/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentTop75.bf is in hyphy-common 2.2.6+dfsg-3build3.
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alignOptions = {};
alignOptions ["SEQ_ALIGN_CHARACTER_MAP"]="ARNDCQEGHILKMFPSTWYV";
ChoiceList (refSeq,"Scoring Matrix",1,SKIP_NONE,"BLOSUM62","Default BLAST BLOSUM62 matrix",
"HIV 5%","Empirically derived 5% divergence HIV matrix",
"HIV 25%","Empirically derived 25% divergence HIV matrix",
"HIV 50%","Empirically derived 50% divergence HIV matrix");
if (refSeq < 0)
{
return 0;
}
if (refSeq == 0)
{
scoreMatrix = {
{7,-3,-3,-3,-1,-2,-2,0,-3,-3,-3,-1,-2,-4,-1,2,0,-5,-4,-1}
{-3,9,-1,-3,-6,1,-1,-4,0,-5,-4,3,-3,-5,-3,-2,-2,-5,-4,-4}
{-3,-1,9,2,-5,0,-1,-1,1,-6,-6,0,-4,-6,-4,1,0,-7,-4,-5}
{-3,-3,2,10,-7,-1,2,-3,-2,-7,-7,-2,-6,-6,-3,-1,-2,-8,-6,-6}
{-1,-6,-5,-7,13,-5,-7,-6,-7,-2,-3,-6,-3,-4,-6,-2,-2,-5,-5,-2}
{-2,1,0,-1,-5,9,3,-4,1,-5,-4,2,-1,-5,-3,-1,-1,-4,-3,-4}
{-2,-1,-1,2,-7,3,8,-4,0,-6,-6,1,-4,-6,-2,-1,-2,-6,-5,-4}
{0,-4,-1,-3,-6,-4,-4,9,-4,-7,-7,-3,-5,-6,-5,-1,-3,-6,-6,-6}
{-3,0,1,-2,-7,1,0,-4,12,-6,-5,-1,-4,-2,-4,-2,-3,-4,3,-5}
{-3,-5,-6,-7,-2,-5,-6,-7,-6,7,2,-5,2,-1,-5,-4,-2,-5,-3,4}
{-3,-4,-6,-7,-3,-4,-6,-7,-5,2,6,-4,3,0,-5,-4,-3,-4,-2,1}
{-1,3,0,-2,-6,2,1,-3,-1,-5,-4,8,-3,-5,-2,-1,-1,-6,-4,-4}
{-2,-3,-4,-6,-3,-1,-4,-5,-4,2,3,-3,9,0,-4,-3,-1,-3,-3,1}
{-4,-5,-6,-6,-4,-5,-6,-6,-2,-1,0,-5,0,10,-6,-4,-4,0,4,-2}
{-1,-3,-4,-3,-6,-3,-2,-5,-4,-5,-5,-2,-4,-6,12,-2,-3,-7,-6,-4}
{2,-2,1,-1,-2,-1,-1,-1,-2,-4,-4,-1,-3,-4,-2,7,2,-6,-3,-3}
{0,-2,0,-2,-2,-1,-2,-3,-3,-2,-3,-1,-1,-4,-3,2,8,-5,-3,0}
{-5,-5,-7,-8,-5,-4,-6,-6,-4,-5,-4,-6,-3,0,-7,-6,-5,16,3,-5}
{-4,-4,-4,-6,-5,-3,-5,-6,3,-3,-2,-4,-3,4,-6,-3,-3,3,11,-3}
{-1,-4,-5,-6,-2,-4,-4,-6,-5,4,1,-4,1,-2,-4,-3,0,-5,-3,7}
};
}
if (refSeq == 1)
{
scoreMatrix =
{
{ 11, 0, 2, 2, -2, 3, -1, 1, 0, -1, 1, 0, 3, -2, 0, 3, 7, 5, -5, -4}
{ 0, 15, -2, -4, 8, 2, 2, -1, -2, 0, -1, 0, -1, -4, 0, 5, 2, 0, 5, 7}
{ 2, -2, 12, 6, -3, 4, 4, -2, 1, -5, -2, 7, -2, -1, -1, 2, 1, 2, -4, 2}
{ 2, -4, 6, 10, -5, 4, 0, -3, 4, -5, 0, 1, -3, 3, 0, -1, 0, 1, -4, -2}
{ -2, 8, -3, -5, 14, 0, 2, 4, -3, 5, 2, -1, -1, -2, -2, 2, 0, 2, 3, 8}
{ 3, 2, 4, 4, 0, 10, -1, -2, 1, -4, -2, 0, -2, -1, 3, 4, 0, 1, 2, -3}
{ -1, 2, 4, 0, 2, -1, 15, 0, 2, 2, 0, 6, 4, 6, 6, 2, 2, -3, 0, 9}
{ 1, -1, -2, -3, 4, -2, 0, 10, 0, 4, 7, 1, -1, -2, 0, 2, 5, 7, -4, 0}
