/usr/share/hyphy/TemplateBatchFiles/SeqAlignment.bf is in hyphy-common 2.2.6+dfsg-3build3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | RequireVersion ("2.0020100903");
ExecuteAFile ("Utility/GrabBag.bf");
#include "SeqAlignShared.ibf";
ASSERTION_BEHAVIOR = 1;
/* END ALIGNMENT SETTINGS */
SetDialogPrompt ("Sequence File:");
doLongestSequence = (refSeq==1);
if (refSeq > 1)
{
DataSet unal2 = ReadDataFile (PROMPT_FOR_FILE);
refSeq = ">" + predefSeqNames [refSeq][0] + "\n" + RefSeqs[refSeq-2];
DataSet refD = ReadFromString (refSeq);
DataSet unal = Combine (refD,unal2);
}
else
{
ChoiceList (refSeq2,"Insert a coordinate reference sequence?",1,SKIP_NONE,predefSeqNames2);
assert (refSeq2 >= 0, "Reference sequence selection");
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);
if (doLongestSequence)
{
doLongestSequence = 2;
}
}
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");
assert (skipOutliers >= 0, "Outlier handling selection");
ChoiceList (doRC, "Try reverse complements?",1,SKIP_NONE,"No","Only align in the provided direction","Yes","Try both each sequences and its reverse complement.");
assert (doRC >= 0, "Reverse complement selection");
// build codon translation table
ExecuteAFile ("TemplateModels/chooseGeneticCode.def");
codonToAAMap = defineCodonToAA();
_handleAlignment ("unal",1);
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