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1 #!/usr/bin/perl
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2
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3
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4 use Getopt::Long;
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5 use Pod::Usage;
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6 use IO::File;
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7 use Data::Dumper;
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8
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9 #require '/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/multi_join_shell.pl'; ##comment this line out when finished testing
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10 #require '/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl';
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11 #require '/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/GetOptWC.pm';
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12
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13 GetOptions(
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14 "log=s" => \$log,
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15 "join_file=s" => \$data_in,
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16 "join_col=s" => \$coljoin,
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17 "time" => \$mTime,
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18 "q|quiet" => \$quiet,
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19 "iteration=i" => \$I,
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20 "totalfiles=i" => \$N,
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21 "with_header=s" => \$header_yes,
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22 "input_name=s" => \$in_name,
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23 "resultsfile=s" => \$out_file,
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24 # "h|help" => \$help
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25 ) or pod2usage( -exitval => 2, -verbose => 2 );
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26
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27
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28 #check parameters and options
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29 my $debug = scalar(@ARGV);
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30
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31 $coljoin--;
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32 #pod2usage(-msg => "To troubleshoot. ARGV should be @ARGV with $debug arguments in it.");
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33 pod2usage(-msg => "Forward probability should be in [0, 1]!", -exitval => 2, -verbose => 2) if ($probF < 0 || $probF > 1);
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34
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35 $N++;
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36
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37 # #
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38 use IO::Handle;
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39 open OUTPUT, '>>',$log or die "cant open this file for OUTPUT: $log. Computer says: $!\n";;
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40 open ERROR, '>>', $log or die "cant open this file for ERROR: $log. Computer says: $!\n";
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41 STDOUT->fdopen( \*OUTPUT, 'a' ) or die "cant open file $!\n"; #cms changing mode from 'w' to 'a' for multiple files in one run
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42 STDERR->fdopen( \*ERROR, 'a' ) or die "cant open file $!\n"; #cms changing mode from 'w' to 'a' for multiple files in one run
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43 # # #
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44
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45 my @options;
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46
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47 my $fileno = $I + 1;
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48
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49 ##Keeping track of the input files (one per iteration of this script) in an external file:
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50 open $Filenames, '>>', "temp_filenames.txt" or die "cannot open the temporary file $!\n";
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51 print $Filenames "$data_in\t";
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52 print $Filenames "$coljoin\n";
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53
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54 if (($I==$N-1)&&($N>=2)) {
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55 ## At the end of the last iteration
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56 close($Filenames);
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57
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58 print "\nLAST ITERATION COMPLETED and at least two input files provided.\n";
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59
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60 ##Read in file temp_filenames.txt
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61 open(my $tmpfile, "<", "temp_filenames.txt") or die "Cannot open temp file: $!";
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62 my @fileArray = <$tmpfile>;
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63 #unshift @fileArray,$conditions; ##don't need to do this since conditions aren't used here
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64 close($tmpfile) or die "what is that??!!! $!";
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65
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66
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67 ##Need to send output file name to shell script:
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68 push @fileArray, $out_file; ##adds out_file to the end of fileArray
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69 ##Also need to send yes/no for keeping header:
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70 push @fileArray, $header_yes;
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71
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72 ##Debug:
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73 print "\nFirst file fileArray[0] is $fileArray[0].";
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74 print "\nOutput file is next-to-last val in fileArray, $fileArray[-2].";
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75 print "\nUse header? is last val in fileArray, $fileArray[-1].";
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76 print "\nSecond file now is fileArray[2], $fileArray[2].";
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77
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78 ##@fileArray has one file per line,output,header_yes, so $N+1 rows
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79 my $f=0;
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80 my @first;
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81 my @second;
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82 do {
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83
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84 @first = split('\t',$fileArray[$f]); ##was filename\tJoinCol
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85 print "\njoin column from first line is $first[1].";
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86
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87 ##CMS DEALING WITH HEADER OR NOT:
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88 if ($header_yes eq "no") {
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89 my $fh1;
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90 $fh1 = IO::File->new("<$first[0]");
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91 my $line1file1 = $fh1->getline();
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92 $line1file1 =~ s/\s+$//;
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93 #print "\nline1file1 is $line1file1\n"; ##DEBUG
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94 @cols = split "\t",$line1file1;
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95 my $numcols1 = @cols;
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96 my $head1;
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97 for (my $i=1; $i<$numcols1; $i++) {
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98 $head1.="C$i\t";
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99 }
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100 $head1.="C$numcols1\n";
