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global_structures.ph
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sub load_color_struct {
my %rgb;
my %color_lookup;
$rgb{33} = "0066FF"; # blue (old = 0000ff)
$rgb{34} = "87ceff"; # lt blue
$rgb{35} = "a0fc8d"; # lt green
$rgb{36} = "ff0000"; # red
$rgb{37} = "8e0000"; # brown
$rgb{38} = "aaaaaa"; # lt gray
$rgb{39} = "347235"; # dk green
$rgb{40} = "ff00ff"; # magenta
$rgb{41} = "ffa0a0"; # salmon
$rgb{42} = "ff8102"; # orange
$rgb{43} = "99c517"; # olive
$rgb{44} = "fdd017"; # gold
$rgb{45} = "666666"; # gray
$rgb{46} = "ffbaff"; # pink
$rgb{47} = "008e8e"; # blue green
$rgb{48} = "8d38c9"; # violet
$rgb{49} = "ede275"; # lt brown
$rgb{50} = "000000"; # black
$rgb{51} = "ffffff"; # diagonal lines
$rgb{52} = "d6dbbf"; # my (Martin Wu) itune color
$rgb{53} = "ff0033"; # Wu red
$rgb{54} = "00f5ff"; # turquoise1
$rgb{55} = "e0e0e0"; # gray88
$rgb{56} = "ff1493"; # DeepPink1
$rgb{57} = "ff4500"; # OrangeRed1
$rgb{58} = "2f4f4f"; # DarkSlateGray
$rgb{59} = "e6e6fa"; # Lavender
$rgb{60} = "FFF8DC"; # regions, cornsilk
$rgb{61} = "e0e0e0"; # monogene, user55
$rgb{62} = "993333"; # brownish purple
$rgb{63} = "996666"; # tanish
$rgb{64} = "B0C4DE"; # Light steel blue
$rgb{65} = "F5D6DA"; # new pastel spectrum 91-100%
$rgb{66} = "E5C5DB"; # new pastel spectrum 81-90%
$rgb{67} = "D0BCD9"; # new pastel spectrum 71-80%
$rgb{68} = "BBB8D2"; # new pastel spectrum 61-70%
$rgb{69} = "AAB7C5"; # new pastel spectrum 51-60%
$rgb{70} = "9EB5B3"; # new pastel spectrum 41-50%
$rgb{71} = "97AFA0"; # new pastel spectrum 31-40%
$rgb{72} = "94A48E"; # new pastel spectrum 21-30%
$rgb{73} = "919481"; # new pastel spectrum 11-20%
$rgb{74} = "8B8378"; # new pastel spectrum 1-10%
$rgb{75} = "CDE472"; # iceberg lettuce
$rgb{76} = "adff2f"; # green yellow
$rgb{77} = "ba55d3"; # med orchid
$color_lookup{"Mobile and extrachromosomal element functions"}= 48;
$color_lookup{"152"}= 39; # Mobile and extrachromosomal element functions: Prophage functions
$color_lookup{"154"}= 40; # Mobile and extrachromosomal element functions: Transposon functions
$color_lookup{"186"}= 53; # Mobile and extrachromosomal element functions: Plasmid functions
$color_lookup{"708"}= 53; # Mobile and extrachromosomal element functions: Other
$color_lookup{"No database match"} = 49;
$color_lookup{"Amino acid biosynthesis"} = 41;
$color_lookup{"70"}= 41; # Amino acid biosynthesis: Aromatic amino acid family
$color_lookup{"71"}= 41; # Amino acid biosynthesis: Aspartate family
$color_lookup{"73"}= 41; # Amino acid biosynthesis: Glutamate family
$color_lookup{"74"}= 41; # Amino acid biosynthesis: Pyruvate family
$color_lookup{"75"}= 41; # Amino acid biosynthesis: Serine family
$color_lookup{"161"}= 41; # Amino acid biosynthesis: Histidine family
$color_lookup{"69"}= 41; # Amino acid biosynthesis: Other
$color_lookup{"Biosynthesis of cofactors, prosthetic groups, and carriers"} = 34;
$color_lookup{"77"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Biotin
$color_lookup{"78"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Folic acid
$color_lookup{"79"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Heme, porphyrin, and cobalamin
