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brianjohnhaasbrianjohnhaas
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update
1 parent 813fb68 commit 1acab80

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+17
-17
lines changed

3 files changed

+17
-17
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‎TransDecoder.LongOrfs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -153,7 +153,7 @@ main: {
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mkdir($checkpoints_dir);
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}
155155

156-
my $pipeliner = new Pipeliner('-verbose' => 2, -checkpoints_dir => $checkpoints_dir);
156+
my $pipeliner = new Pipeliner('-verbose' => 2, -checkpoint_dir => $checkpoints_dir);
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158158
my %gene_trans_map;
159159
if ($gene_trans_map_file) {

‎TransDecoder.Predict‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -241,7 +241,7 @@ main: {
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mkdir($checkpoints_dir);
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}
243243

244-
my $pipeliner = new Pipeliner('-verbose' => 2, -checkpoints_dir => $checkpoints_dir);
244+
my $pipeliner = new Pipeliner('-verbose' => 2, '-checkpoint_dir' => $checkpoints_dir);
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my $prefix = "$workdir/longest_orfs";
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my $cds_file = "$prefix.cds";

‎util/train_start_PWM.pl‎

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -70,38 +70,38 @@
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mkdir($checkpoints_dir) or die $!;
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}
7272

73-
my $pipeliner = new Pipeliner(-verbose => 2);
74-
73+
my $pipeliner = new Pipeliner(-verbose => 2, -checkpoint_dir => $checkpoints_dir);
74+
7575
my $cmd = "$utildir/build_atgPWM_+-.pl "
7676
. " --transcripts $transcripts_file "
7777
. " --selected_orfs $selected_orfs_file "
7878
. " --out_prefix $out_prefix"
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. " --pwm_left $pwm_left --pwm_right $pwm_right ";
8080

81-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/built_init.ok"));
81+
$pipeliner->add_commands(new Command($cmd, "built_init.ok"));
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8383
$cmd = "$utildir/feature_scoring.+-.pl "
8484
. " --features_plus $out_prefix.+.features "
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. " --features_minus $out_prefix.-.features "
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. " --atg_position $pwm_left "
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. " > $out_prefix.feature.scores";
8888

89-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/score_features.ok"));
89+
$pipeliner->add_commands(new Command($cmd, "score_features.ok"));
9090

9191
$cmd = "$utildir/feature_scores_to_ROC.pl $out_prefix.feature.scores > $out_prefix.feature.scores.roc";
92-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/roc_features.ok"));
92+
$pipeliner->add_commands(new Command($cmd, "roc_features.ok"));
9393

9494
$cmd = "$utildir/plot_ROC.Rscript $out_prefix.feature.scores.roc || :";
95-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/rocplot.ok"));
95+
$pipeliner->add_commands(new Command($cmd, "rocplot.ok"));
9696

9797
$cmd = "$utildir/compute_AUC.pl $out_prefix.feature.scores.roc";
98-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/aucplot.ok"));
98+
$pipeliner->add_commands(new Command($cmd, "aucplot.ok"));
9999

100100
$cmd = "$utildir/make_seqLogo.Rscript $out_prefix.+.pwm || :";
101-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/seqlogo.+.ok"));
101+
$pipeliner->add_commands(new Command($cmd, "seqlogo.+.ok"));
102102

103103
$cmd = "$utildir/make_seqLogo.Rscript $out_prefix.-.pwm || :";
104-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/seqlogo.-.ok"));
104+
$pipeliner->add_commands(new Command($cmd, "seqlogo.-.ok"));
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106106

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#################
@@ -113,7 +113,7 @@
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. " --pwm_minus $out_prefix.-.pwm "
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. " --out_prefix $out_prefix.enhanced";
115115

116-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/enhance.ok"));
116+
$pipeliner->add_commands(new Command($cmd, "enhance.ok"));
117117

118118

119119
$cmd = "$utildir/feature_scoring.+-.pl "
@@ -122,20 +122,20 @@
122122
. " --atg_position $pwm_left "
123123
. " > $out_prefix.enhanced.feature.scores";
124124

125-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/enhanced_score_features.ok"));
125+
$pipeliner->add_commands(new Command($cmd, "enhanced_score_features.ok"));
126126

127127

128128
$cmd = "$utildir/feature_scores_to_ROC.pl $out_prefix.enhanced.feature.scores > $out_prefix.enhanced.feature.scores.roc";
129-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/enhanced_roc_features.ok"));
129+
$pipeliner->add_commands(new Command($cmd, "enhanced_roc_features.ok"));
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131131
$cmd = "$utildir/plot_ROC.Rscript $out_prefix.enhanced.feature.scores.roc || :";
132-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/enhanced_rocplot.ok"));
132+
$pipeliner->add_commands(new Command($cmd, "enhanced_rocplot.ok"));
133133

134134
$cmd = "$utildir/compute_AUC.pl $out_prefix.enhanced.feature.scores.roc";
135-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/enhanced_aucplot.ok"));
135+
$pipeliner->add_commands(new Command($cmd, "enhanced_aucplot.ok"));
136136

137137
$cmd = "$utildir/make_seqLogo.Rscript $out_prefix.enhanced.+.pwm || :";
138-
$pipeliner->add_commands(new Command($cmd, "$checkpoints_dir/seqlogo.enhanced.+.ok"));
138+
$pipeliner->add_commands(new Command($cmd, "seqlogo.enhanced.+.ok"));
139139

140140

141141
$pipeliner->run();

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