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101 open(my $fh_sub, '>', './header1.txt') or die "OOPIES: $!\n";
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102 print "\nheader first file $first[0] on next line:\n$head1"; ##DEBUG
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103 print $fh_sub $head1;
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104 close $fh_sub;
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105 system("cat $first[0] >> ./header1.txt"); ##put header in front of file
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106 ##now want to use ./header1.txt instead of what was in $first[0] earlier
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107 $first[0] = "./header1.txt";
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108 }
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109
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110
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111
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112 @second = split('\t',$fileArray[$f+1]);
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113
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114 if ($header_yes eq "no") {
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115 my $fh2;
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116 $fh2 = IO::File->new("<$second[0]");
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117 my $line1file2 = $fh2->getline();
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118 $line1file2 =~ s/\s+$//;
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119 @cols = split "\t",$line1file2;
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120 my $numcols2 = @cols;
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121 my $head2;
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122 for (my $i=1; $i<$numcols2; $i++) {
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123 $head2.="C$i\t";
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124 }
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125 $head2.="C$numcols2\n";
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126 open(my $fh_sub, '>', './header2.txt') or die "OOPIES: $!\n";
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127 print "\nheader from $second[0] on next line:\n$head2"; ##DEBUG
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128 print $fh_sub $head2;
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129 close $fh_sub;
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130 system("cat $second[0] >> ./header2.txt");
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131 $second[0]="./header2.txt";
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132 }
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133
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134 print "\ncommand following:\n";
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135 print "/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl -File1=$first[0] -File2=$second[0] -cola1=$first[1] -cola2=$second[1] -colb1=$first[1] -colb2=$second[1]";
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136 system("/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl", "-File1=$first[0]", "-File2=$second[0]", "-cola1=$first[1]", "-cola2=$second[1]", "-colb1=$first[1]", "-colb2=$second[1]");
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137 print "\nOut from system call on next line:\n$!";
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138 $f+=2;
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139 system("mv file1_file2.txt joined.txt");
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140 if ($header_yes eq "no") {
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141 system("rm ./header2.txt");
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142 system("rm ./header1.txt");
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143 }
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144 } while ($f < 2); ##FIRST TWO ONLY!!!
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145
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146 for ($f; $f<$N; $f++) {
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147 my @current = split('\t',$fileArray[$f]); ##was filename\tJoinCol
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148 print "\njoin column from first line is $first[1].";
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149
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150 if ($header_yes eq "no") {
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151 my $fh;
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152 $fh = IO::File->new("<$current[0]");
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153 my $line1file = $fh->getline();
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154 $line1file =~ s/\s+$//;
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155 @cols = split "\t",$line1file;
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156 my $numcols = @cols;
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157 my $head;
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158 for (my $i=1; $i<$numcols; $i++) {
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159 $head.="C$i\t";
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160 }
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161 $head.="C$numcols\n";
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162 open(my $fh_sub, '>', './header.txt') or die "OOPIES: $!\n";
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163 print "\nheader from file $current[0] on next line:\n$head"; ##DEBUG
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164 print $fh_sub $head;
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165 close $fh_sub;
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166 system("cat $current[0] >> ./header.txt");
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167 $current[0]="./header.txt";
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168 }
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169
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170 print "\ncommand following:\n";
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171 print "/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl -File1=joined.txt -File2=$current[0] -cola1=$first[1] -cola2=$current[1] -colb1=$first[1] -colb2=$current[1]";
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172 system("/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl","-File1=joined.txt", "-File2=$current[0]", "-cola1=$first[1]", "-cola2=$current[1]", "-colb1=$first[1]", "-colb2=$current[1]");
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173 print "\nOut from system call on next line:\n$!";
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174 system("mv file1_file2.txt joined.txt");
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175 if ($header_yes eq "no") {
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176 system("rm ./header.txt");
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177 }
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178 }
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179
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180 system("mv joined.txt $fileArray[-2]");
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181
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182 ##NOT SURE WHAT TO DO WITH THIS FOR THE MULTI-JOIN TOOL:
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183 ##Now, make the EC files from the genes-results files (extract appropriate columns):
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184 #my $condStr = multi_join_shell(@fileArray); ##RSEMgetTPMs needs to take care of carriage returns
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185 ##NEED TO MODIFY RSEMTOEBSEQ_SHELL SO IT TAKES THE OUTPUT FILENAME AS WELL
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186
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187 system("rm temp_filenames.txt");
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188
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189 }
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190 elsif ($N<2) {
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191 print "\n<br /><i>Only one file; not running join.</i>\n";
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192 }
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193
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194
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195
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196 #print "LOG $mv\n";
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