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laserson/gist:321444902ab1fa6698c9229f5f1cf229

Created September 9, 2024 14:19
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OAS schema issues
Raw
gistfile1.txt
Schema 1
num_files 15002
num_seqs 7051351620
sequence,locus,stop_codon,vj_in_frame,v_frameshift,productive,rev_comp,complete_vdj,v_call,d_call,j_call,sequence_alignment,germline_alignment,sequence_alignment_aa,germline_alignment_aa,v_alignment_start,v_alignment_end,d_alignment_start,d_alignment_end,j_alignment_start,j_alignment_end,v_sequence_alignment,v_sequence_alignment_aa,v_germline_alignment,v_germline_alignment_aa,d_sequence_alignment,d_sequence_alignment_aa,d_germline_alignment,d_germline_alignment_aa,j_sequence_alignment,j_sequence_alignment_aa,j_germline_alignment,j_germline_alignment_aa,fwr1,fwr1_aa,cdr1,cdr1_aa,fwr2,fwr2_aa,cdr2,cdr2_aa,fwr3,fwr3_aa,fwr4,fwr4_aa,cdr3,cdr3_aa,junction,junction_length,junction_aa,junction_aa_length,v_score,d_score,j_score,v_cigar,d_cigar,j_cigar,v_support,d_support,j_support,v_identity,d_identity,j_identity,v_sequence_start,v_sequence_end,v_germline_start,v_germline_end,d_sequence_start,d_sequence_end,d_germline_start,d_germline_end,j_sequence_start,j_sequence_end,j_germline_start,j_germline_end,fwr1_start,fwr1_end,cdr1_start,cdr1_end,fwr2_start,fwr2_end,cdr2_start,cdr2_end,fwr3_start,fwr3_end,fwr4_start,fwr4_end,cdr3_start,cdr3_end,np1,np1_length,np2,np2_length,c_region,Redundancy,ANARCI_numbering,ANARCI_status 15002
Schema 2 - the last three columns are ordered differently than Schema 1
num_files 547
num_seqs 3432990
sequence,locus,stop_codon,vj_in_frame,v_frameshift,productive,rev_comp,complete_vdj,v_call,d_call,j_call,sequence_alignment,germline_alignment,sequence_alignment_aa,germline_alignment_aa,v_alignment_start,v_alignment_end,d_alignment_start,d_alignment_end,j_alignment_start,j_alignment_end,v_sequence_alignment,v_sequence_alignment_aa,v_germline_alignment,v_germline_alignment_aa,d_sequence_alignment,d_sequence_alignment_aa,d_germline_alignment,d_germline_alignment_aa,j_sequence_alignment,j_sequence_alignment_aa,j_germline_alignment,j_germline_alignment_aa,fwr1,fwr1_aa,cdr1,cdr1_aa,fwr2,fwr2_aa,cdr2,cdr2_aa,fwr3,fwr3_aa,fwr4,fwr4_aa,cdr3,cdr3_aa,junction,junction_length,junction_aa,junction_aa_length,v_score,d_score,j_score,v_cigar,d_cigar,j_cigar,v_support,d_support,j_support,v_identity,d_identity,j_identity,v_sequence_start,v_sequence_end,v_germline_start,v_germline_end,d_sequence_start,d_sequence_end,d_germline_start,d_germline_end,j_sequence_start,j_sequence_end,j_germline_start,j_germline_end,fwr1_start,fwr1_end,cdr1_start,cdr1_end,fwr2_start,fwr2_end,cdr2_start,cdr2_end,fwr3_start,fwr3_end,fwr4_start,fwr4_end,cdr3_start,cdr3_end,np1,np1_length,np2,np2_length,c_region,ANARCI_numbering,ANARCI_status,Redundancy 547
Schema 3 - missing `v_frameshift` and `complete_vdj` columns
num_files 7
num_seqs 1020645
sequence,locus,stop_codon,vj_in_frame, productive,rev_comp, v_call,d_call,j_call,sequence_alignment,germline_alignment,sequence_alignment_aa,germline_alignment_aa,v_alignment_start,v_alignment_end,d_alignment_start,d_alignment_end,j_alignment_start,j_alignment_end,v_sequence_alignment,v_sequence_alignment_aa,v_germline_alignment,v_germline_alignment_aa,d_sequence_alignment,d_sequence_alignment_aa,d_germline_alignment,d_germline_alignment_aa,j_sequence_alignment,j_sequence_alignment_aa,j_germline_alignment,j_germline_alignment_aa,fwr1,fwr1_aa,cdr1,cdr1_aa,fwr2,fwr2_aa,cdr2,cdr2_aa,fwr3,fwr3_aa,fwr4,fwr4_aa,cdr3,cdr3_aa,junction,junction_length,junction_aa,junction_aa_length,v_score,d_score,j_score,v_cigar,d_cigar,j_cigar,v_support,d_support,j_support,v_identity,d_identity,j_identity,v_sequence_start,v_sequence_end,v_germline_start,v_germline_end,d_sequence_start,d_sequence_end,d_germline_start,d_germline_end,j_sequence_start,j_sequence_end,j_germline_start,j_germline_end,fwr1_start,fwr1_end,cdr1_start,cdr1_end,fwr2_start,fwr2_end,cdr2_start,cdr2_end,fwr3_start,fwr3_end,fwr4_start,fwr4_end,cdr3_start,cdr3_end,np1,np1_length,np2,np2_length,c_region,Redundancy,ANARCI_numbering,ANARCI_status 7
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