-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
--
-
-
-
-
- - mbdoud - - -
-
-
-
- - - - - - - - - - -
- - - - - - -
- - - -
-
-
-
-
-
-
-
-
-
-
-
-
-
- /hyphy
-
-
-
-
- -
-
-
- - - - -
- - - - - - -
- - - - Fork - - 19 - - - - -
-
-
- /hyphy
-
-
- 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Permalink
-
-
-
-
-
-
-
-
-
-
-
-
- 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-| - | ExecuteAFile ("Utility/GrabBag.bf"); | -
| - | ExecuteAFile ("Utility/DBTools.ibf"); | -
| - | - |
| - | - |
| - | alignOptions = {}; | -
| - | - |
| - | SetDialogPrompt ("Sequence File:"); | -
| - | DataSet unal = ReadDataFile (PROMPT_FOR_FILE); | -
| - | BASE_FILE_PATH = LAST_FILE_PATH; | -
| - | DB_FILE_PATH = LAST_FILE_PATH + ".db"; | -
| - | - |
| - | ANALYSIS_DB_ID = _openCacheDB (DB_FILE_PATH); | -
| - | - |
| - | haveTable = _TableExists (ANALYSIS_DB_ID, "SETTINGS"); | -
| - | if (haveTable) | -
| - | { | -
| - | existingSettings = _ExecuteSQL (ANALYSIS_DB_ID, "SELECT * FROM SETTINGS"); | -
| - | } | -
| - | - |
| - | if (Abs(existingSettings)) | -
| - | { | -
| - | existingSettings = existingSettings [0]; | -
| - | ExecuteCommands ("_Genetic_Code = " + existingSettings["GENETIC_CODE"]); | -
| - | ExecuteCommands (existingSettings["OPTIONS"] ^ {{"_hyphyAssociativeArray","alignOptions"}}); | -
| - | masterReferenceSequence = existingSettings["REFERENCE"]; | -
| - | dbSequences = _ExecuteSQL (ANALYSIS_DB_ID, "SELECT SEQUENCE_ID FROM SEQUENCES WHERE STAGE = 0"); | -
| - | unalSequenceCount = Abs(dbSequences); | -
| - | toDoSequences = {unalSequenceCount,1}; | -
| - | for (k = 0; k < unalSequenceCount; k=k+1) | -
| - | { | -
| - | toDoSequences[k] = (dbSequences[k])["SEQUENCE_ID"]; | -
| - | } | -
| - | dbSequences = 0; | -
| - | fprintf (stdout, "[PHASE 1] Reloaded ", unalSequenceCount, " unprocessed sequences\n"); | -
| - | } | -
| - | else | -
| - | { | -
| - | tableDefines = {}; | -
| - | tableDefines ["SETTINGS"] = {}; | -
| - | (tableDefines ["SETTINGS"])["RUN_DATE"] = "DATE"; | -
| - | (tableDefines ["SETTINGS"])["OPTIONS"] = "TEXT"; | -
| - | (tableDefines ["SETTINGS"])["REFERENCE"] = "TEXT"; | -
| - | (tableDefines ["SETTINGS"])["GENETIC_CODE"] = "TEXT"; | -
| - | (tableDefines ["SETTINGS"])["THRESHOLD"] = "REAL"; | -
| - | - |
| - | tableDefines ["SEQUENCES"] = {}; | -
| - | (tableDefines ["SEQUENCES"])["SEQUENCE_ID"] = "TEXT UNIQUE"; | -
| - | (tableDefines ["SEQUENCES"])["LENGTH"] = "INTEGER"; | -
| - | (tableDefines ["SEQUENCES"])["STAGE"] = "INTEGER"; | -
| - | /* | -
| - | 0 - initial import | -
| - | 1 - in frame without a fix | -
| - | 2 - one frame shift / fixed | -
| - | 3 - out-of-frame; not fixed / not aligned | -
| - | */ | -
| - | (tableDefines ["SEQUENCES"])["RAW"] = "TEXT"; | -
| - | (tableDefines ["SEQUENCES"])["ALIGNED_AA"] = "TEXT"; /* aligned aa. sequence */ | -
