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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | # -*- perl -*- | ||
| 4 : | # | ||
| 5 : | # Copyright (c) 2003-2006 University of Chicago and Fellowship | ||
| 6 : | # for Interpretations of Genomes. All Rights Reserved. | ||
| 7 : | # | ||
| 8 : | # This file is part of the SEED Toolkit. | ||
| 9 : | parrello | 1.2 | # |
| 10 : | parrello | 1.1 | # The SEED Toolkit is free software. You can redistribute |
| 11 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 12 : | parrello | 1.2 | # Public License. |
| 13 : | parrello | 1.1 | # |
| 14 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 15 : | # along with this program; if not write to the University of Chicago | ||
| 16 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 17 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 18 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 19 : | # | ||
| 20 : | |||
| 21 : | =head1 SproutGFF | ||
| 22 : | |||
| 23 : | This is a fancy wrapper around B<seed2gff> that can be used to generate the | ||
| 24 : | GFF3 files for the NMPDR. The single parameter is the output directory name. | ||
| 25 : | The files will be organized by NMPDR group. | ||
| 26 : | |||
| 27 : | The currently-supported command-line options are as follows. | ||
| 28 : | |||
| 29 : | =over 4 | ||
| 30 : | |||
| 31 : | =item user | ||
| 32 : | |||
| 33 : | Name suffix to be used for log files. If omitted, the PID is used. | ||
| 34 : | |||
| 35 : | =item trace | ||
| 36 : | |||
| 37 : | Numeric trace level. A higher trace level causes more messages to appear. The | ||
| 38 : | default trace level is 2. Tracing will be directly to the standard output | ||
| 39 : | as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory, | ||
| 40 : | where I<User> is the value of the B<user> option above. | ||
| 41 : | |||
| 42 : | =item sql | ||
| 43 : | |||
| 44 : | If specified, turns on tracing of SQL activity. | ||
| 45 : | |||
| 46 : | =item background | ||
| 47 : | |||
| 48 : | Save the standard and error output to files. The files will be created | ||
| 49 : | in the FIG temporary directory and will be named C<err>I<User>C<.log> and | ||
| 50 : | C<out>I<User>C<.log>, respectively, where I<User> is the value of the | ||
| 51 : | B<user> option above. | ||
| 52 : | |||
| 53 : | =item h | ||
| 54 : | |||
| 55 : | Display this command's parameters and options. | ||
| 56 : | |||
| 57 : | =item scan | ||
| 58 : | |||
| 59 : | If specified, the genomes will be collected and the directories created, but no GFF | ||
| 60 : | files will be output. This is mostly useful for testing. | ||
| 61 : | |||
| 62 : | =item phone | ||
| 63 : | |||
| 64 : | Phone number to message when the script is complete. | ||
| 65 : | |||
| 66 : | =back | ||
| 67 : | |||
| 68 : | =cut | ||
| 69 : | |||
| 70 : | use strict; | ||
| 71 : | use Tracer; | ||
| 72 : | use Cwd; | ||
| 73 : | use File::Copy; | ||
| 74 : | use File::Path; | ||
| 75 : | use SFXlate; | ||
| 76 : | |||
| 77 : | # Get the command-line options and parameters. | ||
| 78 : | my ($options, @parameters) = StandardSetup([qw(Sprout ERDB) ], | ||
| 79 : | { | ||
| 80 : | phone => ["", "phone number (international format) to call when load finishes"], | ||
| 81 : | genome => ["", "genome to process; the default is to process all NMPDR core genomes"], | ||
| 82 : | scan => ["", "if specified, the output directories will be created but no files will be written"], | ||
| 83 : | }, | ||
| 84 : | "<output directory>", | ||
| 85 : | @ARGV); | ||
| 86 : | # Set a variable to contain return type information. | ||
| 87 : | my $rtype; | ||
| 88 : | # Insure we catch errors. | ||
| 89 : | eval { | ||
| 90 : | # Create a Sprout object. | ||
| 91 : | my $sprout = SFXlate->new_sprout_only(); | ||
| 92 : | # Insure the output directory exists. | ||
| 93 : | my $outDir = $parameters[0]; | ||
| 94 : | if (! $outDir) { | ||
| 95 : | Confess("No output directory specified."); | ||
| 96 : | } else { | ||
| 97 : | Insure($outDir, 0777); | ||
