:
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80 for line in file:
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81 cols = line.split()
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82 if len(cols) != 2:
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83 raise Exception("Invalid line in crossreference [%s]." % line)
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84 crossReference.append(dict(core=cols[0], partner=cols[1]))
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85 logFile.write("Loaded crossreference with %d entries.\n" % len(crossReference))
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86 logFile.flush()
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87
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88 for refEntry in crossReference:
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89 coreId = refEntry["core"]
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90 partnerId = refEntry["partner"]
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91 partnerFile = "%s/%s.fasta" % (temp, partnerId)
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92 partnerResultFile = "%s.result" % partnerFile
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93 if partnerId in templates:
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94 refEntry["match"] = partnerId
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95 logFile.write("Found partner in template list alignment [%s].\n" % partnerId)
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96 else:
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97 logFile.write("Processing %s.\n" % partnerId)
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98 if not os.path.isfile(partnerResultFile):
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99 pdbFile, pdbChain = getPDB(partnerId, args)
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100 partnerMol = Molecule(pdbFile)
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101 partnerSeq = partnerMol.getSequence(pdbChain)
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102 with open(partnerFile, "w") as partnerFasta:
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103 partnerFasta.write(">%s\n" % partnerId)
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104 partnerFasta.write("%s" % partnerSeq)
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105 else:
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106 logFile.write("Using existing results. [%s].\n" % partnerId)
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107 matchedId = getHomologue(partnerFile, partnerResultFile,
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108 templateSequenceFile)
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109 if matchedId is None:
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110 logFile.write("Warning: Failed alignment [%s].\n" % partnerId)
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111 else:
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112 logFile.write("Found matching entry %s.\n" % matchedId)
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113 refEntry["match"] = matchedId
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114 logFile.flush()
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115
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116 finalSet = set()
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117 for refEntry in crossReference:
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118 coreId = refEntry["core"]
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119 partnerId = refEntry["partner"]
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120 if "match" in refEntry:
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121 entry = "%s\t%s" % (coreId, refEntry["match"])
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122 if entry not in finalSet:
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123 finalSet.add(entry)
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124 else:
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125 logFile.write("Warning: Skipping failed missing partner match [%s, %s].\n" % (coreId, partnerId))
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126 logFile.write("Found %s cross reference entries.\n" % len(finalSet))
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127 logFile.close()
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128
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129 with open(args.output, 'w') as output_file:
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130 for entry in sorted(finalSet):
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131 output_file.write("%s\n" % entry)
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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 (dbkit_index)', required=True)
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138 parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', 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('-t', '--temp', help='Temporary directory', required=True)
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143 args = parser.parse_args()
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144 main(args)