updated dependencies; addressing #192

requirements.txt

@@ -1,8 +1,8 @@
-numpy>=1.14.6
-numba>=0.52.0
-matplotlib>=2.2
-scipy>=1.3
+numpy>=1.26
+numba>=0.59.0
+matplotlib>=3.7
+scipy>=1.13
 intervaltree>=3.0.0
 h5py>=2.2
-pysam>=0.15.3
-statsmodels>=0.9.0
+pysam>=0.22.0
+statsmodels>=0.14.0

spladder/alt_splice/verify.py

@@ -179,7 +179,7 @@ def verify_intron_retention(event, gene, counts_segments, counts_edges, counts_s
     ### check intron confirmation as sum of valid intron scores
     ### intron score is the number of reads confirming this intron
     # intron conf
-    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon1[-1], seg_exon2[0]], segs.seg_edges.shape))[0]
+    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon1[-1], seg_exon2[0]], segs.seg_edges.shape))[0].item()
     info[4] = counts_edges[idx, 1]
 
     if (info[4] >= options.intron_retention['min_non_retention_count']) or \
@@ -245,19 +245,19 @@ def verify_exon_skip(event, gene, counts_segments, counts_edges, options):
     ### check intron confirmation as sum of valid intron scores
     ### intron score is the number of reads confirming this intron
     # exon_pre_exon_conf
-    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon_pre[-1], seg_exon[0]], segs.seg_edges.shape))[0]
+    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon_pre[-1], seg_exon[0]], segs.seg_edges.shape))[0].item()
     info[4] = counts_edges[idx, 1]
     if (info[4] >= options.exon_skip['min_non_skip_count']) or \
        (options.use_anno_support and intron_pre in gene.introns_anno):
         verified[1] = 1
     # exon_exon_aft_conf
-    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon[-1], seg_exon_aft[0]], segs.seg_edges.shape))[0]
+    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon[-1], seg_exon_aft[0]], segs.seg_edges.shape))[0].item()
     info[5] = counts_edges[idx, 1]
     if (info[5] >= options.exon_skip['min_non_skip_count']) or \
        (options.use_anno_support and intron_aft in gene.introns_anno):
         verified[2] = 1
     # exon_pre_exon_aft_conf
-    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon_pre[-1], seg_exon_aft[0]], segs.seg_edges.shape))[0]
+    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([seg_exon_pre[-1], seg_exon_aft[0]], segs.seg_edges.shape))[0].item()
     info[6] = counts_edges[idx, 1]
     if (info[6] >= options.exon_skip['min_skip_count']) or \
        (options.use_anno_support and intron_skip in gene.introns_anno):
@@ -353,12 +353,10 @@ def verify_alt_prime(event, gene, counts_segments, counts_edges, options):
     ### check intron confirmations as sum of valid intron scores
     ### intron score is the number of reads confirming this intron
     # intron1_conf 
-    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([segs_exon11[-1], segs_exon12[0]], segs.seg_edges.shape))[0]
-    assert(idx.shape[0] > 0)
+    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([segs_exon11[-1], segs_exon12[0]], segs.seg_edges.shape))[0].item()
     info[4] = counts_edges[idx, 1]
     # intron2_conf 
-    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([segs_exon21[-1], segs_exon22[0]], segs.seg_edges.shape))[0]
-    assert(idx.shape[0] > 0)
+    idx = np.where(counts_edges[:, 0] == np.ravel_multi_index([segs_exon21[-1], segs_exon22[0]], segs.seg_edges.shape))[0].item()
     info[5] = counts_edges[idx, 1]
 
     if (min(info[4], info[5]) >= options.alt_prime['min_intron_count']) or \

spladder/spladder_viz.py

@@ -5,7 +5,7 @@
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-plt.style.use('seaborn')
+plt.style.use('seaborn-v0_8-whitegrid')
 import matplotlib.gridspec as gridspec
 import matplotlib.patches as patches
 import numpy as np

spladder/viz/coverage.py

@@ -225,7 +225,7 @@ def cov_from_segments(gene, seg_counts, edge_counts, edge_idx, size_factors, ax,
 
     ### draw grid
     if grid:
-        ax.grid(b=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
+        ax.grid(visible=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
         ax.xaxis.grid(False)
 
     ax.set_ylim([0, int(seg_counts.max() * 1.1)])
@@ -320,7 +320,7 @@ def cov_from_bam(chrm, start, stop, files, subsample=0, verbose=False,
 
     ### draw grid
     if grid:
-        ax.grid(b=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
+        ax.grid(visible=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
         ax.xaxis.grid(False)
 
     if marker_pos is not None:

spladder/viz/genelets.py

@@ -10,7 +10,7 @@ def single(exon_set, ax=None, x_range=None, count=1, color='blue', grid=False, l
 
     ### draw grid
     if grid:
-        ax.grid(b=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
+        ax.grid(visible=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
         ax.yaxis.grid(False)
 
     min_ex = None

spladder/viz/graph.py

@@ -16,7 +16,7 @@ def plot_graph(vertices, edges, ax, xlim=None, highlight=None, highlight_color='
     stop = vertices.ravel().max()
 
     ### draw grid
-    ax.grid(b=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
+    ax.grid(visible=True, which='major', linestyle='--', linewidth=0.2, color='#222222')
     ax.yaxis.grid(False)
 
     ### nodes