Skip to content

Commit

Permalink
remove Math::SigFigs dep
Browse files Browse the repository at this point in the history
  • Loading branch information
@jvolkening
jvolkening committed Jan 20, 2023
1 parent 6c17f6f commit 29fbe5f
Show file tree
Hide file tree
Showing 5 changed files with 23 additions and 24 deletions.
3 changes: 1 addition & 2 deletions Build.PL
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use Module::Build;

my $builder = Module::Build->new(
module_name => 'b2b-utils',
dist_version => 0.015,
dist_version => 0.016,
dist_abstract => 'Utilities from BASE2BIO LLC',
license => 'GPL_3',
dist_author => q{Jeremy Volkening <jeremy.volkening@base2bio.com>},
Expand All @@ -20,7 +20,6 @@ my $builder = Module::Build->new(
requires => {
'BioX::Seq' => 0,
'Bio::TreeIO' => 0,
'Math::SigFigs' => 0,
'List::MoreUtils' => 0,
'PerlIO::gzip' => 0,
},
Expand Down
20 changes: 10 additions & 10 deletions bin/boot2frac
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,14 @@ use 5.012;

use Bio::TreeIO;
use Getopt::Long;
use Math::SigFigs;
use Pod::Usage;

my $fn_in;
my $fn_out;
my $bs;
my $mode = 'decimal'; # decimal or percent
my $sf = 4;
my $force = 0;
my $mode = 'decimal'; # decimal or percent
my $places = 4;
my $force = 0;

