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This commit is contained in:
Eric Coissac
2022-01-13 23:27:39 +01:00
parent dab6549cad
commit f53bf1b804
93 changed files with 11042 additions and 0 deletions
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14
pkg/obiapat/abiapat/CODES/dft_code.h Normal file
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/* ----------------------------------------------- */
/* dft_pat_seq_code.h */
/* default alphabet encoding for alpha */
/* ----------------------------------------------- */
0x00000001 /* A */, 0x00000002 /* B */, 0x00000004 /* C */,
0x00000008 /* D */, 0x00000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000200 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002000 /* N */, 0x00004000 /* O */,
0x00008000 /* P */, 0x00010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00100000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x00800000 /* X */,
0x01000000 /* Y */, 0x02000000 /* Z */

71
pkg/obiapat/abiapat/CODES/dna_code.h Normal file
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/* ----------------------------------------------- */
/* dna_code.h */
/* alphabet encoding for dna/rna */
/* ----------------------------------------- */
/* IUPAC encoding */
/* ----------------------------------------- */
/* G/A/T/C */
/* U=T */
/* R=AG */
/* Y=CT */
/* M=AC */
/* K=GT */
/* S=CG */
/* W=AT */
/* H=ACT */
/* B=CGT */
/* V=ACG */
/* D=AGT */
/* N=ACGT */
/* X=ACGT */
/* EFIJLOPQZ not recognized */
/* ----------------------------------------- */
/* dual encoding */
/* ----------------------------------------- */
/* A=ADHMNRVW */
/* B=BCDGHKMNRSTUVWY */
/* C=BCHMNSVY */
/* D=ABDGHKMNRSTUVWY */
/* G=BDGKNRSV */
/* H=ABCDHKMNRSTUVWY */
/* K=BDGHKNRSTUVWY */
/* M=ABCDHMNRSVWY */
/* N=ABCDGHKMNRSTUVWY */
/* R=ABDGHKMNRSVW */
/* S=BCDGHKMNRSVY */
/* T=BDHKNTUWY */
/* U=BDHKNTUWY */
/* V=ABCDGHKMNRSVWY */
/* W=ABDHKMNRTUVWY */
/* X=ABCDGHKMNRSTUVWY */
/* Y=BCDHKMNSTUVWY */
/* EFIJLOPQZ not recognized */
/* ----------------------------------------------- */
#ifndef USE_DUAL
/* IUPAC */
0x00000001 /* A */, 0x00080044 /* B */, 0x00000004 /* C */,
0x00080041 /* D */, 0x00000000 /* E */, 0x00000000 /* F */,
0x00000040 /* G */, 0x00080005 /* H */, 0x00000000 /* I */,
0x00000000 /* J */, 0x00080040 /* K */, 0x00000000 /* L */,
0x00000005 /* M */, 0x00080045 /* N */, 0x00000000 /* O */,
0x00000000 /* P */, 0x00000000 /* Q */, 0x00000041 /* R */,
0x00000044 /* S */, 0x00080000 /* T */, 0x00080000 /* U */,
0x00000045 /* V */, 0x00080001 /* W */, 0x00080045 /* X */,
0x00080004 /* Y */, 0x00000000 /* Z */
#else
/* DUAL */
0x00623089 /* A */, 0x017e34ce /* B */, 0x01243086 /* C */,
0x017e34cb /* D */, 0x00000000 /* E */, 0x00000000 /* F */,
0x0026244a /* G */, 0x017e348f /* H */, 0x00000000 /* I */,
0x00000000 /* J */, 0x017e24ca /* K */, 0x00000000 /* L */,
0x0166308f /* M */, 0x017e34cf /* N */, 0x00000000 /* O */,
0x00000000 /* P */, 0x00000000 /* Q */, 0x006634cb /* R */,
0x012634ce /* S */, 0x0158248a /* T */, 0x0158248a /* U */,
0x016634cf /* V */, 0x017a348b /* W */, 0x017e34cf /* X */,
0x017c348e /* Y */, 0x00000000 /* Z */
#endif

51
pkg/obiapat/abiapat/CODES/prot_code.h Normal file
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/* ----------------------------------------------- */
/* prot_code.h */
/* alphabet encoding for proteins */
/* ----------------------------------------- */
/* IUPAC encoding */
/* ----------------------------------------- */
/* B=DN */
/* Z=EQ */
/* X=any - {X} */
/* JOU not recognized */
/* ----------------------------------------- */
/* dual encoding */
/* ----------------------------------------- */
/* B=BDN */
/* D=BD */
/* E=EZ */
/* N=BN */
/* Q=QZ */
/* X=any - {X} */
/* Z=EQZ */
/* JOU not recognized */
/* ----------------------------------------------- */
#ifndef USE_DUAL
/* IUPAC */
0x00000001 /* A */, 0x00002008 /* B */, 0x00000004 /* C */,
0x00000008 /* D */, 0x00000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000000 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002000 /* N */, 0x00000000 /* O */,
0x00008000 /* P */, 0x00010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00000000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x037fffff /* X */,
0x01000000 /* Y */, 0x00010010 /* Z */
#else
/* DUAL */
0x00000001 /* A */, 0x0000200a /* B */, 0x00000004 /* C */,
0x0000000a /* D */, 0x02000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000000 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002002 /* N */, 0x00000000 /* O */,
0x00008000 /* P */, 0x02010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00000000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x037fffff /* X */,
0x01000000 /* Y */, 0x02010010 /* Z */
#endif