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karini925karini925
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fixed clean_up files with min num cells
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-8
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‎LeafletSC.egg-info/PKG-INFO‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: LeafletSC
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Version: 0.3.0
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Version: 0.3.1
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Summary: Alternative splicing quantification in single cells with Leaflet
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Home-page: https://github.com/daklab/Leaflet
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Author: Karin Isaev, Columbia University and NYGC

‎LeafletSC/clustering/find_intron_clusters.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -207,7 +207,7 @@ def read_junction_files(junc_files, junc_suffix):
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else:
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junc_files_in_path = [junc_path]
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210-
print(f"The number of junction files to be processed is {len(junc_files_in_path)}")
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#print(f"The number of junction files to be processed is {len(junc_files_in_path)}")
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files_not_read = []
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@@ -229,7 +229,7 @@ def read_junction_files(junc_files, junc_suffix):
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return all_juncs
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232-
def clean_up_juncs(all_juncs, col_names, min_intron, max_intron, num_cells_wjunc):
232+
def clean_up_juncs(all_juncs, col_names, min_intron, max_intron, min_num_cells_wjunc):
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# Apply column names to the DataFrame
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all_juncs.columns = col_names
@@ -455,7 +455,7 @@ def main(junc_files, gtf_file, output_file, sequencing_type, junc_bed_file, thre
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col_names += ["file_name", "cell_type"]
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# 6. Clean up junctions and filter for intron length
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all_juncs = clean_up_juncs(all_juncs, col_names, min_intron, max_intron)
458+
all_juncs = clean_up_juncs(all_juncs, col_names, min_intron, max_intron, min_num_cells_wjunc)
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# 7. Make gr object from ALL junctions across all cell types
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print("Making gr object from all junctions across all cell types")

‎build/lib/LeafletSC/clustering/find_intron_clusters.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -207,7 +207,7 @@ def read_junction_files(junc_files, junc_suffix):
207207
else:
208208
junc_files_in_path = [junc_path]
209209

210-
print(f"The number of junction files to be processed is {len(junc_files_in_path)}")
210+
#print(f"The number of junction files to be processed is {len(junc_files_in_path)}")
211211

212212
files_not_read = []
213213

@@ -229,7 +229,7 @@ def read_junction_files(junc_files, junc_suffix):
229229

230230
return all_juncs
231231

232-
def clean_up_juncs(all_juncs, col_names, min_intron, max_intron, num_cells_wjunc):
232+
def clean_up_juncs(all_juncs, col_names, min_intron, max_intron, min_num_cells_wjunc):
233233

234234
# Apply column names to the DataFrame
235235
all_juncs.columns = col_names
@@ -455,7 +455,7 @@ def main(junc_files, gtf_file, output_file, sequencing_type, junc_bed_file, thre
455455
col_names += ["file_name", "cell_type"]
456456

457457
# 6. Clean up junctions and filter for intron length
458-
all_juncs = clean_up_juncs(all_juncs, col_names, min_intron, max_intron)
458+
all_juncs = clean_up_juncs(all_juncs, col_names, min_intron, max_intron, min_num_cells_wjunc)
459459

460460
# 7. Make gr object from ALL junctions across all cell types
461461
print("Making gr object from all junctions across all cell types")

dist/LeafletSC-0.3.0-py3-none-any.whl renamed to dist/LeafletSC-0.3.1-py3-none-any.whl

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‎dist/leafletsc-0.3.0.tar.gz‎

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‎dist/leafletsc-0.3.1.tar.gz‎

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‎setup.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ def read_requirements():
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setup(
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name='LeafletSC',
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version='0.3.0',
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version='0.3.1',
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author='Karin Isaev, Columbia University and NYGC',
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author_email='ki2255@cumc.columbia.edu',
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description='Alternative splicing quantification in single cells with Leaflet',

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