Merge branch 'development'

Author: akahles

spladder/alt_splice/detect.py

@@ -1,5 +1,4 @@
 from scipy.sparse import lil_matrix
-from numpy.matlib import repmat
 import numpy as np
 import sys
 import operator
@@ -25,7 +24,7 @@ def detect_multipleskips(genes, gidx, log=False, edge_limit=300):
         genes[iix].from_sparse()
         num_exons = genes[iix].splicegraph.get_len()
         edges = genes[iix].splicegraph.edges.copy()
-        labels = repmat(np.arange(num_exons), num_exons, 1).T
+        labels = np.hstack([np.arange(num_exons)[:, np.newaxis]] * num_exons)
         genes[iix].to_sparse()
 
         # adjecency matrix: upper half only
@@ -90,15 +89,15 @@ def detect_multipleskips(genes, gidx, log=False, edge_limit=300):
                         backtrace = np.r_[backtrace, path[exon_idx_first, backtrace[-1]]]
                     backtrace = backtrace[:-1]
                     backtrace = backtrace[::-1]
-                    idx_multiple_skips.append(ix) #repmat(ix, 1, backtrace.shape[0] + 2))
+                    idx_multiple_skips.append(ix) 
                     exon_multiple_skips.append([exon_idx_first, backtrace, exon_idx_last])
                 elif (long_exist_path[exon_idx_first, exon_idx_last] > 2) and np.isfinite(long_exist_path[exon_idx_first, exon_idx_last]):
                     backtrace = np.array([long_path[exon_idx_first, exon_idx_last]])
                     while backtrace[-1] > exon_idx_first:
                         backtrace = np.r_[backtrace, long_path[exon_idx_first, backtrace[-1]]]
                     backtrace = backtrace[:-1]
                     backtrace = backtrace[::-1]
-                    idx_multiple_skips.append(ix) #repmat(ix, 1, backtrace.shape[0] + 2))
+                    idx_multiple_skips.append(ix) 
                     exon_multiple_skips.append([exon_idx_first, backtrace, exon_idx_last])
 
     if log:

spladder/alt_splice/verify.py

@@ -18,7 +18,7 @@ def verify_mult_exon_skip(event, gene, counts_segments, counts_edges, options):
     # (3) avg inclusion count inner exons >= threshold
     # (4) skip count >= threshold
 
-    info = [1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+    info = np.array([1, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype='float')
     # (0) valid, (1) exon_pre_cov, (2) exons_cov, (3) exon_aft_cov
     # (4) exon_pre_exon_conf, (5) exon_exon_aft_conf, (6) exon_pre_exon_aft_conf
     # (7) sum_inner_exon_conf, (8) num_inner_exon, (9) len_inner_exon
@@ -102,7 +102,7 @@ def verify_intron_retention(event, gene, counts_segments, counts_edges, counts_s
     # (0) counts meet criteria for min_retention_cov, min_retention_region and min_retetion_rel_cov 
     # (1) min_non_retention_count >= threshold
 
-    info = [1, 0, 0, 0, 0, 0]
+    info = np.array([1, 0, 0, 0, 0, 0], dtype='float')
     # (0) valid, (1) intron_cov, (2) exon1_cov, (3), exon2_cov
     # (4) intron_conf, (5) intron_cov_region
 
@@ -169,7 +169,7 @@ def verify_exon_skip(event, gene, counts_segments, counts_edges, options):
     # (2) inclusion count of second intron >= threshold
     # (3) skip count of exon >= threshold
 
-    info = [1, 0, 0, 0, 0, 0, 0]
+    info = np.array([1, 0, 0, 0, 0, 0, 0], dtype='float')
     # (0) valid, (1) exon_cov, (2) exon_pre_cov, (3) exon_aft_cov, 
     # (4) exon_pre_exon_conf, (5) exon_exon_aft_conf, (6) exon_pre_exon_aft_conf
 
@@ -236,7 +236,7 @@ def verify_alt_prime(event, gene, counts_segments, counts_edges, options):
     # (0) coverage of diff region is at least FACTOR * coverage constant region
     # (1) both alternative introns are >= threshold 
 
-    info = [1, 0, 0, 0, 0]
+    info = np.array([1, 0, 0, 0, 0], dtype='float')
     # (0) valid, (1) exon_diff_cov, (2) exon_const_cov
     # (3) intron1_conf, (4) intron2_conf
 
@@ -332,7 +332,7 @@ def verify_mutex_exons(event, gene, counts_segments, counts_edges, options):
     # (2) both introns neighboring first alt exon are confirmed >= threshold
     # (3) both introns neighboring second alt exon are confirmed >= threshold
 
-    info = [1, 0, 0, 0, 0, 0, 0, 0, 0]
+    info = np.array([1, 0, 0, 0, 0, 0, 0, 0, 0], dtype='float')
     # (0) valid, (1) exon_pre_cov, (2) exon1_cov, (3) exon2_cov, (4) exon_aft_cov, 
     # (5) exon_pre_exon1_conf, (6) exon_pre_exon2_conf, (7) exon1_exon_aft_conf, (8) exon2_exon_aft_conf
 
@@ -513,9 +513,9 @@ def verify_all_events(ev, strain_idx=None, list_bam=None, event_type=None, optio
 
                 ev[i].verified.append(ver)
                 if s_idx == 0:
-                    counts.append(np.array([info], dtype='float'))
+                    counts.append(info[np.newaxis, :])
                 else:
-                    counts[-1] = np.r_[counts[-1], np.array([info], dtype='float')]
+                    counts[-1] = np.append(counts[-1], info[np.newaxis, :], axis=0) 
             ev[i].verified = np.array(ev[i].verified, dtype='bool')
 
         IN.close()
@@ -532,18 +532,18 @@ def verify_empty(event_type):
 
     if event_type == 'exon_skip':
         verified = [0, 0, 0, 0]
-        info = [1, 0, 0, 0, 0, 0, 0]
+        info = np.array([1, 0, 0, 0, 0, 0, 0], dtype='float')
     elif event_type in ['alt_3prime', 'alt_5prime']:
         verified = [0, 0]
-        info = [1, 0, 0, 0, 0]
+        info = np.array([1, 0, 0, 0, 0], dtype='float')
     elif event_type == 'intron_retention':
         verified = [0, 0]
-        info = [1, 0, 0, 0, 0, 0]
+        info = np.array([1, 0, 0, 0, 0, 0], dtype='float')
     elif event_type == 'mult_exon_skip':
         verified = [0, 0, 0, 0, 0]
-        info = [1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+        info = np.array([1, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype='float')
     elif event_type == 'mutex_exons':
         verified = [0, 0, 0, 0]
-        info = [1, 0, 0, 0, 0, 0, 0, 0, 0]
+        info = np.array([1, 0, 0, 0, 0, 0, 0, 0, 0], dtype='float')
 
     return (verified, info)