| - | (tableDefines ["SEQUENCES"])["ALIGNED"] = "TEXT"; /* aligned nucleotide sequence */ | -
| - | (tableDefines ["SEQUENCES"])["OFFSET"] = "INTEGER"; /* start offset w.r.t the reference sequence */ | -
| - | (tableDefines ["SEQUENCES"])["END_OFFSET"] = "INTEGER"; /* end offset w.r.t the reference sequence */ | -
| - | (tableDefines ["SEQUENCES"])["SCORE"] = "REAL"; | -
| - | (tableDefines ["SEQUENCES"])["FRAME"] = "INTEGER"; | -
| - | - |
| - | _CreateTableIfNeeded (ANALYSIS_DB_ID, "SETTINGS", tableDefines["SETTINGS"], 0); | -
| - | _CreateTableIfNeeded (ANALYSIS_DB_ID, "SEQUENCES", tableDefines["SEQUENCES"], 1); | -
| - | - |
| - | /* START ALIGNMENT SETTINGS */ | -
| - | LoadFunctionLibrary ("SeqAlignShared.ibf"); | -
| - | - |
| - | DataSetFilter filteredData = CreateFilter (unal,1); | -
| - | - |
| - | GetInformation (UnalignedSeqs,filteredData); | -
| - | /* preprocess sequences */ | -
| - | - |
| - | unalSequenceCount = Rows(UnalignedSeqs)*Columns(UnalignedSeqs); | -
| - | GetString (sequenceNames, unal, -1); | -
| - | - |
| - | longestSequence = 0; | -
| - | longestSequenceIDX = 0; | -
| - | - |
| - | seqRecord = {}; | -
| - | - |
| - | fprintf (stdout, "[PHASE 1] Initial Processing of ", unalSequenceCount, " sequences\n"); | -
| - | - |
| - | for (seqCounter = 0; seqCounter < unalSequenceCount; seqCounter = seqCounter+1) | -
| - | { | -
| - | UnalignedSeqs[seqCounter] = UnalignedSeqs[seqCounter]^{{"[^a-zA-Z]",""}}; | -
| - | UnalignedSeqs[seqCounter] = UnalignedSeqs[seqCounter]^{{"^N+",""}}; | -
| - | UnalignedSeqs[seqCounter] = UnalignedSeqs[seqCounter]^{{"N+$",""}}; | -
| - | - |
| - | seqRecord ["SEQUENCE_ID"] = sequenceNames[seqCounter]; | -
| - | seqRecord ["LENGTH"] = Abs (UnalignedSeqs[seqCounter]); | -
| - | seqRecord ["STAGE"] = 0; | -
| - | seqRecord ["RAW"] = UnalignedSeqs[seqCounter]; | -
| - | - |
| - | if (doLongestSequence) | -
| - | { | -
| - | if (doLongestSequence == 1 || seqCounter != unalSequenceCount-1) | -
| - | { | -
| - | if (Abs (UnalignedSeqs[seqCounter]) > longestSequence) | -
| - | { | -
| - | longestSequence = Abs (UnalignedSeqs[seqCounter]); | -
| - | longestSequenceIDX = seqCounter; | -
| - | } | -
| - | } | -
| - | } | -
| - | - |
| - | _InsertRecord (ANALYSIS_DB_ID, "SEQUENCES", seqRecord); | -
| - | SetParameter (STATUS_BAR_STATUS_STRING, "Initial processing ("+seqCounter+"/"+unalSequenceCount+" done)",0); | -
| - | } | -
| - | - |
| - | if (refSeq == 0) | -
| - | { | -
| - | masterReferenceSequence = UnalignedSeqs[0]; | -
| - | } | -
| - | - |
| - | - |
| - | if (doLongestSequence) | -
| - | { | -
| - | fprintf (stdout, "\nSelected sequence ", sequenceNames[longestSequenceIDX], " as reference."); | -
| - | masterReferenceSequence = UnalignedSeqs[longestSequenceIDX]; | -
| - | } | -
| - | - |
| - | incFileName = HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def"; | -
