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Revision 1.6 - (view) (download) (as text)
| 1 : | overbeek | 1.1 | |
| 2 : | use FIG; | ||
| 3 : | my $fig = new FIG; | ||
| 4 : | |||
| 5 : | $usage = "usage: build_initial_objects_for_start_predictions < pegs_in_cluster > initial_objects"; | ||
| 6 : | |||
| 7 : | @pegs = <STDIN>; | ||
| 8 : | chomp @pegs; | ||
| 9 : | # print "NPEGS=", scalar(@pegs), "\n"; | ||
| 10 : | overbeek | 1.5 | |
| 11 : | foreach $peg (@pegs) | ||
| 12 : | overbeek | 1.1 | { |
| 13 : | overbeek | 1.5 | if ($peg =~ /^fig\|\d+\.\d+$/) |
| 14 : | overbeek | 1.1 | { |
| 15 : | overbeek | 1.5 | $genome = $fig->genome_of($peg); |
| 16 : | $loc = $fig->feature_location($peg); | ||
| 17 : | # print "$len{$peg}\t$peg\t$loc\n"; | ||
| 18 : | if ($loc =~ /,/) | ||
| 19 : | { | ||
| 20 : | print STDERR "skipping $peg - do not handle complex locs\n"; | ||
| 21 : | next; | ||
| 22 : | } | ||
| 23 : | overbeek | 1.1 | } |
| 24 : | overbeek | 1.5 | elsif ($peg =~ /^(new\|(\d+\.\d+)\.peg\.\d+)\t(\S+)/) |
| 25 : | { | ||
| 26 : | $peg = $1; | ||
| 27 : | $genome = $2; | ||
| 28 : | $loc = $3; | ||
| 29 : | overbeek | 1.1 | } |
| 30 : | |||
| 31 : | overbeek | 1.5 | ($genome && $loc) || confess $peg; |
| 32 : | |||
| 33 : | overbeek | 1.4 | my $lnC = $fig->contig_ln($genome,$contig); |
| 34 : | overbeek | 1.1 | ($contig,$begin,$end) = $fig->boundaries_of($loc); |
| 35 : | if ($begin < $end) | ||
| 36 : | { | ||
| 37 : | $l = sprintf("%s_%d_%d",$contig,1,$begin-1); | ||
| 38 : | overbeek | 1.4 | if ($end < ($lnC-3)) |
| 39 : | { | ||
| 40 : | $end += 3; | ||
| 41 : | } | ||
| 42 : | overbeek | 1.1 | } |
| 43 : | else | ||
| 44 : | { | ||
| 45 : | overbeek | 1.6 | $l = sprintf("%s_%d_%d",$contig,$fig->contig_ln($genome,$contig),$begin+1); |
| 46 : | overbeek | 1.4 | if ($end > 3) |
| 47 : | { | ||
| 48 : | $end -= 3; | ||
| 49 : | } | ||
| 50 : | overbeek | 1.1 | } |
| 51 : | |||
| 52 : | $loc = join("_",($contig,$begin,$end)); | ||
| 53 : | $seq = uc $fig->dna_seq($genome,$loc); | ||
| 54 : | overbeek | 1.5 | |
| 55 : | overbeek | 1.3 | if (! $seq) |
| 56 : | { | ||
| 57 : | print STDERR &Dumper($peg,$loc,$seq); die "could not get sequence for $peg"; | ||
| 58 : | } | ||
| 59 : | |||
| 60 : | overbeek | 1.1 | # The following hack handles uncertainty about whether SEED gives back the STOP or not |
| 61 : | if (substr($seq,-6,3) =~ /TAA|TAG|TGA/i) | ||
| 62 : | { | ||
| 63 : | overbeek | 1.2 | $end = ($begin < $end) ? $end-3 : $end+3; |
| 64 : | overbeek | 1.1 | $seq = substr($seq,0,length($seq) - 3); |
| 65 : | } | ||
| 66 : | elsif (substr($seq,-3,3) !~ /TAA|TAG|TGA/i) | ||
| 67 : | { | ||
| 68 : | overbeek | 1.4 | warn "BAD STOP: $peg $genome $loc $seq\n"; |
| 69 : | overbeek | 1.1 | } |
| 70 : | |||
| 71 : | overbeek | 1.2 | $loc = join("_",($contig,$begin,$end)); |
| 72 : | overbeek | 1.1 | |
| 73 : | |||
| 74 : | # BACK INTO THE STOP FROM START OF PEG | ||
| 75 : | $pre_peg = uc $fig->dna_seq($genome,$l); | ||
| 76 : | $found = 0; | ||
| 77 : | $len_pre_peg = length($pre_peg); | ||
| 78 : | |||
| 79 : | for ($i=$len_pre_peg-3; $i > 0 && ! $found; $i-=3) | ||
| 80 : | { | ||
| 81 : | $stop = substr($pre_peg,$i,3); | ||
| 82 : | if ($stop eq "TAG" || $stop eq "TAA" || $stop eq "TGA") | ||
| 83 : | { | ||
| 84 : | # print "FOUND $stop for $l\n"; | ||
| 85 : | $orf = substr($pre_peg,$i+3) . $seq; | ||
| 86 : | if (($i-27) > 0) | ||
| 87 : | { | ||
| 88 : | $pre_orf = substr($pre_peg,$i-27,30); | ||
| 89 : | overbeek | 1.5 | my $gs = $fig->genus_species($genome); |
| 90 : | my @aliases = (); | ||
| 91 : | if ($peg =~ /^fig/) | ||
| 92 : | { | ||
| 93 : | @aliases = grep { $_ =~ /^([NXYZA]P_[0-9\.]+)|(uni\|)|(sp\|)/ } $fig->feature_aliases($peg); | ||
| 94 : | } | ||
| 95 : | |||
| 96 : | overbeek | 1.1 | print "ID=$peg\n"; |
| 97 : | print "GENOME=$gs\n"; | ||
| 98 : | if (@aliases > 0) | ||
| 99 : | { | ||
| 100 : | print "ALIASES=",join(",",@aliases),"\n"; | ||
| 101 : | } | ||
| 102 : | print "CONTIG=$contig\n"; | ||
| 103 : | overbeek | 1.5 | |
| 104 : | overbeek | 1.1 | if ($begin < $end) |
| 105 : | { | ||
| 106 : | print "BEGIN=", $begin-($len_pre_peg-$i-3), "\n"; | ||
| 107 : | } | ||
| 108 : | else | ||
| 109 : | { | ||
| 110 : | print "BEGIN=", $begin+($len_pre_peg-$i-3), "\n"; | ||
| 111 : | } | ||
| 112 : | print "END=$end\n"; | ||
| 113 : | print "SEQ=$orf\n"; | ||
| 114 : | print "PREFIX=$pre_orf\n"; | ||
| 115 : | print "OLD_START_POS=", $len_pre_peg-$i-2, "\n"; | ||
| 116 : | print "///\n"; | ||
| 117 : | $found = 1; | ||
| 118 : | } | ||
| 119 : | else | ||
| 120 : | { | ||
| 121 : | print STDERR "skipping $peg - not enough prefix before orf\n"; | ||
| 122 : | } | ||
| 123 : | last; | ||
| 124 : | } | ||
| 125 : | } | ||
| 126 : | if ( ! $found) | ||
| 127 : | { | ||
| 128 : | print STDERR "DID NOT FIND STOP BEFORE $peg $contig $begin $end $l\n"; | ||
| 129 : | } | ||
| 130 : | } |
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