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Revision 1.3 - (view) (download) (as text)
| 1 : | efrank | 1.1 | # -*- perl -*- |
| 2 : | |||
| 3 : | use strict; | ||
| 4 : | use FIG; | ||
| 5 : | my $fig = new FIG; | ||
| 6 : | |||
| 7 : | use DBrtns; | ||
| 8 : | |||
| 9 : | |||
| 10 : | my $temp_dir = "$FIG_Config::temp"; | ||
| 11 : | my($organisms_dir) = "$FIG_Config::organisms"; | ||
| 12 : | |||
| 13 : | my($genome,@types,$type,$id,$loc,@aliases,$aliases,$contig); | ||
| 14 : | |||
| 15 : | # usage: load_features [G1 G2 G3 ... ] | ||
| 16 : | |||
| 17 : | open(REL,">$temp_dir/tmpfeat$$") || die "could not open $temp_dir/tmpfeat$$"; | ||
| 18 : | |||
| 19 : | my $dbf = $fig->{_dbf}; | ||
| 20 : | |||
| 21 : | |||
| 22 : | |||
| 23 : | my @genomes; | ||
| 24 : | if (@ARGV == 0) | ||
| 25 : | { | ||
| 26 : | $dbf->drop_table( tbl => "features" ); | ||
| 27 : | if ($FIG_Config::dbms eq "Pg") | ||
| 28 : | { | ||
| 29 : | $dbf->create_table( tbl => "features", | ||
| 30 : | flds => "id varchar(32) UNIQUE NOT NULL, type varchar(16),genome varchar(16)," . | ||
| 31 : | "location varchar(5000)," . | ||
| 32 : | "contig varchar(96), minloc INTEGER, maxloc INTEGER," . | ||
| 33 : | "aliases TEXT, PRIMARY KEY ( id )" | ||
| 34 : | ); | ||
| 35 : | } | ||
| 36 : | elsif ($FIG_Config::dbms eq "mysql") | ||
| 37 : | { | ||
| 38 : | $dbf->create_table( tbl => "features", | ||
| 39 : | flds => "id varchar(32) UNIQUE NOT NULL, type varchar(16),genome varchar(16)," . | ||
| 40 : | "location TEXT," . | ||
| 41 : | "contig varchar(96), minloc INTEGER, maxloc INTEGER," . | ||
| 42 : | "aliases TEXT, PRIMARY KEY ( id )" | ||
| 43 : | ); | ||
| 44 : | } | ||
| 45 : | |||
| 46 : | $dbf->create_index( idx => "features_org_ix", | ||
| 47 : | tbl => "features", | ||
| 48 : | type => "btree", | ||
| 49 : | flds => "genome" ); | ||
| 50 : | $dbf->create_index( idx => "features_type_ix", | ||
| 51 : | type => "btree", | ||
| 52 : | tbl => "features", | ||
| 53 : | flds => "type" ); | ||
| 54 : | $dbf->create_index( idx => "features_beg_ix", | ||
| 55 : | type => "btree", | ||
| 56 : | tbl => "features", | ||
| 57 : | flds => "genome,contig,minloc" ); | ||
| 58 : | |||
| 59 : | @genomes = $fig->genomes; | ||
| 60 : | } | ||
| 61 : | else | ||
| 62 : | { | ||
| 63 : | @genomes = @ARGV; | ||
| 64 : | overbeek | 1.2 | foreach $genome (@genomes) |
| 65 : | { | ||
| 66 : | $dbf->SQL("DELETE FROM features WHERE ( genome = \'$genome\' )"); | ||
| 67 : | } | ||
| 68 : | efrank | 1.1 | } |
| 69 : | |||
| 70 : | foreach $genome (@genomes) | ||
| 71 : | { | ||
| 72 : | opendir(FEAT,"$organisms_dir/$genome/Features") | ||
| 73 : | || die "could not open $genome/Features"; | ||
| 74 : | @types = grep { $_ =~ /^[a-zA-Z]+$/ } readdir(FEAT); | ||
| 75 : | closedir(FEAT); | ||
| 76 : | |||
| 77 : | foreach $type (@types) | ||
| 78 : | { | ||
| 79 : | if ((-s "$organisms_dir/$genome/Features/$type/tbl") && | ||
| 80 : | open(TBL,"<$organisms_dir/$genome/Features/$type/tbl")) | ||
| 81 : | { | ||
| 82 : | # print STDERR "loading $genome/Features/$type/tbl\n"; | ||
| 83 : | while (defined($_ = <TBL>)) | ||
| 84 : | { | ||
| 85 : | chop; | ||
| 86 : | ($id,$loc,@aliases) = split(/\t/,$_); | ||
| 87 : | if ($id) | ||
| 88 : | { | ||
| 89 : | my($minloc,$maxloc); | ||
| 90 : | if ($loc) | ||
| 91 : | { | ||
| 92 : | $loc =~ s/\s+$//; | ||
| 93 : | ($contig,$minloc,$maxloc) = &FIG::boundaries_of($loc); | ||
| 94 : | if ($minloc && $maxloc) | ||
| 95 : | { | ||
| 96 : | ($minloc < $maxloc) || (($minloc,$maxloc) = ($maxloc,$minloc)); | ||
| 97 : | } | ||
| 98 : | } | ||
| 99 : | |||
| 100 : | if (! $contig) | ||
| 101 : | { | ||
| 102 : | $loc = $contig = $minloc = $maxloc = ""; | ||
| 103 : | } | ||
| 104 : | |||
| 105 : | if (@aliases > 0) | ||
| 106 : | { | ||
| 107 : | $aliases = join(",",grep(/\S/,@aliases)); | ||
| 108 : | } | ||
| 109 : | else | ||
| 110 : | { | ||
| 111 : | $aliases = ""; | ||
| 112 : | } | ||
| 113 : | $minloc = (! $minloc) ? 0 : $minloc; | ||
| 114 : | $maxloc = (! $maxloc) ? 0 : $maxloc; | ||
| 115 : | overbeek | 1.3 | if ((length($loc) < 5000) && (length($contig) < 96) && (length($id) < 32)) |
| 116 : | { | ||
| 117 : | print REL "$id\t$type\t$genome\t$loc\t$contig\t$minloc\t$maxloc\t$aliases\n"; | ||
| 118 : | } | ||
| 119 : | efrank | 1.1 | } |
| 120 : | } | ||
| 121 : | close(TBL); | ||
| 122 : | } | ||
| 123 : | } | ||
| 124 : | } | ||
| 125 : | close(REL); | ||
| 126 : | |||
| 127 : | $dbf->load_table( tbl => "features", | ||
| 128 : | file => "$temp_dir/tmpfeat$$" ); | ||
| 129 : | |||
| 130 : | if (@ARGV == 0) { $dbf->vacuum_it("features") } | ||
| 131 : | unlink("$temp_dir/tmpfeat$$"); |
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