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extractSpacerTypes.pl
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extractSpacerTypes.pl
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#!/usr/bin/perl
use strict;
# I-Fa: grep -wf ../types/ifa.ab ../genes/aba_genes_ssrA_dr2.tsv | cut -f3 | grep "[^,]+,CRISPR,[^,]+" -Eo | grep -v thiE | sus
my $VIR = "unknown5757";
my $BET = "BQ1898_06609";
my $TRA = "unknown1879";
my $IFB = "thiE|csy4";
my $IFA1 = "cas1__2|ssrA";
my $IFA2 = "cas3__2|unknown975";
my %G;
open in, "../types/crispr.ab";
while (<in>) {
chomp;
$G{$_} = 1;
}
close in;
open NS, ">nspacers.tsv";
open REP, ">rep_ab.fasta";
open SP, ">spacers_ab.fasta";
print NS "Array\tFrequency\n";
my %nrep; my %nsp;
open in, "../genes/aba_genes.tsv";
while (<in>) {
chomp;
next unless /CRISPR/;
my ($ab, $id) = split/\t/;
next unless $G{$ab};
$id =~ s/\.\d+$//;
my $type;
my $x = 0;
my @ns; my @type; my @rep; my @sp;
while (/((\w+)\{[a-z][a-z][0-9]{5}_[0-9]{5} \d+ \d+ [+-]\},)?CRISPR\{CRISPR (\d+) (\d+) .\},?(\w+)?/g) {
my ($p1, $p2, $g1, $g2) = ($3, $4, $2, $5);
#print "$ab $id - $p1 $p2 - $g1 $g2\n";
# Classify
if ($g1 eq $VIR || $g2 eq $VIR) {
if ($type eq "ifa2") {
$type[$x-1] = "vir2";
} else {
$type = "vir1";
}
} elsif ($g1 eq $BET || $g2 eq $BET) {
if ($type eq "ifa2") {
$type[$x-1] = "bet2";
}
$type = "bet1";
} elsif ($g1 eq $TRA || $g2 eq $TRA) {
if ($type eq "ifa1") {
$type[$x-1] = "tra1";
$type = "tra2";
} else {
$type = "tra2";
}
} elsif ($IFB =~ /$g1/ || $IFB =~ /$g2/) {
$type = "ifb";
} elsif ($IFA1 =~ /$g1/ || $IFA1 =~ /$g2/) {
if ($type eq "tra1") {
$type[$x-1] = "tra2";
$type = "tra1";
} elsif ($type eq "tra2") {
$type = "tra1";
} else {
$type = "ifa1";
}
} elsif ($IFA2 =~ /$g1/ || $IFA2 =~ /$g2/) {
if ($type eq "vir1") {
$type = "vir2";
} elsif ($type eq "bet1") {
$type = "bet2";
} else {
$type = "ifa2";
}
}
next unless $type;
my $flag = 0;
#open crispr, "/mnt/data/pangenomes/ab/ccfinder/$ab/$id.gff";
open crispr, "/home/ajperez/databases/ab/ccfinder/$ab/$id.gff";
my (@lines) = <crispr>;
close crispr;
foreach my $l (@lines) {
chomp $l;
next if $l =~ /^##/ || $l =~ /^$/;
my ($att, $n1, $n2, $line) = (split/\t/, $l)[2,3,4,8];
if ($att eq "CRISPR") {
next unless $n1 == $p1 && $n2 == $p2;
$flag = 1;
$l =~ m/DR=([ATCG]+);.+Number_of_spacers=(\d+)/;
my ($rep, $ns) = ($1, $2);
#print "# $ns\n";
#print "$rep\n";
$ns[$x] = $ns; $type[$x] = $type; $rep[$x] = $rep;
} elsif ($att eq "CRISPRspacer" && $flag == 1) {
$l =~ m/sequence=([ATCGN]+);/; # tomamos tb N, pero en el _uniq los descartaremos
my $spacer = $1;
#print "$spacer\n";
push @{$sp[$x]}, $spacer;
} elsif ($att eq "RightFLANK") {
$flag = 0;
}
}
$x++;
#print "*** $x\n";
}
# Print
for (my $i = 0; $i <= $#ns; $i++) {
#print "$type[$i] ** $ns[$i]\n";
print NS "$type[$i]\t$ns[$i]\n";
my $seq_id = "$type[$i]_$ab";
$nrep{$seq_id}++;
print REP ">$seq_id\_$nrep{$seq_id}\n";
print REP "$rep[$i]\n";
foreach my $seq_sp (@{$sp[$i]}) {
$nsp{$seq_id}++;
print SP ">$seq_id\_$nsp{$seq_id}\n";
print SP "$seq_sp\n";
}
}
}
close in;
close NS;
close REP;
close SP;
exit;