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lines changed Original file line number Diff line number Diff line change @@ -823,16 +823,12 @@ class Fusion(Model):
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gene_2 = relationship ("Gene" , foreign_keys = "Fusion.gene_2_id" , uselist = False )
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# New columns based on the updated schema
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- profile_id = Column (String , nullable = False )
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total_reads_supporting_fusion = Column (Integer , nullable = False )
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total_fusion_coverage = Column (Integer , nullable = False )
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ffpm = Column (Float , nullable = False )
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split_reads_1 = Column (Integer , nullable = False )
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split_reads_2 = Column (Integer , nullable = False )
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discordant_mates = Column (Integer , nullable = False )
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- strand1 = Column (String , nullable = False )
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- strand2 = Column (String , nullable = False )
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- reading_frame = Column (String , nullable = False )
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@classmethod
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def has_gene (cls , gene_id ):
Original file line number Diff line number Diff line change @@ -272,31 +272,23 @@ class FusionTableSpec:
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"fusion_name" ,
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"gene_1_label" ,
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"gene_2_label" ,
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- "profile_id" ,
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"total_reads_supporting_fusion" ,
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"total_fusion_coverage" ,
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"ffpm" ,
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"split_reads_1" ,
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"split_reads_2" ,
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"discordant_mates" ,
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- "strand1" ,
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- "strand2" ,
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- "reading_frame" ,
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]
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common_renames = {
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"gene_1_label" : "Gene 1" ,
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"gene_2_label" : "Gene 2" ,
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"fusion_name" : "Fusion Name" ,
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- "profile_id" : "Profile ID" ,
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"total_reads_supporting_fusion" : "Total Reads Supporting Fusion" ,
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"total_fusion_coverage" : "Total Fusion Coverage" ,
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"ffpm" : "FFPM" ,
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"split_reads_1" : "Split Reads 1" ,
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"split_reads_2" : "Split Reads 2" ,
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"discordant_mates" : "Discordant Mates" ,
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- "strand1" : "Strand 1" ,
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- "strand2" : "Strand 2" ,
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- "reading_frame" : "Reading Frame" ,
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}
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default_columns = [
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"Cell Line" ,
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