| - | ExecuteCommands ("#include \""+incFileName+"\";"); | -
| - | - |
| - | doLongestSequence = (refSeq==1); | -
| - | aRecord = {}; | -
| - | aRecord["RUN_DATE"] = _ExecuteSQL(ANALYSIS_DB_ID,"SELECT DATE('NOW') AS CURRENT_DATE"); | -
| - | aRecord["RUN_DATE"] = ((aRecord["RUN_DATE"])[0])["CURRENT_DATE"]; | -
| - | aRecord["OPTIONS"] = "" + alignOptions; | -
| - | aRecord["REFERENCE"] = masterReferenceSequence; | -
| - | aRecord["GENETIC_CODE"] = "" + _Genetic_Code; | -
| - | _InsertRecord (ANALYSIS_DB_ID, "SETTINGS", aRecord); | -
| - | toDoSequences = sequenceNames; | -
| - | UnalignedSequences = 0; | -
| - | - |
| - | } | -
| - | - |
| - | skipOutliers = 1; | -
| - | doRC = 1; | -
| - | - |
| - | /* build codon translation table */ | -
| - | - |
| - | codonToAAMap = {}; | -
| - | codeToAA = "FLIMVSPTAYXHQNKDECWRG"; | -
| - | - |
| - | nucChars = "ACGT"; | -
| - | - |
| - | for (p1=0; p1<64; p1=p1+1) | -
| - | { | -
| - | codon = nucChars[p1$16]+nucChars[p1%16$4]+nucChars[p1%4]; | -
| - | ccode = _Genetic_Code[p1]; | -
| - | codonToAAMap[codon] = codeToAA[ccode]; | -
| - | } | -
| - | - |
| - | /* determine reading frames */ | -
| - | ProteinSequences = {}; | -
| - | AllTranslations = {}; | -
| - | ReadingFrames = {}; | -
| - | StopCodons = {}; | -
| - | StopPositions = {}; | -
| - | RC = {}; | -
| - | - |
| - | fprintf (stdout, "\n[PHASE 2] Detecting reading frames for each unprocessed sequence...\n"); | -
| - | frameCounter = {3,2}; | -
| - | stillHasStops = {}; | -
| - | aRecord = {}; | -
| - | - |
| - | for (seqCounter = 0; seqCounter < unalSequenceCount; seqCounter = seqCounter+1) | -
| - | { | -
| - | rawSeq = (_ExecuteSQL(ANALYSIS_DB_ID,"SELECT RAW FROM SEQUENCES WHERE SEQUENCE_ID = '" + toDoSequences[seqCounter] + "'")); | -
| - | aSeq = (rawSeq[0])["RAW"]; | -
| - | seqLen = Abs(aSeq)-2; | -
| - | - |
| - | minStops = 1e20; | -
| - | tString = ""; | -
| - | rFrame = 0; | -
| - | rrc = 0; | -
| - | allTran = {3,2}; | -
| - | stopPosn = {6,2}; | -
| - | - |
| - | for (rc = 0; rc<=doRC; rc = rc+1) | -
| - | { | -
| - | if (rc) | -
| - | { | -
| - | aSeq = nucleotideReverseComplement (aSeq) | -
| - | } | -
| - | for (offset = 0; offset < 3; offset = offset+1) | -
| - | { | -
| - | translString = ""; | -
| - | translString * (seqLen/3+1); | -
| - | for (seqPos = offset; seqPos < seqLen; seqPos = seqPos+3) | -
| - | { | -
| - | codon = aSeq[seqPos][seqPos+2]; | -
| - | prot = codonToAAMap[codon]; | -
| - | if (Abs(prot)) | -
| - | { | -
| - | translString * prot; | -
| - | } | -
| - | else | -
| - | { | -
| - | translString * "?"; | -
| - | } | -
| - | } | -
| - | translString * 0; | -
| - | translString = translString^{{"X$","?"}}; | -
| - | stopPos = translString||"X"; | -
| - | if (stopPos[0]>=0) | -
| - | { | -
| - | stopCount = Rows(stopPos)$2; | -