$color_lookup{"80"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Lipoate
$color_lookup{"81"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Menaquinone and ubiquinone
$color_lookup{"82"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Molybdopterin
$color_lookup{"83"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Pantothenate and coenzyme A
$color_lookup{"84"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Pyridoxine
$color_lookup{"85"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Riboflavin, FMN, and FAD
$color_lookup{"86"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Glutathione
$color_lookup{"162"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Thiamine
$color_lookup{"163"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Pyridine nucleotides
$color_lookup{"191"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Chlorophyll
$color_lookup{"707"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Siderophores
$color_lookup{"76"}= 34; # Biosynthesis of cofactors, prosthetic groups, and carriers: Other
$color_lookup{"Cell envelope"} = 35;
$color_lookup{"88"}= 35; # Cell envelope: Other
$color_lookup{"89"}= 35; # Cell envelope: Biosynthesis of murein sacculus and peptidoglycan
$color_lookup{"90"}= 35; # Cell envelope: Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides
$color_lookup{"91"}= 35; # Cell envelope: Surface structures
$color_lookup{"Cellular processes"} = 36;
$color_lookup{"93"}= 36; # Cellular processes: Cell division
$color_lookup{"94"}= 36; # Cellular processes: Toxin production and resistance
$color_lookup{"96"}= 36; # Cellular processes: Detoxification
$color_lookup{"98"}= 36; # Cellular processes: DNA transformation
$color_lookup{"149"}= 36; # Cellular processes: Adaptations to atypical conditions
$color_lookup{"187"}= 36; # Cellular processes: Pathogenesis
$color_lookup{"188"}= 36; # Cellular processes: Chemotaxis and motility
$color_lookup{"701"}= 36; # Cellular processes: Cell adhesion
$color_lookup{"702"}= 36; # Cellular processes: Conjugation
$color_lookup{"705"}= 36; # Cellular processes: Sporulation and germination
$color_lookup{"706"}= 36; # Cellular processes: Biosynthesis of natural products
$color_lookup{"92"}= 36; # Cellular processes: Other
$color_lookup{"Central intermediary metabolism"} = 37;
$color_lookup{"100"}= 37; # Central intermediary metabolism: Amino sugars
$color_lookup{"103"}= 37; # Central intermediary metabolism: Phosphorus compounds
$color_lookup{"104"}= 37; # Central intermediary metabolism: Polyamine biosynthesis
$color_lookup{"105"}= 37; # Central intermediary metabolism: Sulfur metabolism
$color_lookup{"179"}= 37; # Central intermediary metabolism: Nitrogen fixation
$color_lookup{"160"}= 37; # Central intermediary metabolism: Nitrogen metabolism
$color_lookup{"698"}= 37; # Central intermediary metabolism: One-carbon metabolism
$color_lookup{"709"}= 37; # Central intermediary metabolism: Electron carrier regeneration
$color_lookup{"102"}= 37; # Central intermediary metabolism: Other
$color_lookup{"Energy metabolism"} = 38;
$color_lookup{"109"}= 38; # Energy metabolism: Amino acids and amines
$color_lookup{"111"}= 38; # Energy metabolism: ATP-proton motive force interconversion
