/usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.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 55 56 57 | SetDialogPrompt ("Please choose a data file to convert:");
ChoiceList (SKIP_OMISSIONS,"Deletions",1,SKIP_NONE,"Keep Deletions","Deletions will NOT be filtered from the data.",
"Skip Deletions","Deletions will be pruned out and NOT included in the converted file.");
if (SKIP_OMISSIONS<0)
{
fprintf (stdout, "\n\nExecution Canceled...");
}
DataSet bigDataSet = ReadDataFile (PROMPT_FOR_FILE);
if (IS_TREE_PRESENT_IN_DATA)
{
fprintf (stdout, "\nTree In Data:", DATAFILE_TREE);
}
DataSetFilter dsf = CreateFilter (bigDataSet,1);
fprintf (stdout, "\nRead:\n", bigDataSet);
ChoiceList (DATA_FILE_PRINT_FORMAT,"Output Format",1,SKIP_NONE,
/* 0 */ "# sequential","Sequential format with taxa names preceded by #",
/* 1 */ "# interleaved","Interleaved format with taxa names preceded by #",
/* 2 */ "PHYLIP sequential","PHYLIP Sequential Format. Taxa names are chopped at 10 characters.",
/* 3 */ "PHYLIP interleaved","PHYLIP Interleaved Format. Taxa names are chopped at 10 characters.",
/* 4 */ "NEXUS sequential, labels","NEXUS sequential format with taxa labels present in the data matrix.",
/* 5 */ "NEXUS interleaved, labels","NEXUS interleaved format with taxa labels present in the data matrix.",
/* 6 */ "NEXUS sequential, no labels","NEXUS sequential format without taxa labels in the data matrix.",
/* 7 */ "NEXUS interleaved, no labels","NEXUS interleaved format without taxa labels in the data matrix.",
/* 8 */ "CSV", "Comma separated characters",
/* 9 */ "FASTA sequential","FASTA Sequential Format.",
/* 10 */ "FASTA interleaved","FASTA Interleaved Format.",
/* 11 */ "PAML compatible", "PAML Compatible PHYLIP-like format");
if (DATA_FILE_PRINT_FORMAT<0)
{
fprintf (stdout, "\n\nExecution Canceled...");
}
else
{
if (DATA_FILE_PRINT_FORMAT%2 && DATA_FILE_PRINT_FORMAT < 8 || DATA_FILE_PRINT_FORMAT == 10)
{
fprintf (stdout,"\n How many sites per line in interleaved file:");
fscanf (stdin, "Number", DATA_FILE_DEFAULT_WIDTH);
if (DATA_FILE_PRINT_FORMAT<4)
{
fprintf (stdout,"\n How many sites per cluster:");
fscanf (stdin, "Number", DATA_FILE_GAP_WIDTH);
}
}
SetDialogPrompt ("Write to file:");
fprintf (PROMPT_FOR_FILE, CLEAR_FILE, dsf);
}
|