{ 0, -2, 1, 4, -3, 1, 2, 0, 11, -2, 3, 5, 0, 5, 7, 2, 4, 0, -2, -2}
{ -1, 0, -5, -5, 5, -4, 2, 4, -2, 9, 5, -3, 2, 2, 0, 1, 0, 2, 1, 0}
{ 1, -1, -2, 0, 2, -2, 0, 7, 3, 5, 15, 0, 0, 0, 4, 0, 5, 6, 0, -2}
{ 0, 0, 7, 1, -1, 0, 6, 1, 5, -3, 0, 12, 0, 1, 2, 7, 5, -1, -5, 4}
{ 3, -1, -2, -3, -1, -2, 4, -1, 0, 2, 0, 0, 12, 5, 2, 5, 3, -2, -2, -1}
{ -2, -4, -1, 3, -2, -1, 6, -2, 5, 2, 0, 1, 5, 11, 4, 0, 0, -3, -3, 0}
{ 0, 0, -1, 0, -2, 3, 6, 0, 7, 0, 4, 2, 2, 4, 10, 4, 3, -1, 2, 0}
{ 3, 5, 2, -1, 2, 4, 2, 2, 2, 1, 0, 7, 5, 0, 4, 11, 6, 0, -2, 2}
{ 7, 2, 1, 0, 0, 0, 2, 5, 4, 0, 5, 5, 3, 0, 3, 6, 11, 2, -4, 0}
{ 5, 0, 2, 1, 2, 1, -3, 7, 0, 2, 6, -1, -2, -3, -1, 0, 2, 11, -5, -2}
{ -5, 5, -4, -4, 3, 2, 0, -4, -2, 1, 0, -5, -2, -3, 2, -2, -4, -5, 14, 3}
{ -4, 7, 2, -2, 8, -3, 9, 0, -2, 0, -2, 4, -1, 0, 0, 2, 0, -2, 3, 14}
};
}
if (refSeq == 2)
{
scoreMatrix =
{
{ 11, -2, 1, 0, -5, 1, -3, -1, -3, -3, -2, -2, 1, -4, -1, 2, 5, 4, -8, -7}
{ -2, 16, -6, -7, 6, 0, 0, -4, -6, -3, -5, -2, -4, -7, -1, 4, 0, 0, 3, 6}
{ 1, -6, 12, 4, -6, 2, 2, -5, -2, -8, -5, 6, -5, -4, -5, 0, -1, 0, -7, 0}
{ 0, -7, 4, 10, -8, 2, -2, -6, 2, -8, -2, -1, -6, 1, -2, -5, -2, 0, -7, -4}
{ -5, 6, -6, -8, 14, -1, 0, 2, -5, 4, 0, -4, -4, -5, -6, 0, -4, 0, 1, 7}
{ 1, 0, 2, 2, -1, 10, -4, -6, 0, -8, -5, -1, -5, -4, 2, 2, -1, 0, 0, -7}
{ -3, 0, 2, -2, 0, -4, 15, -3, 0, 1, -2, 5, 3, 4, 5, 0, 0, -6, -2, 7}
{ -1, -4, -5, -6, 2, -6, -3, 10, -1, 2, 5, 0, -4, -6, 0, 0, 4, 5, -7, -2}
{ -3, -6, -2, 2, -5, 0, 0, -1, 11, -4, 1, 4, -3, 4, 5, 0, 3, -2, -5, -6}
{ -3, -3, -8, -8, 4, -8, 1, 2, -4, 9, 3, -6, 1, 0, -1, 0, -3, 0, 0, -2}
{ -2, -5, -5, -2, 0, -5, -2, 5, 1, 3, 15, -3, -4, -1, 2, -3, 4, 4, -2, -6}
{ -2, -2, 6, -1, -4, -1, 5, 0, 4, -6, -3, 12, -3, 0, 0, 5, 4, -4, -8, 2}
{ 1, -4, -5, -6, -4, -5, 3, -4, -3, 1, -4, -3, 12, 3, 0, 3, 1, -5, -4, -4}
{ -4, -7, -4, 1, -5, -4, 4, -6, 4, 0, -1, 0, 3, 12, 2, -2, -1, -6, -5, -2}
{ -1, -1, -5, -2, -6, 2, 5, 0, 5, -1, 2, 0, 0, 2, 11, 2, 2, -4, 0, -3}
{ 2, 4, 0, -5, 0, 2, 0, 0, 0, 0, -3, 5, 3, -2, 2, 12, 4, -3, -5, 0}
{ 5, 0, -1, -2, -4, -1, 0, 4, 3, -3, 4, 4, 1, -1, 2, 4, 11, 0, -7, -3}
{ 4, 0, 0, 0, 0, 0, -6, 5, -2, 0, 4, -4, -5, -6, -4, -3, 0, 11, -8, -5}
{ -8, 3, -7, -7, 1, 0, -2, -7, -5, 0, -2, -8, -4, -5, 0, -5, -7, -8, 14, 2}
{ -7, 6, 0, -4, 7, -7, 7, -2, -6, -2, -6, 2, -4, -2, -3, 0, -3, -5, 2, 14}