$color_lookup{"112"}= 38; # Energy metabolism: Electron transport
$color_lookup{"118"}= 38; # Energy metabolism: Pyruvate dehydrogenase
$color_lookup{"108"}= 38; # Energy metabolism: Aerobic
$color_lookup{"110"}= 38; # Energy metabolism: Anaerobic
$color_lookup{"113"}= 38; # Energy metabolism: Entner-Doudoroff
$color_lookup{"114"}= 38; # Energy metabolism: Fermentation
$color_lookup{"116"}= 38; # Energy metabolism: Glycolysis/gluconeogenesis
$color_lookup{"117"}= 38; # Energy metabolism: Pentose phosphate pathway
$color_lookup{"119"}= 38; # Energy metabolism: Sugars
$color_lookup{"120"}= 38; # Energy metabolism: TCA cycle
$color_lookup{"159"}= 38; # Energy metabolism: Methanogenesis
$color_lookup{"105"}= 38; # Energy metabolism: Biosynthesis and degradation of polysaccharides
$color_lookup{"164"}= 38; # Energy metabolism: Photosynthesis
$color_lookup{"180"}= 38; # Energy metabolism: Chemoautotrophy
$color_lookup{"184"}= 38; # Energy metabolism: Other
$color_lookup{"Nitrogen metabolism"} = 38;
$color_lookup{"Methanogenesis"} = 38;
$color_lookup{"Fatty acid and phospholipid metabolism"} = 40;
$color_lookup{"176"}= 48; # Fatty acid and phospholipid metabolism: Biosynthesis
$color_lookup{"177"}= 48; # Fatty acid and phospholipid metabolism: Degradation
$color_lookup{"121"}= 48; # Fatty acid and phospholipid metabolism: Other
$color_lookup{"Purines, pyrimidines, nucleosides, and nucleotides"} = 42;
$color_lookup{"123"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: 2'-Deoxyribonucleotide metabolism
$color_lookup{"124"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: Nucleotide and nucleoside interconversions
$color_lookup{"125"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: Purine ribonucleotide biosynthesis
$color_lookup{"126"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: Pyrimidine ribonucleotide biosynthesis
$color_lookup{"127"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: Salvage of nucleosides and nucleotides
$color_lookup{"128"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: Sugar-nucleotide biosynthesis and conversions
$color_lookup{"122"}= 42; # Purines, pyrimidines, nucleosides, and nucleotides: Other
$color_lookup{"Regulatory functions"} = 43;
$color_lookup{"129"}= 43; # Regulatory functions: Other
$color_lookup{"261"}= 43; # Regulatory functions: DNA interactions
$color_lookup{"262"}= 43; # Regulatory functions: RNA interactions
$color_lookup{"263"}= 43; # Regulatory functions: Protein interactions
$color_lookup{"264"}= 43; # Regulatory functions: Small molecule interactions
$color_lookup{"129"}= 43; # Regulatory functions: Other
$color_lookup{"Signal transduction"} = 43;
$color_lookup{"699"}= 43; # Signal transduction: Two-component systems
$color_lookup{"700"}= 43; # Signal transduction: PTS
$color_lookup{"710"}= 43; # Signal transduction: Other
$color_lookup{"DNA metabolism"} = 44;
$color_lookup{"130"}= 44; # DNA metabolism: Other
$color_lookup{"131"}= 44; # DNA metabolism: Degradation of DNA
$color_lookup{"132"}= 44; # DNA metabolism: DNA replication, recombination, and repair
$color_lookup{"170"}= 44; # DNA metabolism: Chromosome-associated proteins
$color_lookup{"183"}= 44; # DNA metabolism: Restriction/modification
