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Add status and score to JSON output #173

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Add status and score to JSON output #173

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8 changes: 5 additions & 3 deletions bin/mlst
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ use MLST::Requirements qw(require_exe);
#..............................................................................
# Globals

my $VERSION = '2.32.3';
my $VERSION = '2.32.4';
my $EXE = path($FindBin::RealScript)->basename;
my $AUTHOR = 'Torsten Seemann';
my $URL = 'https://github.com/tseemann/mlst';
Expand Down Expand Up @@ -208,8 +208,10 @@ for my $argv (@ARGV) {
'filename' => $argv,
'scheme' => $sch,
'sequence_type' => $ST,
'alleles' => $sch eq '-'
? undef
'status' => status_column($ST, $score, @code),
'score' => $score,
'alleles' => $sch eq '-'
? undef
: { (pairwise { ($a=>$b) } @{$scheme{$sch}->genes}, @code) },
};
}
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4 changes: 3 additions & 1 deletion test/test.sh
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Expand Up @@ -139,7 +139,9 @@ setup() {
local outfile="${BATS_TMPDIR}/$name.json"
run -0 $exe --json "$outfile" example.fna.gz
[[ -r "$outfile" ]]
run -0 grep 'sequence_type' "$outfile"
run -0 grep '"sequence_type"' "$outfile"
run -0 grep '"status"' "$outfile"
run -0 grep '"score"' "$outfile"
}
@test "Using --outfile" {
local outfile="${BATS_TMPDIR}/$name.tsv"
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