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Revision 1.3 - (view) (download) (as text)
| 1 : | disz | 1.1 | use CGI; |
| 2 : | my $cgi = new CGI; | ||
| 3 : | use FIG; | ||
| 4 : | |||
| 5 : | my $fig = new FIG; | ||
| 6 : | |||
| 7 : | disz | 1.3 | #open (PEGS, "rosspegs"); |
| 8 : | open (PEGS, $ARGV[0]); | ||
| 9 : | my %pegs; | ||
| 10 : | |||
| 11 : | while (<PEGS>) { | ||
| 12 : | $pegs[$_] = 1; | ||
| 13 : | } | ||
| 14 : | olson | 1.2 | |
| 15 : | #fig|169963.1.peg.1 NC_003210 318_1673 NP_463534.1 isu,icw(1),ff dnaA Chromosomal replication initiator protein dnaA CDD:pfam00004,CDD:pfam00308,CDD:pfam01695,CDD:smart00382,GeneID:984365,InterPro:IPR001957,InterPro:IPR003593,NCBI_gi:16802049,Pfam:PF00308,SMART:Q8YAW2,SMART:SM00382,UniProtKB:Q8YAW2 http://www.nmpdr.org/linkin.cgi?id=fig|169963.1.peg.1 MQSIED | ||
| 16 : | |||
| 17 : | disz | 1.1 | while (defined($_ = <STDIN>)) |
| 18 : | { | ||
| 19 : | chop; | ||
| 20 : | disz | 1.3 | ($peg,$contig_refseq,$contig_refseq_coords,$refseq,$ev, $gene, $fixed_func, $dbxref, $kegg, $subsystems, $link, $seq) = split(/\t/,$_); |
| 21 : | disz | 1.1 | $funcSeed = $fig->function_of($peg,undef,1); |
| 22 : | my($func1,$ecs1) = &fix_func($funcSeed); | ||
| 23 : | disz | 1.3 | if (! $pegs[$peg]) |
| 24 : | #if (0) | ||
| 25 : | olson | 1.2 | #if (($func1 ne $fixed_func) || ($ecs1 ne $ecs)) |
| 26 : | #if ($func1 ne $fixed_func) | ||
| 27 : | disz | 1.1 | { |
| 28 : | print STDERR &Dumper($fixed_func,$func1,$ecs,$ecs1); | ||
| 29 : | print STDERR "$_\n"; | ||
| 30 : | } | ||
| 31 : | else | ||
| 32 : | { | ||
| 33 : | disz | 1.3 | my ($evcodes, $subs, $structured_english) = $fig->to_structured_english($fig,$peg); |
| 34 : | disz | 1.1 | my $text = $cgi->unescape($structured_english); |
| 35 : | olson | 1.2 | |
| 36 : | my $nmpdr_id_text = "nmpdr_id=$peg"; | ||
| 37 : | my $contig_refseq_text= "reference_contig_refseq=$contig_refseq"; | ||
| 38 : | my $refseq_coords_text = "reference_contig_refseq_coordinates=$contig_refseq_coords"; | ||
| 39 : | my $refseq_id_text= "reference_protein_refseq=$refseq"; | ||
| 40 : | my $evc_text= "evidence_code=$ev"; | ||
| 41 : | my $gene_symbol_text = "gene_symbol=$gene"; | ||
| 42 : | my $desc_text = "description=\"$func1\""; | ||
| 43 : | #my $desc_text = "description=\"$fixed_func\""; | ||
| 44 : | my $dbxref_text = "dbxref=$dbxref"; | ||
| 45 : | my $kegg_text = "kegg=$kegg"; | ||
| 46 : | disz | 1.3 | my $subsystem_text = "subsystem=$subs"; |
| 47 : | olson | 1.2 | my $nmpdr_link_text = "nmpdr_web_page=\"$link\""; |
| 48 : | my $structured_eng_text= "structured_description=\`$structured_english\`"; | ||
| 49 : | my $seq_text= "protein_sequence=\"$seq\""; | ||
| 50 : | |||
| 51 : | if ($structured_english && $seq) | ||
| 52 : | disz | 1.1 | { |
| 53 : | disz | 1.3 | print join("\n",($nmpdr_id_text, $contig_refseq_text, $refseq_coords_text, $refseq_id_text, $evc_text, $gene_symbol_text, $desc_text, $dbxref_text, $subsystem_text, $nmpdr_link_text, $structured_eng_text, $seq_text)), "\n//\n"; |
| 54 : | olson | 1.2 | #print join("\n",($nmpdr_id_text, $contig_refseq_text, $refseq_coords_text, $refseq_id_text, $evc_text, $gene_symbol_text, $desc_text, $dbxref_text, $kegg_text, $subsystem_text, $nmpdr_link_text, $structured_eng_text, $seq_text)), "\n"; |
| 55 : | #print join("\t",($peg,$refseq,$seq,'',$fixed_func,$ecs,$structured_english,'','')),"\n"; | ||
| 56 : | disz | 1.1 | } |
| 57 : | } | ||
| 58 : | } | ||
| 59 : | |||
| 60 : | |||
| 61 : | |||
| 62 : | sub fix_func { | ||
| 63 : | my($func) = @_; | ||
| 64 : | my($ecs); | ||
| 65 : | |||
| 66 : | $ecs = {}; | ||
| 67 : | while ($func =~ /^(.*\S)\s*\(EC ([^\)]+)\)(.*)$/) | ||
| 68 : | { | ||
| 69 : | $ecs->{$2} = 1; | ||
| 70 : | $func = $3 ? $1 . $3 : $1; | ||
| 71 : | } | ||
| 72 : | $func =~ s/\s+\@\s+/ AND /g; | ||
| 73 : | $func =~ s/;\s+/ AND\/OR /g; | ||
| 74 : | return ($func,join(";",sort keys(%$ecs))); | ||
| 75 : | } |
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