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1 #!/usr/bin/perl
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2 # blat_wrapper.pl
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3 # Joachim Jacob - joachim.jacob@gmail.com - 2013
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4
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5 use strict;
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6 use File::Temp 'tempdir';
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7 use File::Copy qw(move);
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8 use File::Basename;
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9 use File::Spec qw(join);
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10 use Log::Log4perl qw(:easy);
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11
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12 # ---------------------- Prepping Logging -----------------------------#
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13 ########################################################################
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14 # Log levels: $DEBUG $INFO $WARN $ERROR $FATAL
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15 # ConversionPattern: %d %-5p %F{1} [%M] (line %L): %m%n%n
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16 my $log_conf = q/
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17 log4perl.category = ERROR, Screen
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18 log4perl.appender.Screen.stderr=1
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19 log4perl.appender.Screen.layout=Log::Log4perl::Layout::PatternLayout
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20 log4perl.appender.Screen.layout.ConversionPattern = %d %-5p %m%n
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21 log4perl.appender.Screen = Log::Log4perl::Appender::Screen
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22 /;
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23
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24 Log::Log4perl::init( \$log_conf );
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25 my $logger = get_logger();
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26
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27 # ----------------- Getting parameters file ---------------------------#
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28 ########################################################################
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29 my ($configfile) = @ARGV;
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30 my (%para);
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1
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31 open(CONFIG,"<",$configfile);
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0
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32 while (<CONFIG>) {
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33 if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; }
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34 }
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35 close(CONFIG);
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36
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37 =Excerpt Config parameters
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1
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38
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0
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39 ## first we pass some galaxy environment variables
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40 galtemp==${__new_file_path__}
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41
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42 #if $refGenomeSource.genomeSource == "indexed"
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43 referencepath==${refGenomeSource.index.fields.path}
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44 range=$refGenomeSource.range
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45 #else
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46 referencepath==${refGenomeSource.ownFile}
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47 #end if
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48
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49 input==$input
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50 output==$output
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51 q==$q
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52 t==$t
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53
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54 advanced_params.use==$advanced_params.use
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55 #if $advanced_params.use=="yes"
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56 tileSize==$advanced_params.tileSize
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57 stepSize==$advanced_params.stepSize
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58 oneOff==$advanced_params.oneOff
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59 minMatch==$advanced_params.minMatch
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60 minScore==$advanced_params.minScore
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61 maxGap==$advanced_params.maxGap
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62 mask==$advanced_params.mask
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63 qMask==$advanced_params.qMask
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64 repeats==$advanced_params.repeats
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65 trimT==$advanced_params.trimT
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66 noTrimA==$advanced_params.noTrimA
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67 fine==$advanced_params.fine
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68 maxIntron==$advanced_params.maxIntron
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69 extendThroughN==$advanced_params.extendThroughN
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70 #end if
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71 =cut
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72
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73 for my $para (keys %para){
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74 INFO "$para\tset to\t$para{$para}";
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75 }
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76
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77 # ---------------------- Prepping temp dir ----------------------------#
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78 ########################################################################
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79 # within the temporary directory of Galaxy, we create a temporary dir
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80
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81 my $galtemp = $para{'galtemp'};
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82 delete($para{'galtemp'});
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83 DEBUG "\nReceived Galaxy temporary directory:\n$galtemp";
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84
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85
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86 my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1);
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87 mkdir "$tempdir", 077 unless -d "$tempdir";
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88 INFO "\nTemporary directory:\n$tempdir";
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89
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1
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90 # --------------------- Checking executable ---------------------------#
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91 ########################################################################
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92 #~ my $command = "which blat ";
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93 #~ run_process($command, "Testing path", $tempdir);
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0
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94
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95 # -------------------- Assembling command ----------------------------#
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96 ########################################################################
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1
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97 my $command = "blat "; # this will ultimately be executed
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98 $command .= " $para{'referencepath'}";
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99 if ( $para{'range'} ) {
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100 ## format checking of the provided range
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101 if ($para{'range'} !~ //){
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102 ERROR "Range has be wrongly formatted: $para{'range'}";
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103 } else {
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104 $command .= ":$para{'range'}";
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105 }
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106 }
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107
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108 $command .= " $para{'input'}";
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109 delete($para{'referencepath'});
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110 delete($para{'range'});
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111 delete($para{'input'});
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112
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113 $command .= " -out=blast9 -q=$para{'q'} -t=$para{'t'}";
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114 delete($para{'q'});
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115 delete($para{'t'});
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116
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117 my $output = " $para{'output'}";
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118 delete($para{'output'});
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119
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120 if ( $para{'advanced_params.use'} eq "yes" ){
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121 delete($para{'advanced_params.use'});
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1
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122 $command .= " -minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'} -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} -stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} ";
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0
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123 if($para{'repeats'} eq 'yes' ){
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124 $command .= " -repeats=$para{'qMask'}";
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125 }
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126 if($para{'extendThroughN'} eq 'yes' ){
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127 $command .= " -extendThroughN";
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128 }
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129 if($para{'fine'} eq 'yes' ){
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130 $command .= " -fine";
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131 }
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132 if($para{'trimT'} eq 'yes' ){
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133 $command .= " -trimT";
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134 }
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135 if($para{'noTrimA'} eq 'yes' ){
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136 $command .= " -noTrimA";
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137 }
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138 }
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139
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140 $command .= " $output";
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141
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142
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143 # --------------------- Executing command ----------------------------#
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144 ########################################################################
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145 run_process($command, "BLAT alignment", $tempdir);
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146
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147 # --------------------------- Exiting --------------------------------#
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148 ########################################################################
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149 exit 0;
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150
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151
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152 ### Subroutines ###
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153 ########################################################################
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154 sub run_process {
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155 my ($command, $name, $tempdir)= @_;
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156 my $logger = get_logger();
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157 INFO "\nProcess to launch:\n $command\n";
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158 system("cd $tempdir; $command 2>/dev/null") == 0 or die "$name failed\nExit status $?\nCommand: $command";
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159 if ($? == -1) {
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160 print "failed to execute: $!\n";
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161 } elsif ($? & 127) {
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162 printf "child died with signal %d, %s coredump\n", ($? & 127), ($? & 128) ? 'with' : 'without';
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163 } else {
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164 printf "$name executed successfully\n", $? >> 8;
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165 }
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166 }
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167
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168
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