| - | stopPosn[3*rc+offset][0] = stopPos[0]; | -
| - | stopPosn[3*rc+offset][1] = stopPos[stopCount*2-1]; | -
| - | } | -
| - | else | -
| - | { | -
| - | stopCount = 0; | -
| - | } | -
| - | if (stopCount<minStops) | -
| - | { | -
| - | minStops = stopCount; | -
| - | rFrame = offset; | -
| - | rrc = rc; | -
| - | tString = translString; | -
| - | } | -
| - | allTran[offset][rc] = translString; | -
| - | } | -
| - | } | -
| - | - |
| - | ReadingFrames [seqCounter] = rFrame; | -
| - | ProteinSequences [seqCounter] = tString; | -
| - | frameCounter [rFrame][rrc] = frameCounter[rFrame][rrc]+1; | -
| - | StopPositions [seqCounter] = stopPosn; | -
| - | AllTranslations [seqCounter] = allTran; | -
| - | RC [seqCounter] = rrc; | -
| - | - |
| - | SetParameter (STATUS_BAR_STATUS_STRING, "Reading frame analysis ("+seqCounter+"/"+unalSequenceCount+" done)",0); | -
| - | } | -
| - | - |
| - | _closeCacheDB (ANALYSIS_DB_ID); | -
| - | 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]; | -
| - | seqName = sequenceNames[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 = {}; | -
| - | - |
| - | 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[Abs(alignmentScores)] = aligned[0]/Abs(aligned[1]); | -
| - | 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; | -
| - | } | -
| - | } | -
| - | } | -
| - | } | -
| - | - |
| - | alignmentScoresM = avlToMatrix ("alignmentScores"); | -
| - | ExecuteAFile ("Utility/DescriptiveStatistics.bf"); | -
| - | distInfo = GatherDescriptiveStats (alignmentScoresM); | -
| - | /*lowerCuttoff = 0.25;*/ | -
| - | distInfo["Mean"] - 2*distInfo["Std.Dev"]; | -
| - | /* 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; | -
| - | - |
| - | return 0; | -
| - | - |
| - | refLength = Abs(fullRefSeq); | -
| - | - |
| - | SetDialogPrompt ("Save alignment to:"); | -
| - | - |
| - | seqName=sequenceNames[0]; | -
| - | fprintf (PROMPT_FOR_FILE,CLEAR_FILE,">",seqName,"\n",fullRefSeq); | -
| - | fName = LAST_FILE_PATH; | -
| - | fNameC = fName+".nuc"; | -
| - | fprintf (fNameC,CLEAR_FILE,">",seqName,"\n",fullRefSeqN); | -
| - | - |
| - | alCounter = 0; | -
| - | - |
| - | for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter = seqCounter+1) | -
| - | { | -
| - | if (skipSeqs[seqCounter] == 0) | -
| - | { | -
| - | if (skipOutliers == 0 && alignmentScoresM[alCounter] < lowerCuttoff) | -
| - | { | -
| - | seqName=sequenceNames[seqCounter]; | -
| - | fprintf (stdout, "Sequence ", seqName ," was skipped because of a poor alignment score.\n"); | -
| - | skipSeqs[seqCounter] = 1; | -
| - | alCounter = alCounter + 1; | -
| - | continue; | -
| - | } | -
| - | alCounter = alCounter + 1; | -
| - | seqName=sequenceNames[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]) | -
| - | { | -
| - | seqName=sequenceNames[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; | -
| - | } | -
| - | - |