};
}
if (refSeq == 3)
{
scoreMatrix =
{
{ 10, 1, 4, 3, 0, 4, 0, 3, 1, 0, 3, 3, 4, 0, 2, 5, 7, 6, -2, -1}
{ 1, 15, 0, -2, 9, 3, 4, 0, 0, 1, 0, 2, 0, -1, 2, 6, 3, 2, 6, 8}
{ 4, 0, 12, 7, -1, 5, 5, 0, 3, -3, 0, 8, 0, 1, 0, 4, 3, 3, -2, 3}
{ 3, -2, 7, 10, -3, 5, 1, 0, 5, -3, 0, 3, 0, 4, 2, 0, 1, 2, -2, 0}
{ 0, 9, -1, -3, 13, 1, 5, 5, -1, 6, 4, 0, 1, 0, 0, 3, 1, 3, 4, 9}
{ 4, 3, 5, 5, 1, 10, 1, 0, 3, -2, 0, 2, 0, 0, 4, 5, 2, 2, 3, -1}
{ 0, 4, 5, 1, 5, 1, 14, 1, 4, 3, 2, 7, 5, 7, 7, 4, 3, 0, 1, 10}
{ 3, 0, 0, 0, 5, 0, 1, 9, 1, 5, 7, 2, 0, 0, 2, 3, 6, 7, -1, 1}
{ 1, 0, 3, 5, -1, 3, 4, 1, 10, 0, 4, 6, 1, 6, 8, 3, 5, 1, 0, 0}
{ 0, 1, -3, -3, 6, -2, 3, 5, 0, 9, 6, 0, 4, 3, 1, 2, 1, 3, 2, 2}
{ 3, 0, 0, 0, 4, 0, 2, 7, 4, 6, 15, 2, 1, 2, 5, 2, 6, 7, 0, 0}
{ 3, 2, 8, 3, 0, 2, 7, 2, 6, 0, 2, 11, 2, 3, 4, 7, 6, 0, -2, 5}
{ 4, 0, 0, 0, 1, 0, 5, 0, 1, 4, 1, 2, 12, 6, 3, 6, 4, 0, -1, 0}
{ 0, -1, 1, 4, 0, 0, 7, 0, 6, 3, 2, 3, 6, 11, 5, 1, 2, -1, -1, 2}
{ 2, 2, 0, 2, 0, 4, 7, 2, 8, 1, 5, 4, 3, 5, 10, 5, 4, 0, 3, 1}
{ 5, 6, 4, 0, 3, 5, 4, 3, 3, 2, 2, 7, 6, 1, 5, 11, 6, 1, 0, 3}
{ 7, 3, 3, 1, 1, 2, 3, 6, 5, 1, 6, 6, 4, 2, 4, 6, 10, 4, -2, 1}
{ 6, 2, 3, 2, 3, 2, 0, 7, 1, 3, 7, 0, 0, -1, 0, 1, 4, 10, -2, 0}
{ -2, 6, -2, -2, 4, 3, 1, -1, 0, 2, 0, -2, -1, -1, 3, 0, -2, -2, 13, 5}
{ -1, 8, 3, 0, 9, -1, 10, 1, 0, 2, 0, 5, 0, 2, 1, 3, 1, 0, 5, 14}
};
}
alignOptions ["SEQ_ALIGN_SCORE_MATRIX"] = scoreMatrix;
alignOptions ["SEQ_ALIGN_GAP_OPEN"] = 40;
alignOptions ["SEQ_ALIGN_GAP_OPEN2"] = 20;
alignOptions ["SEQ_ALIGN_GAP_EXTEND"] = 10;
alignOptions ["SEQ_ALIGN_GAP_EXTEND2"] = 5;
alignOptions ["SEQ_ALIGN_AFFINE"] = 1;
ChoiceList (refSeq,"Prefix/Suffix Indels",1,SKIP_NONE,"No penalty","Do not penalize prefix and suffix Indels","Normal penalty","Treat prefix and suffix indels as any other indels");
if (refSeq < 0)
{
return 0;
}
alignOptions ["SEQ_ALIGN_NO_TP"] = 1-refSeq;
/* END ALIGNMENT SETTINGS */
/* REFERENCE SEQUENCES OPTIONS */
predefSeqNames = {{"First in file", "Use the first sequence in the data file as a reference"}
/*0*/ {"HXB2_env", "Use HIV-1 HXB2 reference strain envelope sequence (K03455)"}
/*1*/ {"HXB2_nef", "Use HIV-1 HXB2 reference strain NEF sequence (K03455)"}
/*2*/ {"HXB2_gag", "Use HIV-1 HXB2 reference strain gag sequence (K03455)"}
/*3*/ {"HXB2_vpr", "Use HIV-1 HXB2 reference strain vpr sequence (K03455)"}