$color_lookup{"Transcription"} = 45;
$color_lookup{"134"}= 45; # Transcription: Degradation of RNA
$color_lookup{"135"}= 45; # Transcription: DNA-dependent RNA polymerase
$color_lookup{"165"}= 45; # Transcription: Transcription factors
$color_lookup{"166"}= 45; # Transcription: RNA processing
$color_lookup{"133"}= 45; # Transcription: Other
$color_lookup{"Protein fate"} = 46;
$color_lookup{"97"}= 46; # Protein fate: Protein and peptide secretion and trafficking
$color_lookup{"140"}= 46; # Protein fate: Protein modification and repair
$color_lookup{"95"}= 46; # Protein fate: Protein folding and stabilization
$color_lookup{"138"}= 46; # Protein fate: Degradation of proteins, peptides, and glycopeptides
$color_lookup{"189"}= 46; # Protein fate: Other
$color_lookup{"Protein synthesis"} = 46;
$color_lookup{"137"}= 46; # Protein synthesis: tRNA aminoacylation
$color_lookup{"158"}= 46; # Protein synthesis: Ribosomal proteins: synthesis and modification
$color_lookup{"168"}= 46; # Protein synthesis: tRNA and rRNA base modification
$color_lookup{"169"}= 46; # Protein synthesis: Translation factors
$color_lookup{"136"}= 46; # Protein synthesis: Other
$color_lookup{"Transport and binding proteins"} = 47;
$color_lookup{"141"}= 47; # Transport and binding proteins: Unknown substrate
$color_lookup{"142"}= 47; # Transport and binding proteins: Amino acids, peptides and amines
$color_lookup{"143"}= 47; # Transport and binding proteins: Anions
$color_lookup{"144"}= 47; # Transport and binding proteins: Carbohydrates, organic alcohols, and acids
$color_lookup{"145"}= 47; # Transport and binding proteins: Cations and iron carrying compounds
$color_lookup{"146"}= 47; # Transport and binding proteins: Nucleosides, purines and pyrimidines
$color_lookup{"182"}= 47; # Transport and binding proteins: Porins
$color_lookup{"147"}= 47; # Transport and binding proteins: Other
$color_lookup{"Other categories"} = 50;
$color_lookup{"Hypothetical proteins"} = 51;
$color_lookup{"NULL"}= 7; # hypothetical proteins (white, was 51, diagonal)
$color_lookup{"Conserved hypothetical proteins"} = 52;
$color_lookup{"156"}= 52; # Hypothetical proteins: Conserved
$color_lookup{"704"}= 52; # Hypothetical proteins: Domain
$color_lookup{"Unknown"} = 50; # genes with Unknown assignment, are grouped into other, if that makes sense.
$color_lookup{"Unknown function"} = 50; # genes with Unknown assignment, are grouped into other, if that makes sense.
$color_lookup{"157"}= 50; # Unknown function: General
$color_lookup{"703"}= 50; # Unknown function: Enzymes of unknown specificity
$color_lookup{"Unclassified"} = 50; # genes with Unknown assignment, are grouped into other, if that makes sense.
$color_lookup{"185"}= 50; # Unclassified
$color_lookup{"Disrupted reading frame"} = 50; # genes with Unknown assignment, are grouped into other, if that makes sense.
$color_lookup{"270"}= 50; # Disrupted reading frame
#######################################################
# dfouts phage roles
#######################################################
$color_lookup{"1000"}= 64; # Regulatory functions: DNA interactions [magenta]
$color_lookup{"1015"}= 35; # Regulatory functions: protein interactions (eg anti-repressor) [lt green]