| 98 : | # Create the genome map. This lists all the genomes we want along with the corresponding | ||
| 99 : | # output file name. | ||
| 100 : | my %genomes; | ||
| 101 : | # Check for a single-genome situation. | ||
| 102 : | if ($options->{genome}) { | ||
| 103 : | # Get the genome name. | ||
| 104 : | my $genomeID = $options->{genome}; | ||
| 105 : | my $genomeName = $sprout->GenusSpecies($genomeID); | ||
| 106 : | # Compute the file name. | ||
| 107 : | my $fileName = CleanGenomeName($genomeName); | ||
| 108 : | $genomes{$genomeID} = "$outDir/$fileName.gff"; | ||
| 109 : | } else { | ||
| 110 : | # Here we want all the core organisms, split into super-groups. First, we get the | ||
| 111 : | # genomes for each group in a hash. | ||
| 112 : | my %baseGroups = $sprout->GetGroups(); | ||
| 113 : | # Fix it into a hash by super-group. | ||
| 114 : | parrello | 1.2 | my %coreGroups = $sprout->Fix(%baseGroups); |
| 115 : | parrello | 1.1 | for my $coreGroup (keys %coreGroups) { |
| 116 : | # Compute the directory and isure it exists. | ||
| 117 : | my $superDirectory = "$outDir/$coreGroup"; | ||
| 118 : | Insure($superDirectory, 0777); | ||
| 119 : | # Put all of this group's genomes in the output hash. | ||
| 120 : | for my $coreGenome (@{$coreGroups{$coreGroup}}) { | ||
| 121 : | my $fileName = CleanGenomeName($sprout->GenusSpecies($coreGenome)); | ||
| 122 : | $genomes{$coreGenome} = "$superDirectory/$fileName.gff"; | ||
| 123 : | } | ||
| 124 : | } | ||
| 125 : | } | ||
| 126 : | # Now we loop through %genomes, creating GFF files. | ||
| 127 : | for my $genome (sort keys %genomes) { | ||
| 128 : | my $fileName = $genomes{$genome}; | ||
| 129 : | if ($options->{scan}) { | ||
| 130 : | Trace("$genome would be written to $fileName") if T(2); | ||
| 131 : | } else { | ||
| 132 : | Trace("Writing $genome to $fileName.") if T(3); | ||
| 133 : | # Do the conversion. | ||
| 134 : | my @output = `seed2gff -g $genome -o "$fileName" -s -t all -nmpdr`; | ||
| 135 : | # At trace level 3, we show the output. | ||
| 136 : | Trace("Output from seed2gff:\n" . join("\n", @output)) if T(3) && scalar(@output); | ||
| 137 : | } | ||
| 138 : | } | ||
| 139 : | } | ||
| 140 : | |||
| 141 : | }; | ||
| 142 : | if ($@) { | ||
| 143 : | Trace("Script failed with error: $@") if T(0); | ||
| 144 : | $rtype = "error"; | ||
| 145 : | } else { | ||
| 146 : | Trace("Script complete.") if T(2); | ||
| 147 : | $rtype = "no error"; | ||
| 148 : | } | ||
| 149 : | if ($options->{phone}) { | ||
| 150 : | my $msgID = Tracer::SendSMS($options->{phone}, "SproutGFF terminated with $rtype."); | ||
| 151 : | if ($msgID) { | ||
| 152 : | Trace("Phone message sent with ID $msgID.") if T(2); | ||
| 153 : | } else { | ||
| 154 : | Trace("Phone message not sent.") if T(2); | ||
| 155 : | } | ||
| 156 : | } | ||
| 157 : | |||
| 158 : | =head3 CleanGenomeName | ||
| 159 : | |||
| 160 : | parrello | 1.2 | my $cleaned = CleanGenomeName($name); |
| 161 : | parrello | 1.1 | |
| 162 : | Clean up a genome name so it can be used as a file name. | ||
| 163 : | |||
| 164 : | =over 4 | ||
| 165 : | |||
| 166 : | =item name | ||
| 167 : | |||
| 168 : | Name of the genome, for cleaning purposes. | ||
| 169 : | |||
| 170 : | =item RETURN | ||
| 171 : | |||
| 172 : | Returns the incoming name with all its evil characters converted to dots. | ||
| 173 : | |||
| 174 : | =back | ||
| 175 : | |||
| 176 : | =cut | ||
| 177 : | |||
| 178 : | sub CleanGenomeName { | ||
| 179 : | # Get the parameters. | ||
| 180 : | my ($name) = @_; | ||
| 181 : | # Declare the return variable. | ||
| 182 : | my $retVal = $name; | ||
| 183 : | # Convert spaces to dots. | ||
| 184 : | $retVal =~ s/\s+/\./g; | ||
| 185 : | # Convert double dots to dots. | ||
| 186 : | $retVal =~ s/\.\./\./g; | ||
| 187 : | # Convert other bad guys to underscores. | ||
| 188 : | $retVal =~ tr/():/___/; | ||
| 189 : | # Return the result. | ||
| 190 : | return $retVal; | ||
| 191 : | } | ||
| 192 : | |||
| 193 : | |||
| 194 : | parrello | 1.2 | 1; |
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