my $NAME = 'boot2frac';
my $VERSION = '0.001';
Expand All @@ -26,7 +25,7 @@ GetOptions(
'bs=i' => \$bs,
'force' => \$force,
'mode=s' => \$mode,
'sig_figs=i' => \$sf,
'places=i' => \$places,
'help' => sub{ pod2usage( -verbose => 2 ) },
'version' => sub{ print "This is $NAME v$VERSION\n" and exit },
) or pod2usage( -msg => $err_msg, -verbose => 1 );
Expand Down Expand Up @@ -56,8 +55,8 @@ while (my $tree = $in->next_tree) {
if ($support !~ /^\d+$/);
die "Branch support value greater than supplied bootstrap count"
if ($support > $bs);
my $label = $mode eq 'decimal' ? FormatSigFigs($support/$bs, $sf)
: $mode eq 'percent' ? FormatSigFigs($support/$bs*100, $sf)
my $label = $mode eq 'decimal' ? sprintf("%0.*f", $places, $support/$bs)
: $mode eq 'percent' ? sprintf("%0.*f", $places-2, $support/$bs*100)
: die "Unsupported mode: $mode\n";
$node->id($label);
}
Expand Down Expand Up @@ -99,10 +98,11 @@ The number of bootstraps actually run (i.e. the denominator)
The format in which to write support values (either 'decimal', e.g. '0.658', or
'percent', e.g. '65.8') (default: decimal)
=item B<--sig_figs>
=item B<--places>
The number of significant figures to use in writing support values (default:
4)
The number of decimal places to use in writing support values. Note that this
is calculated before conversion to percent, so it is more like a
quasi-significant digits format (default: 4)
=item B<--help>
Expand Down
20 changes: 10 additions & 10 deletions t/boot2frac.t
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,11 @@ $cmp = 't/test_data/test.newick.out.bs500.sf3.md';
$out = File::Temp->new(UNLINK => 1);
$ret = system(
$bin,
'--in' => $in,
'--out' => $out,
'--bs' => 500,
'--sig_figs' => 3,
'--mode' => 'decimal',
'--in' => $in,
'--out' => $out,
'--bs' => 500,
'--places' => 3,
'--mode' => 'decimal',
'--force',
);
ok( ! $ret, "test $i call succeeded" );
Expand All @@ -39,11 +39,11 @@ $cmp = 't/test_data/test.newick.out.bs600.sf4.mp';
$out = File::Temp->new(UNLINK => 1);
$ret = system(
$bin,
'--in' => $in,
'--out' => $out,
'--bs' => 600,
'--sig_figs' => 4,
'--mode' => 'percent',
'--in' => $in,
'--out' => $out,
'--bs' => 600,
'--places' => 4,
'--mode' => 'percent',
'--force',
);
ok( ! $ret, "test $i call succeeded" );
Expand Down
2 changes: 1 addition & 1 deletion t/test_data/test.newick.out.bs500.sf3.md
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
(((((((((AtHA5:0.16080899,(MtHA8:0.03443625,((MtHA12:0.02826669,MtHA7:0.02709547)1.00:0.08989073,MtHA3:0.06339041)0.534:0.00701517)0.852:0.02276584)0.972:0.03197485,(OsHA7:0.08006951,OsHA5:0.25690155)0.312:0.02878130)0.112:0.01295698,((AtHA3:0.10543546,(AtHA1:0.04142886,AtHA2:0.02761315)0.988:0.03563662)0.990:0.06764772,(MtHA5:0.09200765,MtHA4:0.07789138)0.966:0.03545207)0.290:0.01796465)0.460:0.01852368,((((AtHA6:0.07194197,AtHA8:0.11257159)0.918:0.03073821,((OsHA10:0.13981792,OsHA6:0.07666544)1.00:0.11941131,(MtHA11:0.08529923,MtHA10:0.09271545)0.950:0.04893483)0.378:0.03379257)0.716:0.05655055,(AtHA9:0.11955304,MtHA13:0.10217084)0.870:0.03953478)0.530:0.02368979,OsHA4:0.20774605)0.630:0.01574769)0.978:0.05308309,((((PPHA2:0.04481490,PPHA1:0.02480662)0.918:0.01176811,PPHA3:0.04191167)1.00:0.04305698,PPHA5:0.11571686)0.602:0.01423941,PPHA4:0.07601305)1.00:0.07611264)0.590:0.01993966,((OsHA9:0.20439369,MtHA9:0.08955643)0.492:0.02900198,AtHA10:0.18014107)1.00:0.17131650)0.524:0.03247169,PPHA8:0.18494231)0.292:0.01262039,((OsHA8:0.18783906,(AtHA7:0.20676650,MtHA1:0.13094007)0.598:0.04413065)1.00:0.08733036,(((OsHA3:0.03530415,OsHA1:0.03099337)0.998:0.04250190,OsHA2:0.04918639)0.826:0.01985323,(((AtHA4:0.03968310,AtHA11:0.02879809)0.972:0.02744878,MtHA2:0.04309439)0.468:0.00792143,MtHA6:0.09287388)0.966:0.03434016)0.900:0.02639269)0.938:0.02439334)1.00:0.38093515,PPHA7:0.38745225,PPHA6:0.24048235);
