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1 import subprocess
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2 import os
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3 import sys
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4
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5 ## Prepare profiles databank and create command to search profiles from a profiles databank in a nucleotides databank
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6 #
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7 class ProfilesSearch(object):
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8
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9 ## launch command to prepare profiles bank
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10 #
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11 # @param launch_1 string corresponding to pre command
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12 # @param launch_2 string corresponding to post command
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13 # @param config configParser object instance
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14 # @param cDir string current directory
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15 # @param verbose int (default = 0)
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16 #
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17 def prepareProfilesBank(self, launch_1, launch_2, config, cDir, verbose = 0):
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18 bank = self._getBankBaseName(config)
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19 prg = "hmmpress"
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20 if verbose > 0:
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21 print "prepare bank '%s'..." % ( bank ); sys.stdout.flush()
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22 cmd = ""
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23 cmd += prg + " -f "
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24 cmd += "%s/%s " % ( cDir, bank )
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25 process = subprocess.Popen(cmd, shell = True)
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26 process.communicate()
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27 if process.returncode != 0:
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28 raise Exception("ERROR when launching '%s'" % cmd)
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29
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30 ## create command to detect Hmm profiles in a nt sequence file
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31 #
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32 # @param inFileName string name of input file
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33 # @param launch_1 string corresponding to pre command
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34 # @param launch_2 string corresponding to post command
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35 # @param cDir string current directory
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36 # @param tmpDir string temporary directory
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37 # @param config configParser object instance
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38 # @return cmd string command to launch
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39 #
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40 def detectHmmProfiles(self, inFileName, launch_1, launch_2, cDir, tmpDir, config):
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41 bank = self._getBankBaseName(config)
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42 evalueMax = config.get("detect_features","TE_HMMER_evalue")
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43
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44 cmd = ""
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45
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46 cmd += launch_1
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47 cmd += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
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48 cmd += " -i %s" % ( inFileName )
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49 cmd += " -o %s_translated" % ( inFileName )
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50 cmd += launch_2
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51
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52 cmd += launch_1
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53 cmd += "hmmscan "
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54 cmd += " -o %s_tr.hmmScanOut" % ( inFileName )
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55 cmd += " --domtblout %s_tr.hmmScanOutTab" % ( inFileName )
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56 cmd += " --noali -E " + evalueMax
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57 cmd += " --cpu 1 "
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58 cmd += "%s/%s" % ( cDir, bank ) + " " + "%s_translated" % ( inFileName )
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59 cmd += launch_2
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60
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61 cmd += "if os.path.exists( \"%s_translated\" ):\n" % ( inFileName )
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62 cmd += "\tos.remove( \"%s_translated\" )\n" % ( inFileName )
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63
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64 cmd += launch_1
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65 cmd += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py"
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66 cmd += " -i %s_tr.hmmScanOutTab" % ( inFileName )
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67 cmd += " -o %s_profiles_%s.align" % ( inFileName, bank )
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68 cmd += " -T %s" % ( inFileName )
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69 cmd += " -p hmmscan"
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70 cmd += " -c"
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71 cmd += launch_2
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72
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73 cmd += launch_1
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74 cmd += os.environ["REPET_PATH"] + "/bin/matcher"
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75 cmd += " -m %s_profiles_%s.align" % ( inFileName, bank )
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76 cmd += " -j"
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77 cmd += " -E 10"
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78 cmd += " -L 0"
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79 cmd += " -v 1"
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80 cmd += launch_2
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81
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82 cmd += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( cDir, inFileName, bank )
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83 cmd += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inFileName, bank, cDir )
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84 cmd += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( cDir, inFileName, bank )
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85 cmd += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inFileName, bank, cDir )
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86 cmd += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inFileName, bank )
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87 cmd += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inFileName, bank )
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88 cmd += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inFileName, bank )
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89 cmd += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inFileName, bank )
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90 cmd += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inFileName )
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91 cmd += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inFileName )
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92
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93 if tmpDir != cDir:
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94 cmd += "if os.path.exists( \"%s\" ):\n" % ( bank )
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95 cmd += "\tos.remove( \"%s\" )\n" % ( bank )
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96
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97 return cmd
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98
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99 def _getBankBaseName(self, config):
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100 profilsHmmBank = config.get("detect_features", "TE_HMM_profiles")
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101 bank = os.path.basename(profilsHmmBank)
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102 return bank
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103
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