#!/usr/bin/env perl package NAST_to_Eco_coords; use strict; use warnings; use Carp; require Exporter; our @ISA = qw(Exporter); our @EXPORT = qw(NAST_to_Eco_coord); our @NAST_TO_ECO_COORD; our @ECO_TO_NAST_COORD; our $ECO_NAST_SEQ; our $ECO_SEQ; #### sub NAST_to_Eco_coord { my @coords = @_; my @ret_coords; foreach my $coord (@coords) { if ($coord >= length($ECO_NAST_SEQ)) { confess "Error, nast coord $coord >= nast alignment length: " . length($ECO_NAST_SEQ); } push (@ret_coords, $NAST_TO_ECO_COORD[$coord]); } return(@ret_coords); } #### sub Eco_to_NAST_coord { my @coords = @_; my @ret_coords; foreach my $coord (@coords) { if ($coord >= length($ECO_SEQ)) { confess "Error, coordinate $coord of E. coli refseq is >= length of sequence:" . length($ECO_SEQ); } push (@ret_coords, $ECO_TO_NAST_COORD[$coord]); } return(@ret_coords); } sub get_Eco_NAST_alignment { return($ECO_NAST_SEQ); } sub Eco_to_Vregion_string { my ($coord) = @_; my %ranges = ("1-49" => "-V1", "50-100" => "V1", "101-180" => "V1-V2", "181-220" => "V2", "221-399" => "V2-V3", "400-500" => "V3", "501-599" => "V3-V4", "600-650" => "V4", "651-819" => "V4-V5", "820-860" => "V5", "861-999" => "V5-V6", "1000-1050" => "V6", "1051-1119" => "V6-V7", "1120-1150" => "V7", "1151-1239" => "V7-V8", "1240-1290" => "V8", "1291-1409" => "V8-V9", "1410-1480" => "V9", "1481-1600" => "V9+", # should change this to proper length coordinate ); foreach my $range (keys %ranges) { my $region = $ranges{$range}; my ($lend, $rend) = split(/-/, $range); if ($coord >= $lend && $coord <= $rend) { return($region); } } confess "Coordinate $coord out of range of E. coli sequence"; } BEGIN { #>7000004128537908 Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia my $eco_NAST = "............................................................ ................................................AGAGTTT-GA-- T-CA-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--A ACACA-T-GC-A-AGT-CGA-A-CG----------G-TAA-CA-G--------------- -------------AAAG-A-AG-------------------------------------- --------------CTT-G----------------------------------------- -----------------------------------------CTT-CTTT----------- -----G-CT--G--AC--G--AG-T-GG-C-GG-A--C-------------GGG-TGAGT -A--AT-GT-C-T-G-GG---A-A--A-CT-G--C-C-TGA--TG-G------------- -----------------------------------------------------A-GG--- -GGG-AT-AA-CTA-------------------------C-T-G---------------- -------GAA-A---CGG-TAG-CTAA-TA---CC-G--C-AT-A----------A---- ----------------C-------------------------------------GT-C-- ------------------------------------------------------------ ---------------------------------------------------------G-C A-A--------------------------------------------------------- ------------------------------------------------------------ -----------------G-A-C-------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------CAAA--G-A-G-GG-----G--GA-C--C------------------------ ------------------------------------------------------------ --------------------------------TTC-G----------------------- ------------------------------------------------------------ -----------------------------------G-G--CC-TC--T---T-G------ --------C----C-A---T-CG-G---AT---G-T-----G-CCC-AGA--T-GGG--A ------TT--A--G-CT-T----G---TTGG-T-G-GG-G-T----AAC-GG-C-T-C-A CCA--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT- G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G -G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TT GCA-C-AA-T-GG--GC-GC-A----A-G-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T ---G-T-A--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G -T--A---AA-G-TAC--------TT-TC-A-G--C-GGG----GA-G--G---AA-GGG A---GTAA-AG----T--T--AA-T---A----C-----CT-T-TGC-TCA-TT-GA-CG -TT-A-C-CC-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA--- C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT -GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-AC- -G-CA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-A---G-ATG -TG-A-AA-TC--CC-CGG-G--------------------------------------- -----------------------------CTTC-AA------------------------ -------------------------------------------------CC-T-G-GG-A A-C----T-G-C-A-T-C--------T--GA-T-A-C-T-G-GCA--A-G-C-------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -T-T-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG --AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG- A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G -AC-GA------------------------------------------------------ --------AG-A-C-T--GA--CG-----CT-CA-GG--T-G-CGA--AA-G-C------ --------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA- G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--GA-CT---------T-GG--A --G-G-TT-G-TG-C--C------------------------------------------ --------------------------------------------CTT-GA---------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------G-G-C-GT--G-G-C-T-TC-C------GG--A----GC-TAA- -CG-C-G-T--T--AA-GT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG----- C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G- CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G- ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TGGTC-TT-G-AC-A-T-C------- -------CAC-G-G-------------A-AG-T-T-T--TC--A-GA-G-A-T--G-A-G --A-A-T-G--T-G-----CC-------------------------------------T- -TC-G------------------------------------------GG----A----A- --CC-GTG---A--GA-------------------------------------------- -------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G --TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC -C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--G--T--------------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------CCG----------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------G----C----C -G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G- -AC-T-G-CCA--G-T------------------------------------G-A---TA A----------------------------------A-C-T-G--G-A-GG-A--AGG-T- -GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AC-C -A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA ------------------------------------------------------------ --------------------------------------A-G-C-G-A--C-CTCG-C--G ---------------------------------------A-GA-G-C-----------A- -A-G-CG---G----------A--CCT-C------A-T-AAAGT-GC-G-T-C-G-TAG- TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C---------------------- ------------------------------------------------------------ ---------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT- C-G-T----GGA-TC-A-G--A------AT--GCC-AC-G-GT-G-AAT-ACGT-T-CCC GGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G--- TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C------ -------------------------------------------------------T-TC- G----------------------------------------------------------- -------------------------------------------GG-A--GG-G--C---G C-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG-- ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CC.......................... ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ ............................................................ .."; $eco_NAST =~ s/\s+//g; $ECO_NAST_SEQ = $eco_NAST; my @chars = split (//, $eco_NAST); ## convert to an Ecoli sequence reference coord system: my $counter = -1; for (my $i = 0; $i <= $#chars; $i++) { my $char = $chars[$i]; if ($char =~ /\w/) { $counter++; $ECO_TO_NAST_COORD[$counter] = $i; } $NAST_TO_ECO_COORD[$i] = $counter; } # create unaligned sequence $ECO_SEQ = $ECO_NAST_SEQ; $ECO_SEQ =~ s/[\.\-]//g; } 1; #EOM