bed annotation supports positive base shift

src/bed_annotation.py

@@ -55,9 +55,37 @@ def draw_bed_annotation(p, bed_content, sig_algn_data, draw_data, base_limit, tr
     annotation_box_details = {'left': [], 'right': [], 'fill_color': []}
     annotation_label = []
     annotation_label_x = []
-    location_plot = 0
-    x_coordinate = 0
-    initial_x_coordinate = x_coordinate
+
+    initial_location_plot = 0
+    if draw_data["base_shift"] > 0:
+        abs_base_shift = abs(draw_data["base_shift"])
+        count_bases = 0
+        for i in moves:
+            if 'D' in i:
+                i = re.sub('D', '', i)
+                if count_bases + int(i) > abs_base_shift:
+                    initial_location_plot += (abs_base_shift - count_bases) * draw_data["fixed_base_width"]
+                    break
+                initial_location_plot += int(i) * draw_data["fixed_base_width"]
+                count_bases += int(i)
+            elif 'I' in i:
+                i = re.sub('I', '', i)
+                if draw_data['fixed_width']:
+                    pass
+                else:
+                    initial_location_plot += int(i)
+            else:
+                if draw_data['fixed_width']:
+                    initial_location_plot += draw_data["fixed_base_width"]
+                else:
+                    initial_location_plot += int(i)
+                count_bases += 1
+            if count_bases == abs_base_shift:
+                break
+
+    initial_x_coordinate = 0
+    x_coordinate = initial_x_coordinate
+    location_plot = initial_location_plot
     flag_base_index_bound = 0
 
     bed_index = 0

src/metric.py

@@ -86,7 +86,9 @@ def get_metric(args, fout, metric_record, read_id, signal_tuple, sig_algn_data,
             break
         if x_coordinate - initial_x_coordinate > draw_data["sig_plot_limit"]:
             break
-    signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
+    signal_start = initial_x_coordinate
+    if draw_data["base_shift"] < 0:
+        signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
     if sig_algn_data["data_is_rna"] == 1:
         ref_region = "{}:{}-{}".format(sig_algn_data["ref_name"], sig_algn_data["ref_end"], sig_algn_data["ref_end"] - base_index+1)
         signal_region = "{}-{}".format(x_real[signal_start], x_real[x_coordinate - 1])

src/plot.py

@@ -204,7 +204,9 @@ def plot_function(p, read_id, signal_tuple, sig_algn_data, fasta_sequence, base_
     hover.mode = 'mouse'
 
     indt = "\t\t\t\t\t\t\t\t"
-    signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
+    signal_start = initial_x_coordinate
+    if draw_data["base_shift"] < 0:
+        signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
     if sig_algn_data["data_is_rna"] == 1:
         plot_title = f'{sig_algn_data["tag_name"]}[{sig_algn_data["ref_end"]:,}-{sig_algn_data["ref_end"] - base_index+1:,}]{indt}signal: [{int(x_real[signal_start])}-{int(x_real[x_coordinate - 1])}]{indt}deletions(bases): {num_Ds} insertions(samples): {num_Is}{indt}{read_id}{indt}signal dir:{draw_data["sig_dir"]}'
     else:
@@ -407,7 +409,9 @@ def plot_function_fixed_width(p, read_id, signal_tuple, sig_algn_data, fasta_seq
     hover.tooltips = [("x", "@x_real"), ("y", "@y")]
     hover.mode = 'mouse'
     indt = "\t\t\t\t\t\t\t\t"
-    signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
+    signal_start = initial_x_coordinate
+    if draw_data["base_shift"] < 0:
+        signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
     if sig_algn_data["data_is_rna"] == 1:
         plot_title = f'{sig_algn_data["tag_name"]}[{sig_algn_data["ref_end"]:,}-{sig_algn_data["ref_end"] - base_index+1:,}]{indt}signal: [{int(x_real[signal_start])}-{int(x_real[x_coordinate - 1])}]{indt}deletions(bases): {num_Ds} insertions(samples): {num_Is}{indt}{read_id}{indt}signal dir:{draw_data["sig_dir"]}'
     else:

src/plot_pileup.py

@@ -236,7 +236,9 @@ def plot_function_fixed_width_pileup(read_id, signal_tuple, sig_algn_data, fasta
 
     signal_region = ""
     indels = f'deletions(bases): {num_Ds} insertions(samples): {num_Is}'
-    signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
+    signal_start = initial_x_coordinate
+    if draw_data["base_shift"] < 0:
+        signal_start = abs(draw_data["base_shift"]) * draw_data["fixed_base_width"]
     signal_region = f'[{int(x_real[signal_start])}-{int(x_real[x_coordinate - 1])}]'
     y_plot = y[:x_coordinate]+y_shift
     y_median = np.nanmedian(y_plot)

src/plot_utils.py

@@ -76,6 +76,10 @@ def adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dat
         moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
         sig_algn_data['ss'] = moves_prefix + sig_algn_data['ss']
 
+    base_shift_seq = 'N' * draw_data['base_shift']
+    if draw_data["base_shift"] > 0:
+        fasta_seq = base_shift_seq + fasta_seq[:-1*draw_data["base_shift"]]
+
     return signal_tuple, region_tuple, sig_algn_data, fasta_seq
 def create_figure(args, plot_mode):
     p_defualt = None