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move common code inside a function
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@hiruna72
hiruna72 committed Jan 29, 2024
1 parent 86f914f commit 7d1ec0f
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Showing 4 changed files with 23 additions and 113 deletions.
45 changes: 3 additions & 42 deletions src/metric.py
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Original file line number Diff line number Diff line change
Expand Up @@ -409,20 +409,7 @@ def run(args):
sig_algn_dic['ss'] = moves
sig_algn_dic['ref_name'] = ""

signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

draw_data['y_min'] = np.nanmin(y)
draw_data['y_max'] = np.nanmax(y)
Expand Down Expand Up @@ -612,20 +599,7 @@ def run(args):

# print(len(moves))
# print(fasta_seq)
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

# print(len(sig_algn_dic['ss']))
draw_data['y_min'] = np.nanmin(y)
Expand Down Expand Up @@ -824,20 +798,7 @@ def run(args):
sig_algn_dic['ref_name'] = ref_name
sig_algn_dic['ref_pos_dic'] = ref_pos_dic

signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

# print(len(moves))
# print(fasta_seq)
Expand Down
45 changes: 3 additions & 42 deletions src/plot.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -677,20 +677,7 @@ def run(args):
sig_algn_dic['data_is_rna'] = data_is_rna
sig_algn_dic['ss'] = moves

signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

if args.fixed_width:
sig_algn_dic['tag_name'] = args.tag_name + indt + "base_shift: " + str(draw_data["base_shift"]) + indt + "scale:" + scaling_str + indt + "fixed_width: " + str(args.base_width) + indt + strand_dir + indt + "region: "
Expand Down Expand Up @@ -902,20 +889,7 @@ def run(args):
sig_algn_dic['ss'] = moves
# print(len(moves))
# print(fasta_seq)
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

if args.fixed_width:
sig_algn_dic['tag_name'] = args.tag_name + indt + "base_shift: " + str(draw_data["base_shift"]) + indt + "scale:" + scaling_str + indt + "fixed_width: " + str(args.base_width) + indt + strand_dir + indt + "region: " + ref_name + ":"
Expand Down Expand Up @@ -1120,20 +1094,7 @@ def run(args):
sig_algn_dic['data_is_rna'] = data_is_rna
sig_algn_dic['ss'] = moves

signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

if args.fixed_width:
sig_algn_dic['tag_name'] = args.tag_name + indt + "base_shift: " + str(draw_data["base_shift"]) + indt + "scale:" + scaling_str + indt + "fixed_width: " + str(args.base_width) + indt + strand_dir + indt + "region: " + ref_name + ":"
Expand Down
30 changes: 2 additions & 28 deletions src/plot_pileup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -573,22 +573,9 @@ def run(args):
sig_algn_dic['ss'] = moves
# print(len(moves))
# print(fasta_seq)
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)
# print(len(sig_algn_dic['ss']))

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']

sig_algn_dic['tag_name'] = args.tag_name + indt + "base_shift: " + str(draw_data["base_shift"]) + indt + "scale:" + scaling_str + indt + "fixed_width: " + str(args.base_width) + indt + strand_dir + indt + "region: " + ref_name + ":"

y_min = math.floor(np.nanmin(y))
Expand Down Expand Up @@ -803,20 +790,7 @@ def run(args):
sig_algn_dic['ss'] = moves
# print(len(moves))
# print(fasta_seq)
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_dic['ss'] = moves_prefix + sig_algn_dic['ss']
signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq, draw_data)

sig_algn_dic['tag_name'] = args.tag_name + indt + "base_shift: " + str(draw_data["base_shift"]) + indt + "scale:" + scaling_str + indt + "fixed_width: " + str(args.base_width) + indt + strand_dir + indt + "region: " + ref_name + ":"

Expand Down
16 changes: 15 additions & 1 deletion src/plot_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ def get_base_color_map():
base_color_map = {'A': '#d6f5d6', 'C': '#ccccff', 'T': '#ffcccc', 'G': '#ffedcc', 'U': '#ffcccc', 'N': '#fafafe', 'M': '#000000', 'R': '#000000', 'W': '#000000', 'S': '#000000', 'Y': '#000000', 'K': '#000000', 'V': '#000000', 'H': '#000000', 'D': '#000000', 'B': '#000000'}
return base_color_map

def adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_data, fasta_seq):
def adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_data, fasta_seq, draw_data):
if sig_algn_data["data_is_rna"]:
ref_region_start_diff = region_tuple[1] - region_tuple[3]
else:
Expand Down Expand Up @@ -62,6 +62,20 @@ def adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dat
y = signal_tuple[2][eat_signal:]
signal_tuple = (x, x_real, y)
sig_algn_data['ss'] = moves

if draw_data["base_shift"] < 0:
abs_base_shift = abs(draw_data["base_shift"])
x = signal_tuple[0]
x_real = signal_tuple[1]
y = signal_tuple[2]
y_prefix = [np.nan] * abs_base_shift * draw_data["fixed_base_width"]
y = np.concatenate((y_prefix, y), axis=0)
x_real = np.concatenate(([1] * abs_base_shift * draw_data["fixed_base_width"], x_real), axis=0)
x = list(range(1, len(x) + 1 + abs_base_shift * draw_data["fixed_base_width"]))
signal_tuple = (x, x_real, y)
moves_prefix = [str(draw_data["fixed_base_width"])] * abs_base_shift
sig_algn_data['ss'] = moves_prefix + sig_algn_data['ss']

return signal_tuple, region_tuple, sig_algn_data, fasta_seq
def create_figure(args, plot_mode):
p_defualt = None
Expand Down

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