fixed prediction bug at bigger batch sizes

Hughes-Genome-Group · May 24, 2021 · caf15e4 · caf15e4
1 parent 5f0f6ff
commit caf15e4
Show file tree

Hide file tree

Showing 14 changed files with 21 additions and 23 deletions.
diff --git a/legacy_version_tf1.8/run_deploy_shape_combination_deepCregr.py b/legacy_version_tf1.8/run_deploy_shape_combination_deepCregr.py
@@ -120,7 +120,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/legacy_version_tf1.8/run_deploy_shape_deepCregr.py b/legacy_version_tf1.8/run_deploy_shape_deepCregr.py
@@ -130,7 +130,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/legacy_version_tf1.8/run_get_saliency.py b/legacy_version_tf1.8/run_get_saliency.py
@@ -1,4 +1,4 @@
-'''DESCRIPTION:
+seqs_placeholder: seqs[test_batch_range],'''DESCRIPTION:
 Run Get Saliency Scores:  Gradient of Output with respect to inout and/or intermediate layers.
 # FORMAT
 chr start end replacer --> will work like variant deploy in terms of apllying variants
@@ -181,7 +181,7 @@ def map_saliency(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow1_version/run_deploy_shape_combination_deepCregr.py b/tensorflow1_version/run_deploy_shape_combination_deepCregr.py
@@ -120,7 +120,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow1_version/run_deploy_shape_deepCregr.py b/tensorflow1_version/run_deploy_shape_deepCregr.py
@@ -138,7 +138,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow1_version/run_get_saliency.py b/tensorflow1_version/run_get_saliency.py
@@ -181,7 +181,7 @@ def map_saliency(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow1_version/run_training_deepCregr.py b/tensorflow1_version/run_training_deepCregr.py
@@ -18,7 +18,7 @@
 # Basic model parameters as external flags -------------------------------------
 flags = tf.app.flags
 FLAGS = flags.FLAGS
-flags.DEFINE_boolean('help', False, 'For help.')
+# flags.DEFINE_boolean('help', False, 'For help.')
 flags.DEFINE_string('data_file', '', 'Input data: pseudo bed format: chr start end and comma separated classes')
 # TRAININGS SETTINGS
 flags.DEFINE_string('test_chroms', 'chr12, chr13', 'Comma seperated list of test chromosoems to use ...')
@@ -76,8 +76,8 @@
 BP_CONTEXT = FLAGS.bp_context
 NUM_CLASSES = FLAGS.num_classes
 
-if FLAGS.help:
-    print(FLAGS.__dict__['__flags'])
+# if FLAGS.help:
+#     print(FLAGS.__dict__['__flags'])
 
 # SET RANDOM SEED --------------------------------------------------------------
 np.random.seed(FLAGS.seed)  # use same seed for numpy --> for shuffeling

diff --git a/tensorflow2.0_compatibility_version/run_deploy_shape_combination_deepCregr.py b/tensorflow2.0_compatibility_version/run_deploy_shape_combination_deepCregr.py
@@ -122,7 +122,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow2.0_compatibility_version/run_deploy_shape_deepCregr.py b/tensorflow2.0_compatibility_version/run_deploy_shape_deepCregr.py
@@ -140,7 +140,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow2.0_compatibility_version/run_get_saliency.py b/tensorflow2.0_compatibility_version/run_get_saliency.py
@@ -183,7 +183,7 @@ def map_saliency(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow2.1plus_compatibility_version/run_deploy_shape_combination_deepCregr.py b/tensorflow2.1plus_compatibility_version/run_deploy_shape_combination_deepCregr.py
@@ -122,7 +122,7 @@ def predict(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow2.1plus_compatibility_version/run_deploy_shape_deepCregr.py b/tensorflow2.1plus_compatibility_version/run_deploy_shape_deepCregr.py
@@ -320,9 +320,12 @@ def predict(sess,
                     js = patch_start + i * half_bin_size
                     je = patch_start + i * half_bin_size + FLAGS.bp_context
                     jseq = seq[(i*half_bin_size):((i)*half_bin_size + FLAGS.bp_context)]
-                    run_starts.append(js)
-                    run_ends.append(je)
-                    run_seqs.append(jseq)
+                    if len(jseq) == FLAGS.bp_context:
+                        run_starts.append(js)
+                        run_ends.append(je)
+                        run_seqs.append(jseq)
+                    else:
+                        print('Extracted seq for %s-%s is smaller then bp_context ... skipping' % (js, je))
                     i += 1
 
             # Predict ----------------------------------------------------------------

diff --git a/tensorflow2.1plus_compatibility_version/run_get_saliency.py b/tensorflow2.1plus_compatibility_version/run_get_saliency.py
@@ -183,7 +183,7 @@ def map_saliency(sess,
         test_batch_end = step * FLAGS.batch_size + FLAGS.batch_size
         test_batch_range=range(test_batch_start, test_batch_end)
         feed_dict = {
-              seqs_placeholder: np.expand_dims(seqs[test_batch_range][0], axis=0),
+              seqs_placeholder: seqs[test_batch_range],
               keep_prob_inner_placeholder: 1.0,
               keep_prob_outer_placeholder: 1.0
               }

diff --git a/tensorflow2.1plus_compatibility_version/run_training_deepCregr.py b/tensorflow2.1plus_compatibility_version/run_training_deepCregr.py
@@ -22,8 +22,6 @@
 flags = tf.app.flags
 FLAGS = flags.FLAGS
 
-#flags.DEFINE_boolean('help', False, 'For help.')
-
 flags.DEFINE_string('data_file', '', 'Input data: pseudo bed format: chr start end and comma separated classes')
 
 # TRAININGS SETTINGS
@@ -82,9 +80,6 @@
 BP_CONTEXT = FLAGS.bp_context
 NUM_CLASSES = FLAGS.num_classes
 
-#if FLAGS.help:
-#    print(FLAGS.__dict__['__flags'])
-
 # SET RANDOM SEED --------------------------------------------------------------
 np.random.seed(FLAGS.seed)  # use same seed for numpy --> for shuffeling