forked from sanger-pathogens/SPN-Resistance_Sanger
-
Notifications
You must be signed in to change notification settings - Fork 0
/
SPN_Target2MIC.pl
executable file
·217 lines (206 loc) · 7.22 KB
/
SPN_Target2MIC.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
#use Getopt::Long;
use Getopt::Std;
use File::Copy qw(copy);
use Env;
###Start Doing Stuff###
my $Res_output = "RES-MIC_".$ARGV[1];
open(my $fh,'>',$Res_output) or die "Could not open file '$Res_output' $!";
#print STDERR Dumper \@ARGV;
print STDERR "Output file name is: $Res_output\n";
my %Res_hash;
my $RES_full_name = $ARGV[0];
open(MYINPUTFILE, "$RES_full_name");
while(<MYINPUTFILE>) {
#next if $. < 2;
my $line = $_;
chomp($line);
#print STDERR "$line\n";
my @res_arr;
@res_arr = split('\t',$line);
$Res_hash{$res_arr[0]} = $res_arr[1];
}
close MYINPUTFILE;
while (my ($key, $val) = each %Res_hash) {
my @val_arr = split(':',$val);
my @val_sort = sort(@val_arr);
my $val_out = join(':',@val_sort);
print STDERR "$key\t$val_out\n";
}
print STDERR "\n";
print STDERR Dumper \%Res_hash;
my %drug;
my %Out_hash;
###ER_CL Category###
$drug{ERY} = "=,0.06,S";
$drug{CLI} = "=,0.06,S";
$drug{SYN} = "<=,1.0,S";
$drug{LZO} = "<=,2.0,S";
$drug{ERY_CLI} = "neg";
my @Res_targs = split(':',$Res_hash{EC});
my $left_side = "no";
if ($Res_hash{"EC"} eq "neg") {
#print STDERR "ER_CL,$Res_hash{EC},".$drug{ERY}.",".$drug{CLI}.",".$drug{SYN}.",".$drug{LZO}.",".$drug{ERY_CLI}."\n";
$Out_hash{EC} = "$Res_hash{EC},$drug{ERY},$drug{CLI},$drug{SYN},$drug{LZO},$drug{ERY_CLI}";
} elsif (!grep(/R23S1.*(A(21|29)G|C(5|9)T)/i,@Res_targs) && !grep(/RPLD1.*(5K|G9R|Q5K|K6E)/i,@Res_targs)) {
if (grep (/(R23S1|RPLD1|RPLV)/i,@Res_targs)) {
print STDERR "I'm in the right side of the EC decision tree\n";
#flag everything
#Run the ERMB+ERMBS code to overite flags
$drug{ERY} = "Flag,Flag,Flag";
$drug{CLI} = "Flag,Flag,Flag";
$drug{SYN} = "Flag,Flag,Flag";
$drug{LZO} = "Flag,Flag,Flag";
$drug{ERY_CLI} = "Flag";
if (grep (/ERM/i,@Res_targs) && !grep(/ERMBS/i,@Res_targs)) {
$drug{ERY} = ">,32,R";
$drug{CLI} = ">,2,R";
$drug{ERY_CLI} = "pos";
if (grep (/LSA/i,@Res_targs)) {
$drug{SYN} = "Flag,Flag,Flag";
}
}
#print STDERR "ER_CL,$Res_hash{EC},".$drug{ERY}.",".$drug{CLI}.",".$drug{SYN}.",".$drug{LZO}.",".$drug{ERY_CLI}."\n";
$Out_hash{EC} = "$Res_hash{EC},$drug{ERY},$drug{CLI},$drug{SYN},$drug{LZO},$drug{ERY_CLI}";
} else {
$left_side = "yes";
}
} else {
$left_side = "yes";
}
if ($left_side eq "yes") {
print STDERR "I'm in the left side of the EC decision tree\n";
#Go to left side of decision tree
#Check for 3 known R23S Mutations (not R23SA21G)
if (grep (/R23S1.*(A29G|C(5|9)T)/i,@Res_targs)) {
print STDERR "Found R23S1\n";
$drug{ERY} = "<=,0.25,S";
$drug{CLI} = "<=,0.25,S";
}
#Check for 4 known RPLD mutations
if (grep (/RPLD1.*(5K|G9R|Q5K|K6E)/i,@Res_targs)) {
print STDERR "Found RPLD1\n";
$drug{ERY} = "<=,0.25,S";
$drug{CLI} = "<=,0.25,S";
}
#Check for MEF
if (grep(/MEF/i,@Res_targs)) {
print STDERR "Found MEF\n";
$drug{ERY} = "=,8,R";
}
#Check for LSA/LNU
if (grep(/LSA/i,@Res_targs)) {
print STDERR "Found LSA\n";
$drug{CLI} = ">=,1,R";
}
if (grep(/LNU/i,@Res_targs)) {
print STDERR "Found LNU\n";
$drug{CLI} = "Flag,Flag,Flag";
}
#Check for R32SA21G and ERMB+ERMBS targets
if (grep (/R23S1.*A21G/i,@Res_targs)) {
print STDERR "Found R23S1-A21G\n";
$drug{ERY} = ">,32.0,R";
$drug{CLI} = "=,1.0,R";
$drug{ERY_CLI} = "pos";
}
if (grep(/ERM/i,@Res_targs) && !grep(/ERMBS/i,@Res_targs)) {