$color_lookup{"1034"}= 76; # Regulatory functions: anti-termination [green yellow]
$color_lookup{"1001"}= 6; # DNA metabolism: DNA recombination [yellow]
$color_lookup{"1002"}= 44; # DNA metabolism: DNA integration [gold]
$color_lookup{"1032"}= 59; # DNA metabolism: DNA excision [lavender]
$color_lookup{"1003"}= 2; # DNA metabolism: DNA replication [green]
$color_lookup{"1004"}= 54; # DNA metabolism: Restriction/modification [turquoise1]
$color_lookup{"1016"}= 42; # DNA metabolism: DNA interactions (eg SSB) [orange]
$color_lookup{"1034"}= 75; # DNA metabolism: DNA segregation (eg SpoIIIE/FtsK) [iceberg lettice]
$color_lookup{"1005"}= 30; # Capsid structural components and assembly: small terminase [lt pink]
$color_lookup{"1006"}= 28; # Capsid structural components and assembly: large terminase [pink]
$color_lookup{"1007"}= 8; # Capsid structural components and assembly: portal [dark blue]
$color_lookup{"1008"}= 39; # Capsid structural components and assembly: protease (scaffold protein) [dk green]
$color_lookup{"1009"}= 48; # Capsid structural components and assembly: major capsid [violet]
$color_lookup{"1017"}= 43; # Capsid structural components and assembly: minor capsid [olive]
$color_lookup{"1026"}= 58; # Capsid structural components and assembly: other [dark slate gray]
$color_lookup{"1010"}= 25; # Tail and baseplate assembly: tape measure [brown]
$color_lookup{"1011"}= 47; # Tail and baseplate assembly: tail component [blue green]
$color_lookup{"1033"}= 70; # Tail and baseplate assembly: tail fiber [lt turquoise]
$color_lookup{"1035"}= 77; # Tail and baseplate assembly: receptor-binding [med orchid]
$color_lookup{"1012"}= 53; # Host cell lysis: endolysin/lysin [red]
$color_lookup{"1013"}= 20; # Host cell lysis: holin [lt red]
$color_lookup{"1014"}= 60; # putative fitness factor [cornsilk]
$color_lookup{"1018"}= 45; # Conserved phage protein (hit in phage db, no known function) [gray]
$color_lookup{"1019"}= 33; # Target gene for integration [blue]
$color_lookup{"1020"}= 38; # Conserved hypothetical (No matches to reference phage genome (or phage db but matches in other db)) [lt gray]
$color_lookup{"1021"}= 34; # DNA metabolism: nucleotide degradation (nucleases) [lt blue]
$color_lookup{"1027"}= 10; # DNA metabolism: Salvage of nucleosides and nucleotides [blue]
$color_lookup{"1022"}= 49; # DNA metabolism: DNA ligase [lt brown]
$color_lookup{"1023"}= 46; # Transposon functions [pink]
$color_lookup{"1024"}= 40; # Introns [salmon]
$color_lookup{"1025"}= 37; # Drug resistance and toxin production [brown]
$color_lookup{"1028"}= 50; # Hypothetical Phage protein (novel CDS) [black]
$color_lookup{"1029"}= 57; # Transcription: Transcription factors [orangered1]
$color_lookup{"1030"}= 62; # Plasmid-like functions: Addiction: toxin (ie pemK of R100, phd of phage P1) [brownish purple]
$color_lookup{"1031"}= 63; # Plasmid-like functions: Addiction: anti-toxin (ie pemI of R100, doc of phage P1) [tanish]
$color_lookup{"2000"}= 7; # (white) different ORF call by other facility [white]
#######################################################
return(\%rgb, \%color_lookup);
}
sub load_global_struct {
my %s;
# debugging and options things
$s{'debug'} = 0;
$s{'prog'} = $0;
$s{'prog'} =~ s/.*\///;