(((((((((AtHA5:0.16080899,(MtHA8:0.03443625,((MtHA12:0.02826669,MtHA7:0.02709547)1.000:0.08989073,MtHA3:0.06339041)0.534:0.00701517)0.852:0.02276584)0.972:0.03197485,(OsHA7:0.08006951,OsHA5:0.25690155)0.312:0.02878130)0.112:0.01295698,((AtHA3:0.10543546,(AtHA1:0.04142886,AtHA2:0.02761315)0.988:0.03563662)0.990:0.06764772,(MtHA5:0.09200765,MtHA4:0.07789138)0.966:0.03545207)0.290:0.01796465)0.460:0.01852368,((((AtHA6:0.07194197,AtHA8:0.11257159)0.918:0.03073821,((OsHA10:0.13981792,OsHA6:0.07666544)1.000:0.11941131,(MtHA11:0.08529923,MtHA10:0.09271545)0.950:0.04893483)0.378:0.03379257)0.716:0.05655055,(AtHA9:0.11955304,MtHA13:0.10217084)0.870:0.03953478)0.530:0.02368979,OsHA4:0.20774605)0.630:0.01574769)0.978:0.05308309,((((PPHA2:0.04481490,PPHA1:0.02480662)0.918:0.01176811,PPHA3:0.04191167)1.000:0.04305698,PPHA5:0.11571686)0.602:0.01423941,PPHA4:0.07601305)1.000:0.07611264)0.590:0.01993966,((OsHA9:0.20439369,MtHA9:0.08955643)0.492:0.02900198,AtHA10:0.18014107)1.000:0.17131650)0.524:0.03247169,PPHA8:0.18494231)0.292:0.01262039,((OsHA8:0.18783906,(AtHA7:0.20676650,MtHA1:0.13094007)0.598:0.04413065)1.000:0.08733036,(((OsHA3:0.03530415,OsHA1:0.03099337)0.998:0.04250190,OsHA2:0.04918639)0.826:0.01985323,(((AtHA4:0.03968310,AtHA11:0.02879809)0.972:0.02744878,MtHA2:0.04309439)0.468:0.00792143,MtHA6:0.09287388)0.966:0.03434016)0.900:0.02639269)0.938:0.02439334)1.000:0.38093515,PPHA7:0.38745225,PPHA6:0.24048235);
2 changes: 1 addition & 1 deletion t/test_data/test.newick.out.bs600.sf4.mp
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
(((((((((AtHA5:0.16080899,(MtHA8:0.03443625,((MtHA12:0.02826669,MtHA7:0.02709547)83.33:0.08989073,MtHA3:0.06339041)44.50:0.00701517)71.00:0.02276584)81.00:0.03197485,(OsHA7:0.08006951,OsHA5:0.25690155)26.00:0.02878130)9.333:0.01295698,((AtHA3:0.10543546,(AtHA1:0.04142886,AtHA2:0.02761315)82.33:0.03563662)82.50:0.06764772,(MtHA5:0.09200765,MtHA4:0.07789138)80.50:0.03545207)24.17:0.01796465)38.33:0.01852368,((((AtHA6:0.07194197,AtHA8:0.11257159)76.50:0.03073821,((OsHA10:0.13981792,OsHA6:0.07666544)83.33:0.11941131,(MtHA11:0.08529923,MtHA10:0.09271545)79.17:0.04893483)31.50:0.03379257)59.67:0.05655055,(AtHA9:0.11955304,MtHA13:0.10217084)72.50:0.03953478)44.17:0.02368979,OsHA4:0.20774605)52.50:0.01574769)81.50:0.05308309,((((PPHA2:0.04481490,PPHA1:0.02480662)76.50:0.01176811,PPHA3:0.04191167)83.33:0.04305698,PPHA5:0.11571686)50.17:0.01423941,PPHA4:0.07601305)83.33:0.07611264)49.17:0.01993966,((OsHA9:0.20439369,MtHA9:0.08955643)41.00:0.02900198,AtHA10:0.18014107)83.33:0.17131650)43.67:0.03247169,PPHA8:0.18494231)24.33:0.01262039,((OsHA8:0.18783906,(AtHA7:0.20676650,MtHA1:0.13094007)49.83:0.04413065)83.33:0.08733036,(((OsHA3:0.03530415,OsHA1:0.03099337)83.17:0.04250190,OsHA2:0.04918639)68.83:0.01985323,(((AtHA4:0.03968310,AtHA11:0.02879809)81.00:0.02744878,MtHA2:0.04309439)39.00:0.00792143,MtHA6:0.09287388)80.50:0.03434016)75.00:0.02639269)78.17:0.02439334)83.33:0.38093515,PPHA7:0.38745225,PPHA6:0.24048235);
(((((((((AtHA5:0.16080899,(MtHA8:0.03443625,((MtHA12:0.02826669,MtHA7:0.02709547)83.33:0.08989073,MtHA3:0.06339041)44.50:0.00701517)71.00:0.02276584)81.00:0.03197485,(OsHA7:0.08006951,OsHA5:0.25690155)26.00:0.02878130)9.33:0.01295698,((AtHA3:0.10543546,(AtHA1:0.04142886,AtHA2:0.02761315)82.33:0.03563662)82.50:0.06764772,(MtHA5:0.09200765,MtHA4:0.07789138)80.50:0.03545207)24.17:0.01796465)38.33:0.01852368,((((AtHA6:0.07194197,AtHA8:0.11257159)76.50:0.03073821,((OsHA10:0.13981792,OsHA6:0.07666544)83.33:0.11941131,(MtHA11:0.08529923,MtHA10:0.09271545)79.17:0.04893483)31.50:0.03379257)59.67:0.05655055,(AtHA9:0.11955304,MtHA13:0.10217084)72.50:0.03953478)44.17:0.02368979,OsHA4:0.20774605)52.50:0.01574769)81.50:0.05308309,((((PPHA2:0.04481490,PPHA1:0.02480662)76.50:0.01176811,PPHA3:0.04191167)83.33:0.04305698,PPHA5:0.11571686)50.17:0.01423941,PPHA4:0.07601305)83.33:0.07611264)49.17:0.01993966,((OsHA9:0.20439369,MtHA9:0.08955643)41.00:0.02900198,AtHA10:0.18014107)83.33:0.17131650)43.67:0.03247169,PPHA8:0.18494231)24.33:0.01262039,((OsHA8:0.18783906,(AtHA7:0.20676650,MtHA1:0.13094007)49.83:0.04413065)83.33:0.08733036,(((OsHA3:0.03530415,OsHA1:0.03099337)83.17:0.04250190,OsHA2:0.04918639)68.83:0.01985323,(((AtHA4:0.03968310,AtHA11:0.02879809)81.00:0.02744878,MtHA2:0.04309439)39.00:0.00792143,MtHA6:0.09287388)80.50:0.03434016)75.00:0.02639269)78.17:0.02439334)83.33:0.38093515,PPHA7:0.38745225,PPHA6:0.24048235);

0 comments on commit 29fbe5f

Please sign in to comment.