print STDERR "Found ERM and no ERMBS\n";
$drug{ERY} = ">,32,R";
$drug{CLI} = ">,2,R";
$drug{ERY_CLI} = "pos";
if (grep (/LSA/i,@Res_targs)) {
$drug{SYN} = "Flag,Flag,Flag";
}
}
#print STDERR "ER_CL,$Res_hash{EC},".$drug{ERY}.",".$drug{CLI}.",".$drug{SYN}.",".$drug{LZO}.",".$drug{ERY_CLI}."\n";
$Out_hash{EC} = "$Res_hash{EC},$drug{ERY},$drug{CLI},$drug{SYN},$drug{LZO},$drug{ERY_CLI}";
}
###COT Category###
$drug{SXT} = "=,0.5,S";
@Res_targs = split(':',$Res_hash{COT});
my $newTarg = "no";
if ($Res_hash{"COT"} eq "neg") {
$Out_hash{"COT"} = "$Res_hash{COT},$drug{SXT}";
} else {
#if (grep(/^FOLA-I20L$/i,@Res_targs)) {
if (grep(/FOLA.*I20L/i,@Res_targs)) {
if (grep(/FOLP_.*-ins/i,@Res_targs)) {
print STDERR "Found I20L AND FOLP insert\n";
$drug{SXT} = ">=,4,R";
} else {
print STDERR "Found I20L\n";
$drug{SXT} = "=,2,I";
}
#} elsif (grep(/FOLP_.*-ins/i,@Res_targs) && (!grep(/FOLA/i,@Res_targs) || grep(/^FOLA-(I20L|D12N)$/i,@Res_targs))) {
} elsif (grep(/FOLP_.*-ins/i,@Res_targs) && (!grep(/FOLA/i,@Res_targs) || grep(/^FOLA-D12N$/i,@Res_targs))) {
print STDERR "Found FOLP insert\n";
$drug{SXT} = "=,2,I";
} elsif (!grep(/^FOLA-D12N$/i,@Res_targs)) {
print STDERR "Found new COT target\n";
$drug{SXT} = "Flag,Flag,Flag";
}
$Out_hash{"COT"} = "$Res_hash{COT},$drug{SXT}";
}
###TET Category###
$drug{TET} = "<=,0.25,S";
$drug{DOX} = "<=,0.25,S";
if ($Res_hash{"TET"} eq "neg") {
$Out_hash{"TET"} = "$Res_hash{TET},$drug{TET},$drug{DOX}";
} else {
my @Res_targs = split(':',$Res_hash{TET});
if ( grep( /TET/i, @Res_targs ) ) {
$drug{TET} = ">,8,R";
$drug{DOX} = ">=,1,R";
$Out_hash{"TET"} = "$Res_hash{TET},$drug{TET},$drug{DOX}";
}
}
###FQ Category###
$drug{CIP} = "NA,NA,NA";
$drug{LFX} = "<=,2,S";
@Res_targs = split(':',$Res_hash{FQ});
if ($Res_hash{"FQ"} eq "neg") {
$Out_hash{"FQ"} = "$Res_hash{FQ},$drug{CIP},$drug{LFX}";
} elsif (!grep(/GYRA/i,@Res_targs) && grep(/PARC-S2[F|Y]/i,@Res_targs)) {
$Out_hash{"FQ"} = "$Res_hash{FQ},$drug{CIP},$drug{LFX}";
} else {
$drug{LFX} = "Flag,Flag,Flag";
$Out_hash{"FQ"} = "$Res_hash{FQ},$drug{CIP},$drug{LFX}";
}
###OTHER Category###
$drug{CHL} = "<=,2,S";
$drug{RIF} = "<=,1,S";
$drug{VAN} = "=,0.5,S";
$drug{DAP} = "NA,NA,NA";
if ($Res_hash{"OTHER"} eq "neg") {
print STDERR "OTHER,$Res_hash{OTHER},".$drug{CHL}.",".$drug{RIF}.",".$drug{VAN}.",".$drug{DAP}."\n";
$Out_hash{"OTHER"} = "$Res_hash{OTHER},$drug{CHL},$drug{RIF},$drug{VAN},$drug{DAP}";
} else {
my @Res_targs = split(':',$Res_hash{OTHER});
if ($Res_hash{OTHER} ne "ant(6)-Ia:Ant6-Ia_AGly:aph(3')-III:Aph3-III_AGly:Sat4A_Agly" && $Res_hash{OTHER} ne "aph(3')-III:Aph3-III_AGly:Sat4A_AGly" && $Res_hash{OTHER} ne "msr(D):MsrD_MLS") {
foreach my $target (@Res_targs) {
if ($target =~ m/CAT|RPOB|MSR/i) {
if ($target =~ m/CAT/i) {
print STDERR "Found CAT\n";
$drug{CHL} = ">=,8,R";
} elsif ($target =~ m/RPOB/i) {
print STDERR "Found RPOB\n";
$drug{RIF} = "Flag,Flag,Flag";
}
} elsif ($target !~ m/CAT|RPOB|MSR/i) {
print STDERR "Found an ARGANNOT/RESFINDER target. Flag everything\n";
$drug{CHL} = "Flag,Flag,Flag";
$drug{RIF} = "Flag,Flag,Flag";
$drug{VAN} = "Flag,Flag,Flag";
last;
}
}
}
print STDERR "OTHER,$Res_hash{OTHER},".$drug{CHL}.",".$drug{RIF}.",".$drug{VAN}.",".$drug{DAP}."\n";
$Out_hash{"OTHER"} = "$Res_hash{OTHER},$drug{CHL},$drug{RIF},$drug{VAN},$drug{DAP}";
}
print $fh $Out_hash{EC}.",". $Out_hash{COT}.",".$Out_hash{TET}.",".$Out_hash{FQ}.",".$Out_hash{OTHER}."\n";
print STDERR "$Out_hash{EC}||$Out_hash{COT}||$Out_hash{TET}||$Out_hash{FQ}||$Out_hash{OTHER}\n";