/*4*/ {"HXB2_vif", "Use HIV-1 HXB2 reference strain vif sequence (K03455)"}
/*5*/ {"HXB2_vpu", "Use HIV-1 HXB2 reference strain vpu sequence (K03455)"}
/*6*/ {"HXB2_pr", "Use HIV-1 HXB2 reference strain protease sequence (K03455)"}
/*7*/ {"HXB2_rt", "Use HIV-1 HXB2 reference strain reverse transcriptase sequence (K03455)"}
/*8*/ {"HXB2_int", "Use HIV-1 HXB2 reference strain integrase sequence (K03455)"}
/*9*/ {"HXB2_rev", "Use HIV-1 HXB2 reference strain rev (exons 1 and 2)sequence (K03455)"}
/*10*/ {"HXB2_tat", "Use HIV-1 HXB2 reference strain tat (exons 1 and 2) sequence (K03455)"}
/*11*/ {"HXB2_prrt", "Use HIV-1 HXB2 reference strain protease+rt sequence (K03455)"}
/*12*/ {"NL4_3prrt", "Use HIV-1 NL4-3 reference strain pr+rt sequence"}
};
predefSeqNames2 = {{"No", "No reference coordinate sequences"}
/*0*/ {"HXB2_env", "Use HIV-1 HXB2 reference strain envelope sequence (K03455)"}
/*1*/ {"HXB2_nef", "Use HIV-1 HXB2 reference strain NEF sequence (K03455)"}
/*2*/ {"HXB2_gag", "Use HIV-1 HXB2 reference strain gag sequence (K03455)"}
/*3*/ {"HXB2_vpr", "Use HIV-1 HXB2 reference strain vpr sequence (K03455)"}
/*4*/ {"HXB2_vif", "Use HIV-1 HXB2 reference strain vif sequence (K03455)"}
/*5*/ {"HXB2_vpu", "Use HIV-1 HXB2 reference strain vpu sequence (K03455)"}
/*6*/ {"HXB2_pr", "Use HIV-1 HXB2 reference strain protease sequence (K03455)"}
/*7*/ {"HXB2_rt", "Use HIV-1 HXB2 reference strain reverse transcriptase sequence (K03455)"}
/*8*/ {"HXB2_int", "Use HIV-1 HXB2 reference strain integrase sequence (K03455)"}
/*9*/ {"HXB2_rev", "Use HIV-1 HXB2 reference strain rev (exons 1 and 2)sequence (K03455)"}
/*10*/ {"HXB2_tat", "Use HIV-1 HXB2 reference strain tat (exons 1 and 2) sequence (K03455)"}
/*11*/ {"HXB2_prrt", "Use HIV-1 HXB2 reference strain protease+rt sequence (K03455)"}
/*12*/ {"NL4_3prrt", "Use HIV-1 NL4-3 reference strain pr+rt sequence"}
};
RefSeqs = {};
RefSeqs [0] = "ATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTGGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTA";
RefSeqs [1] = "ATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGAT---CAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGC";
RefSeqs [2] = "ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAA";
RefSeqs [3] = "ATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCC";
