ImmPort/Check Alignment Deltas

up to ImmPort/Demo_sketch

exercise: parse alignment data; check that there's a delta between each allele Done in alignment_parser.py r1172:

~/projects/packages/hla$ for f in ,cache/*nuc.txt; do echo $f; python alignment_parser.py $f; done ,cache/A_nuc.txt 770 alleles found ,cache/B_nuc.txt 1185 alleles found ,cache/ClassI_nuc.txt 0 alleles found ,cache/C_nuc.txt 444 alleles found ,cache/DMA_nuc.txt 4 alleles found ,cache/DMB_nuc.txt 7 alleles found ,cache/DOA_nuc.txt 12 alleles found ,cache/DOB_nuc.txt 9 alleles found ,cache/DPA_nuc.txt 27 alleles found ,cache/DPB_nuc.txt 135 alleles found ,cache/DQA_nuc.txt 34 alleles found ,cache/DQB_nuc.txt 99 alleles found ,cache/DRA_nuc.txt 3 alleles found ,cache/DRB_nuc.txt 719 alleles found ,cache/E_nuc.txt 9 alleles found ,cache/F_nuc.txt 21 alleles found ,cache/G_nuc.txt 43 alleles found ,cache/H_nuc.txt 12 alleles found ,cache/J_nuc.txt 9 alleles found ,cache/K_nuc.txt 6 alleles found ,cache/L_nuc.txt 5 alleles found ,cache/MICA_nuc.txt 67 alleles found ,cache/MICB_nuc.txt 30 alleles found ,cache/TAP1_nuc.txt 7 alleles found ,cache/TAP2_nuc.txt 4 alleles found ,cache/V_nuc.txt 3 alleles found

At the protein level, we note some so-called "silent" mutations - where the dna has changed but where the change doesn't have an impact on translation:

~/projects/packages/hla$ for f in ,cache/*_prot.txt; do echo $f; python alignment_parser.py $f; done ,cache/A_prot.txt 770 alleles found no diff in A*010102 no diff in A*010103 no diff in A*010104 no diff in A*010105 ,cache/B_prot.txt 1185 alleles found no diff in B*070203 no diff in B*070204 no diff in B*070205 no diff in B*070206 no diff in B*070207 no diff in B*070209 ,cache/ClassI_prot.txt 0 alleles found ,cache/C_prot.txt 444 alleles found ,cache/DMA_prot.txt 4 alleles found ,cache/DMB_prot.txt 7 alleles found ,cache/DOA_prot.txt 12 alleles found no diff in DOA*01010201 no diff in DOA*01010202 no diff in DOA*01010203 no diff in DOA*010103 no diff in DOA*01010401 no diff in DOA*01010402 no diff in DOA*010105 no diff in DOA*010106 ,cache/DOB_prot.txt 9 alleles found no diff in DOB*01010102 no diff in DOB*010102 no diff in DOB*010103 ,cache/DPA_prot.txt 27 alleles found no diff in DPA1*010302 no diff in DPA1*010303 no diff in DPA1*010304 ,cache/DPB_prot.txt 135 alleles found no diff in DPB1*010102 no diff in DPB1*010103 ,cache/DQA_prot.txt 34 alleles found no diff in DQA1*010102 ,cache/DQB_prot.txt 99 alleles found no diff in DQB1*050102 ,cache/DRA_prot.txt 3 alleles found ,cache/DRB_prot.txt 709 alleles found no diff in DRB1*010102 no diff in DRB1*010103 no diff in DRB1*010104 no diff in DRB1*010105 no diff in DRB1*010106 no diff in DRB1*010107 no diff in DRB1*010108 no diff in DRB1*010109 no diff in DRB1*010110 ,cache/E_prot.txt 9 alleles found no diff in E*01010102 no diff in E*01010103 ,cache/F_prot.txt 21 alleles found no diff in F*01010102 no diff in F*01010103 no diff in F*01010104 no diff in F*01010105 no diff in F*01010106 no diff in F*01010107 no diff in F*01010108 no diff in F*01010201 no diff in F*01010202 no diff in F*01010203 no diff in F*01010204 no diff in F*01010205 no diff in F*01010301 no diff in F*01010302 no diff in F*01010303 no diff in F*01010304 ,cache/G_prot.txt 43 alleles found no diff in G*01010102 no diff in G*01010103 no diff in G*01010104 no diff in G*01010105 no diff in G*01010106 no diff in G*01010201 no diff in G*01010202 no diff in G*01010301 no diff in G*010104 no diff in G*010105 no diff in G*010106 no diff in G*010107 no diff in G*010108 no diff in G*010109 no diff in G*010111 no diff in G*010112 no diff in G*010113 no diff in G*010114 no diff in G*010115 no diff in G*010116 no diff in G*010117 no diff in G*010118 no diff in G*010119 ,cache/MICA_prot.txt 67 alleles found ,cache/MICB_prot.txt 30 alleles found ,cache/TAP1_prot.txt 7 alleles found ,cache/TAP2_prot.txt 4 alleles found