$s{'seq_line_toggle'} = 1;
$s{'trna_name_toggle'} = 0;
$s{'truncate_name_toggle'} = 0;
$s{'short_gene_toggle'} = 0;
$s{'object_spacing'} = 22;
$s{'locus_toggle'} = 0;
$s{'gene_sym_toggle'} = 0;
$s{'xml_toggle'} = 0;
$s{'block_toggle'} = 1;
$s{'select_genes_toggle'} = 0;
# color things
$s{'color_start'} = 33;
$s{'black'} = 0;
$s{'blue'} = 1;
$s{'green'} = 2;
$s{'cyan'} = 3;
$s{'red'} = 4;
$s{'magenta'} = 5;
$s{'yellow'} = 6;
$s{'white'} = 7;
$s{'pink'} = 30;
$s{'cornsilk'} = 60;
$s{'user55'} = 61;
$s{'gray'} = 45;
$s{'crosshatch'} = 51;
$s{'regions'} = 60;
# general layout things
$s{'tick'} = 100; # make tick mark every 100 bp
$s{'major_tick'} = 2000; # make major tick mark every 2000 bp
$s{'minor_tick'} = 1000; # make minor tick mark every 2000 bp
$s{'x_border'} = 500;
$s{'y_border'} = 2000;
$s{'line_spacing'} = 4000;
$s{'point_size'} = 12;
$s{'char_width'} = 105;
$s{'line_offset'} = 500;
$s{'forward'} = 1;
$s{'reverse'} = 2;
$s{'label_height'} = 150;
$s{'label_offset'} = 70;
$s{'row_depth'} = 105; # 105
$s{'block_depth'} = 120;
$s{'gene_depth'} = 100;
$s{'gene_height'} = 600;
$s{'gene_offset'} = 75;
$s{'gene_arrow_height'} = $s{'gene_height'} * 2;
$s{'gene_arrow_width'} = $s{'gene_height'} * 0.5;
$s{'gene_total'} = ($s{'gene_height'} + $s{'gene_offset'});
$s{'cross_hatch_offset'} = 75;
$s{'cross_hatch_depth'} = 95;
$s{'chi_position'} = $s{'gene_height'};
$s{'chi_height'} = $s{'line_spacing'} - 3*$s{'gene_height'};
$s{'arrow_offset'} = 125;
$s{'tick_offset'} = 75;
$s{'insertion_arrow_pad_x'} = 30;
$s{'insertion_arrow_pad_y'} = 30;
$s{'insertion_arrow_len'} = 200;
$s{'range_height'} = 200;
$s{'range_offset'} = 75;
$s{'range_total'} = $s{'range_height'} / 2;
$s{'transport_height'} = 450;
$s{'transport_width'} = 100;
$s{'transport_offset'} = 30;
$s{'transport_total'} = ($s{'transport_height'} + $s{'transport_offset'} + $s{'label_height'} + $s{'label_offset'});
$s{'legend_height'} = 250;
$s{'legend_width'} = 500;
$s{'legend_inc'} = 75;
$s{'legend_offset'} = 250;
$s{'trna_height'} = 550;
$s{'trna_width'} = 500;
$s{'trna_pad'} = 0;
$s{'trna_total'} = ($s{'trna_height'} + $s{'trna_offset'} + $s{'label_height'} + $s{'label_offset'});
$s{'rrna_height'} = 250;
$s{'rrna_pad'} = 0;
$s{'srna_height'} = 250;
$s{'srna_pad'} = 0;
$s{'repeat_height'} = 180;
$s{'repeat_offset'} = 140;
$s{'repeat_total'} = ($s{'repeat_height'}/2 + $s{'repeat_offset'} + $s{'label_height'} + $s{'label_offset'});
$s{'mem_squiggle1'} = [0, -0.5, -0.5, -0.291666666666667, 0.5, 0.125, 0, 0.5];
$s{'mem_squiggle2'} = [0, 0.5, 0.5, 0.125, -0.5, -0.291666666666667, 0, -0.5];
$s{'hairpin'} = [0.277777777777778, 0.99537037037037, 0.277777777777778, 0.671296296296296, 0.277777777777778, 0.361111111111111, 0, 0.277777777777778, 0, 0.12037037037037, 0.277777777777778, 0, 0.722222222222222, 0, 1, 0.12037037037037, 1, 0.277777777777778, 0.722222222222222, 0.361111111111111, 0.722222222222222, 0.671296296296296, 0.722222222222222, 0.99537037037037];
$s{'cleave_squiggle'} = [-0.5, -0.5, 0.5, -0.327586206896552, -0.5, -0.189655172413793, 0.5, -0.0517241379310345, -0.5, 0.0862068965517241, 0.5, 0.224137931034483, -0.5, 0.362068965517241, 0.5, 0.5];
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return(\%s);
}
1;