RefSeqs [4] = "ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACAC";
RefSeqs [5] = "ACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATC";
RefSeqs [6] = "CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT";
RefSeqs [7] = "CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC";
RefSeqs [8] = "TTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGAT";
RefSeqs [9] = "ATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTAACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGA";
RefSeqs[10] = "ATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGAT";
RefSeqs[11] = "CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC";
RefSeqs[12] = "CCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAGGACAGTATGATCAGATACTCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACAGTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAAGGGTGCCCACACTAATGATGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCATAATAGGAGCAGAAACTTTC";
ChoiceList (refSeq,"Choose a reference sequence",1,SKIP_NONE,predefSeqNames);
if (refSeq < 0)
{
return 0;
}
SetDialogPrompt ("Sequence File:");
if (refSeq > 0)
{
DataSet unal2 = ReadDataFile (PROMPT_FOR_FILE);
refSeq = ">" + predefSeqNames [refSeq][0] + "\n" + RefSeqs[refSeq-1];
DataSet refD = ReadFromString (refSeq);
DataSet unal = Combine (refD,unal2);
}
else
{
ChoiceList (refSeq2,"Insert a coordinate reference sequence?",1,SKIP_NONE,predefSeqNames2);
if (refSeq2 < 0)
{
return 0;
}
if (refSeq2)
{
DataSet unal2 = ReadDataFile (PROMPT_FOR_FILE);
refSeq = ">" + predefSeqNames [refSeq2][0] + "\n" + RefSeqs[refSeq2-1];
DataSet refD = ReadFromString (refSeq);
DataSet unal = Combine (unal2,refD);
}
else
{
DataSet unal = ReadDataFile (PROMPT_FOR_FILE);
}
}
ChoiceList (skipOutliers,"Include outliers?",1,SKIP_NONE,"No","Skip sequences with unusually poor alignment scores","Yes","Include all alignable sequences");
if (skipOutliers<0)
{
return 0;
}
DataSetFilter filteredData = CreateFilter (unal,1);
GetInformation (UnalignedSeqs,filteredData);
/* preprocess sequences */
unalSequenceCount = Rows(UnalignedSeqs)*Columns(UnalignedSeqs);
for (seqCounter = 0; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)
{
aSeq = UnalignedSeqs[seqCounter];
/*for (siteCounter = Abs(aSeq)-1; siteCounter>0; siteCounter=siteCounter-1)
{
if (aSeq[siteCounter]!="?")
