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Revision 1.4 - (view) (download) (as text)
| 1 : | overbeek | 1.2 | # -*- perl -*- |
| 2 : | overbeek | 1.1 | |
| 3 : | use FIG; | ||
| 4 : | my $fig = new FIG; | ||
| 5 : | |||
| 6 : | overbeek | 1.4 | $usage = "usage: make_PHOBs_for_subsystems Dir [SimilarityCutoff FracCoverage] < FileOf_SS-Role-PEG-Func"; |
| 7 : | overbeek | 1.1 | |
| 8 : | ( | ||
| 9 : | ($dir = shift @ARGV) && (! -d $dir) | ||
| 10 : | ) | ||
| 11 : | || die $usage; | ||
| 12 : | |||
| 13 : | overbeek | 1.4 | if (@ARGV == 2) |
| 14 : | { | ||
| 15 : | $sim_cutoff = shift @ARGV; | ||
| 16 : | $frac_cov = shift @ARGV; | ||
| 17 : | } | ||
| 18 : | |||
| 19 : | overbeek | 1.1 | mkdir($dir,0777) || die "could not make $dir"; |
| 20 : | while (defined($_ = <STDIN>)) | ||
| 21 : | { | ||
| 22 : | chop; | ||
| 23 : | ($ss,$role,$peg) = split(/\t/,$_); | ||
| 24 : | push(@{$subH{$ss}->{$role}},$peg); | ||
| 25 : | } | ||
| 26 : | |||
| 27 : | $tmpF = "/tmp/pegs$$.fasta"; | ||
| 28 : | |||
| 29 : | open(INDEXSS,">$dir/index") || die "could not open $dir/index"; | ||
| 30 : | $ssN = 0; | ||
| 31 : | foreach $ss (sort keys(%subH)) | ||
| 32 : | { | ||
| 33 : | ++$ssN; | ||
| 34 : | mkdir("$dir/$ssN",0777) || die "could not make $dir/$ssN"; | ||
| 35 : | print INDEXSS "$ssN\t$ss\n"; | ||
| 36 : | |||
| 37 : | open(INDEXR,">$dir/$ssN/index") || die "could not open $dir/$ssN/index"; | ||
| 38 : | $roleN = 0; | ||
| 39 : | foreach $role (sort keys(%{$subH{$ss}})) | ||
| 40 : | { | ||
| 41 : | ++$roleN; | ||
| 42 : | overbeek | 1.2 | |
| 43 : | overbeek | 1.1 | $pegs = $subH{$ss}->{$role}; |
| 44 : | overbeek | 1.4 | if (@$pegs < 8) |
| 45 : | overbeek | 1.2 | { |
| 46 : | print STDERR "Skipping $dir/$ssN/$roleN, role $role --- only ", (scalar @$pegs), " pegs\n"; | ||
| 47 : | next; | ||
| 48 : | } | ||
| 49 : | |||
| 50 : | overbeek | 1.4 | print INDEXR "$roleN\t$role\n"; |
| 51 : | |||
| 52 : | overbeek | 1.1 | open(TMP,">$tmpF") || die "could not open $tmpF"; |
| 53 : | foreach $peg (@$pegs) | ||
| 54 : | { | ||
| 55 : | if ($pseq = $fig->get_translation($peg)) | ||
| 56 : | { | ||
| 57 : | print TMP ">$peg\n$pseq\n"; | ||
| 58 : | } | ||
| 59 : | else | ||
| 60 : | { | ||
| 61 : | print STDERR "failed to get translation for $peg\n"; | ||
| 62 : | } | ||
| 63 : | } | ||
| 64 : | close(TMP); | ||
| 65 : | |||
| 66 : | mkdir("$dir/$ssN/$roleN",0777) || die "could not make $dir/$ssN/$roleN"; | ||
| 67 : | overbeek | 1.4 | &FIG::run("split_and_trim_sequences $dir/$ssN/$roleN/split_info $sim_cutoff $frac_cov < $tmpF"); |
| 68 : | overbeek | 1.1 | |
| 69 : | overbeek | 1.3 | if (-s "$dir/$ssN/$roleN/split_info/set.sizes") |
| 70 : | overbeek | 1.1 | { |
| 71 : | overbeek | 1.3 | open(SZ,"<$dir/$ssN/$roleN/split_info/set.sizes") || die " could not open $dir/$ssN/$roleN/split_info/set.sizes"; |
| 72 : | overbeek | 1.2 | while (defined($_ = <SZ>)) |
| 73 : | overbeek | 1.1 | { |
| 74 : | overbeek | 1.2 | if (($_ =~ /^(\d+)\t(\d+)/) && ($2 > 3)) |
| 75 : | { | ||
| 76 : | $n = $1; | ||
| 77 : | &FIG::run("make_phob_from_seqs $dir/$ssN/$roleN/$n < $dir/$ssN/$roleN/split_info/$n"); | ||
| 78 : | } | ||
| 79 : | overbeek | 1.1 | } |
| 80 : | overbeek | 1.2 | close(SZ); |
| 81 : | } | ||
| 82 : | else | ||
| 83 : | { | ||
| 84 : | system("rmdir $dir/$ssN/$roleN") && warn "Could not rmdir $dir/$ssN/$roleN"; | ||
| 85 : | print STDERR "Skipping role $role in $dir/$ssN/$roleN\n"; | ||
| 86 : | overbeek | 1.1 | } |
| 87 : | } | ||
| 88 : | close(INDEXR); | ||
| 89 : | } | ||
| 90 : | close(INDEXSS); | ||
| 91 : | unlink($tmpF); |
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