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Fixed some bugs in the feature_generation.py #17

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Fixed some bugs in the feature_generation.py #17

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f015de7
chrom:pos as the unique window ID instead of chrompos.
Ckenen Oct 27, 2024
c54cf80
Fixed: incorrect header when statistic is enabled.
Ckenen Oct 27, 2024
4ab8f4e
Fixed: the raw read counts forgot to substract 1.
Ckenen Oct 27, 2024
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8 changes: 4 additions & 4 deletions src/ashleyslib/feature_generation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ def get_header(windows_list, use_statistics):
feature_names = []
regular_features = ['W10', 'W20', 'W30', 'W40', 'W50', 'W60', 'W70', 'W80', 'W90', 'W100', 'total']
if use_statistics:
statistics_features = ['stdev', 'mean', 'n_stdev', 'n_mean']
statistics_features = ['stdev', 'mean', 'var', 'median', 'n_stdev', 'n_mean', 'n_var', 'n_median']
regular_features = regular_features + statistics_features
mb = 1000000
for w in windows_list:
Expand Down Expand Up @@ -94,7 +94,7 @@ def get_wc_composition(total_window_collection_wc, total_window_collection, wind
wc_difference.append(last_window - current_window)
last_window = current_window

values.append(total_window_collection[i])
values.append(total_window_collection[i] - 1)

if total == 0:
zero_list = ['0.0'] * 10
Expand Down Expand Up @@ -126,7 +126,7 @@ def get_read_features(chrom, bamfile_name, window_size, mapq_threshold):
# count reads in each window of size stepsize
for i in range(0, length, step_size):
window_count += 1
s = str(chrom) + str(i)
s = str(chrom) + ":" + str(i)
window_collection.update({s: 1})
window_collection_wc.update({s: 1})
window_collection_wc.update({s+'W': 1})
Expand Down Expand Up @@ -167,7 +167,7 @@ def get_read_features(chrom, bamfile_name, window_size, mapq_threshold):
window_collection_wc.update({s+'C': 1})

if not i == 0:
last_window = str(chrom) + str(i-step_size)
last_window = str(chrom) + ":" + str(i-step_size)
diff = window_collection[last_window] - window_collection[s]
neighbor_difference.append(diff)

Expand Down