{
break;
}
}
UnalignedSeqs[seqCounter] = aSeq[0][siteCounter];*/
UnalignedSeqs[seqCounter] = aSeq^{{"[^a-zA-Z]",""}};
UnalignedSeqs[seqCounter] = UnalignedSeqs[seqCounter]^{{"^N+",""}};
UnalignedSeqs[seqCounter] = UnalignedSeqs[seqCounter]^{{"N+$",""}};
}
/* build codon translation table */
incFileName = HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def";
ExecuteCommands ("#include \""+incFileName+"\";");
codonToAAMap = {};
codeToAA = "FLIMVSPTAYXHQNKDECWRG";
nucChars = "ACGT";
for (p1=0; p1<64; p1=p1+1)
{
codon = nucChars[p1$16]+nucChars[p1%16$4]+nucChars[p1%4];
ccode = _Genetic_Code[p1];
codonToAAMap[codon] = codeToAA[ccode];
}
/* determine reading frames */
ProteinSequences = {};
AllTranslations = {};
ReadingFrames = {};
StopCodons = {};
StopPositions = {};
fprintf (stdout, "\nDetecting reading frames for each sequence...\n");
frameCounter = {3,1};
stillHasStops = {};
for (seqCounter = 0; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)
{
aSeq = UnalignedSeqs[seqCounter];
seqLen = Abs(aSeq)-2;
minStops = 1e20;
tString = "";
rFrame = 0;
stopPosn = {3,2};
allTran = {3,1};
for (offset = 0; offset < 3; offset = offset+1)
{
translString = "";
translString * (seqLen/3+1);
for (seqPos = offset; seqPos < seqLen; seqPos = seqPos+3)
{
codon = aSeq[seqPos][seqPos+2];
prot = codonToAAMap[codon];
if (Abs(prot))
{
translString * prot;
}
else
{
translString * "?";
}
}
translString * 0;
translString = translString^{{"X$","?"}};
stopPos = translString||"X";
if (stopPos[0]>=0)
{
stopCount = Rows(stopPos)$2;
stopPosn[offset][0] = stopPos[0];
stopPosn[offset][1] = stopPos[stopCount*2-1];
}
else
{
stopCount = 0;
}
if (stopCount<minStops)
{
minStops = stopCount;
rFrame = offset;
tString = translString;
}
allTran[offset] = translString;
}
ReadingFrames[seqCounter] = rFrame;
ProteinSequences[seqCounter] = tString;
frameCounter[rFrame] = frameCounter[rFrame]+1;
StopPositions[seqCounter] = stopPosn;
AllTranslations [seqCounter] = allTran;
if (minStops>0)
{
stillHasStops[Abs(stillHasStops)] = seqCounter;
if (seqCounter == 0)
{
fprintf (stdout, "Reference sequence must not contain frameshifts\n");
return 0;
}
}
}
s1 = ProteinSequences[0];
fprintf (stdout, "\nFound:\n\t", frameCounter[0], " sequences in reading frame 1\n\t",frameCounter[1], " sequences in reading frame 2\n\t",frameCounter[2], " sequences in reading frame 3\n\nThere were ", Abs(stillHasStops), " sequences with apparent frameshift/sequencing errors\n");
skipSeqs = {};
for (k=0; k<Abs(stillHasStops); k=k+1)
{
seqCounter = stillHasStops[k];
GetString (seqName, unal, seqCounter);
fprintf (stdout,"Sequence ", seqCounter+1, " (", seqName, ") seems to have");
stopPosn = StopPositions[seqCounter];
fStart = -1;
fEnd = -1;
fMin = 1e10;
frame1 = 0;
frame2 = 0;
checkFramePosition (stopPosn[0][1],stopPosn[1][0],0,1);
checkFramePosition (stopPosn[1][1],stopPosn[0][0],1,0);
checkFramePosition (stopPosn[0][1],stopPosn[2][0],0,2);
checkFramePosition (stopPosn[2][1],stopPosn[0][0],2,0);
checkFramePosition (stopPosn[2][1],stopPosn[1][0],2,1);
checkFramePosition (stopPosn[1][1],stopPosn[2][0],1,2);
if (fStart>=0)
{
allTran = AllTranslations[seqCounter];
useq = UnalignedSeqs[seqCounter];
fprintf (stdout, " a shift from frame ", frame2+1, " to frame ", frame1+1, " between a.a. positions ", fStart, " and ", fEnd, ".");
fStart2 = Max(fStart-1,0);
fEnd2 = Min(fEnd+1,Min(Abs(allTran[frame1]),Abs(allTran[frame2]))-1);
tempString = allTran[frame2];
fprintf (stdout, "\n\tRegion ", fStart2, "-", fEnd2, " in frame ", frame2+1, ":\n\t", tempString[fStart2][fEnd2]);
fprintf (stdout, "\n\t", useq[3*fStart2+frame2][3*fEnd2+frame2-1]);
tempString = allTran[frame1];
fprintf (stdout, "\n\tRegion ", fStart2, "-", fEnd2, " in frame ", frame1+1, ":\n\t", tempString[fStart2][fEnd2]);
fprintf (stdout, "\n\t", useq[3*fStart2+frame1][3*fEnd2+frame1-1]);
fprintf (stdout, "\n\t\tAttempting to resolve by alignment to reference. ");
f1s = allTran[frame1];
f2s = allTran[frame2];
f1l = Abs(f1s);
bestScore = -1e10;
bestSplice = -1;
for (k2=fStart; k2<fEnd; k2=k2+1)
{
s2 = f2s[0][k2]+f1s[k2+1][Abs(f1s)];
inStr = {{s1,s2}};
AlignSequences(aligned, inStr, alignOptions);
aligned = aligned[0];
aligned = aligned[0];
if (aligned > bestScore)
{
bestScore = aligned;
bestSplice = k2;
bestString = s2;
}
}
fprintf (stdout, "Best splice site appears to be at a.a. position ", bestSplice, "\n");
/* update best spliced string */
ProteinSequences[seqCounter] = bestString;
ReadingFrames[seqCounter] = 0;
UnalignedSeqs[seqCounter] = useq[frame2][frame2+3*bestSplice+2] + useq[frame1+3*bestSplice+3][Abs(useq)-1] + "---";
}
else
{
fprintf (stdout, " multiple frameshifts\n");
skipSeqs[seqCounter] = 1;
}
}
SeqAlignments = {};
startingPosition = {unalSequenceCount,2};
refLength = Abs(ProteinSequences[0]);
refInsertions = {refLength,1};
fprintf (stdout,"\nPerforming pairwise alignment with reference sequences\n");
alignmentScores = {unalSequenceCount-1,2};
for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)
{
if (skipSeqs[seqCounter] == 0)
{
s2 = ProteinSequences[seqCounter];
inStr = {{s1,s2}};
AlignSequences(aligned, inStr, alignOptions);
aligned = aligned[0];
SeqAlignments[seqCounter] = aligned;
alignmentScores[seqCounter-1][0] = aligned[0];
alignmentScores[seqCounter-1][1] = seqCounter;
aligned = aligned[1];
myStartingPosition = aligned$"[^-]";
myEndingPosition = Abs (aligned)-1;
while (aligned[myEndingPosition]=="-")
{
myEndingPosition = myEndingPosition - 1;
}
myStartingPosition = myStartingPosition[0];
startingPosition[seqCounter][0] = myStartingPosition;
startingPosition[seqCounter][1] = myEndingPosition;
aligned = aligned[myStartingPosition][myEndingPosition];
refInsert = aligned||"-+";
if (refInsert[0]>0)
{
insCount = Rows (refInsert)/2;
offset = 0;
for (insN = 0; insN < insCount; insN = insN+1)
{
insPos = refInsert[insN*2];
insLength = refInsert[insN*2+1]-insPos+1;
insPos = insPos-offset;
if (refInsertions[insPos]<insLength)
{
refInsertions[insPos]=insLength;
}
offset = offset + insLength;
}
}
}
}
alignmentScores = alignmentScores%0;
/* produce a fully gapped reference sequence */
fprintf (stdout,"\nMerging pairwise alignments into a MSA\n");
fullRefSeq = "";
fullRefSeq * refLength;
fullRefSeq * (s1[0]);
s1N = UnalignedSeqs[0];
fullRefSeqN = "";
fullRefSeqN * (3*refLength);
fullRefSeqN * (s1N[0][2]);
frameShift = ReadingFrames[0];
for (seqCounter=1;seqCounter<refLength;seqCounter=seqCounter+1)
{
gapCount = refInsertions[seqCounter];
for (k=0; k<gapCount;k=k+1)
{
fullRefSeq*("-");
fullRefSeqN*("---");
}
fullRefSeq * (s1[seqCounter]);
fullRefSeqN * (s1N[frameShift+seqCounter*3][frameShift+seqCounter*3+2]);
}
fullRefSeq * 0;
fullRefSeqN * 0;
refLength = Abs(fullRefSeq);
SetDialogPrompt ("Save alignment to:");
GetString (seqName,unal,0);
fprintf (PROMPT_FOR_FILE,CLEAR_FILE,">",seqName,"\n",fullRefSeq);
fName = LAST_FILE_PATH;
fNameC = fName+".nuc";
fprintf (fNameC,CLEAR_FILE,">",seqName,"\n",fullRefSeqN);
/*for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)*/
for (seqID = 0; seqID < 75; seqID = seqID + 1)
{
seqCounter = alignmentScores[unalSequenceCount-2-seqID][1];
if (skipSeqs[seqCounter] == 0)
{
GetString (seqName,unal,seqCounter);
aligned = SeqAlignments[seqCounter];
aligned1 = aligned[1];
aligned2 = aligned[2];
s2 = startingPosition[seqCounter][0];
e2 = startingPosition[seqCounter][1];
gappedSeq = "";
gappedSeq * Abs(aligned2);
k=0;
while (k<refLength)
{
while (fullRefSeq[k]!=aligned1[s2])
{
gappedSeq*("-");
k=k+1;
}
gappedSeq*(aligned2[s2]);
s2=s2+1;
k=k+1;
}
gappedSeq * 0;
gappedSeqN = "";
gappedSeqN * (3*Abs(aligned2));
frameShift = ReadingFrames[seqCounter];
s1N = UnalignedSeqs[seqCounter];
s2N = ProteinSequences[seqCounter];
s2 = startingPosition[seqCounter][0];
k = 0;
e2 = Abs(gappedSeq);
k = 0;
while (k<e2)
{
while ((s2N[s2]!=gappedSeq[k])&&(k<e2))
{
gappedSeqN * ("---");
k=k+1;
}
if (k<e2)
{
gappedSeqN * s1N[frameShift+s2*3][frameShift+s2*3+2];
s2 = s2+1;
k=k+1;
}
}
gappedSeqN * 0;
if (refSeq2 && seqCounter == unalSequenceCount-1)
{
fscanf (fName, "Raw", soFar);
fprintf (fName, CLEAR_FILE,">",seqName,"\n",gappedSeq,"\n",soFar);
fscanf (fNameC, "Raw", soFar);
fprintf (fNameC,CLEAR_FILE,">",seqName,"\n",gappedSeqN,"\n",soFar);
}
else
{
fprintf (fName,"\n>",seqName,"\n",gappedSeq);
fprintf (fNameC,"\n>",seqName,"\n",gappedSeqN);
}
}
}
if (Abs(skipSeqs))
{
fName = fName+".bad";
for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)
{
if (skipSeqs[seqCounter])
{
GetString (seqName,unal,seqCounter);
fprintf (fName,">",seqName,"\n",UnalignedSeqs[seqCounter],"\n");
}
}
}
function checkFramePosition (pos1, pos2, fr1, fr2)
{
fSpan = pos2-pos1;
if (fSpan>1) /* first followed by second*/
{
if (fSpan < fMin)
{
fMin = fSpan;
frame1 = fr1;
frame2 = fr2;
fStart = pos1+1;
fEnd = pos2;
}
}
return 0;
}
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