tagdigger_script

For the input and output formats of tagdigger_script.py, see tagdigger_interactive.py. This is a command-line program with the following options:

• -h, --help: Display the list of options
• -e, --enzyme: Name of the restriction enzyme whose cut site is expected immediately after the barcode. Options are currently None, ApeKI, EcoT22I, NcoI, NsiI, PstI, SbfI.
• -c, --cutsite: Sequence of the restriction cut site that is expected immediately after the barcode. This does not have to supplied if the -e option is used. If both -e and -c are used, the program will check for consistency and throw an exception if the enzyme name and cut site do not match. If the -e option is not used, the -c option must be used.
• -w, --directory: Working directory.
• -b, --barcodefile: Name of the barcode key file.
• -o, --outputcounts: Output file name for read counts.
• -g, --outputgen (optional): Output file name for numeric genotypes.
• -k, --tokeep (optional): Name of text file listing names of markers to keep.
• --binaryOnly (optional): 'T' to retain only binary markers; 'F' to retain all markers. Default 'F'.
• --TASSELkeyFile (optional, only used if --TASSELSAM used): Name of output file matching tag names to SNP names in TASSEL.

Options for specifying file containing tag sequences:

• --UNEAKtags
• --MergedTags
• --ColumnTags
• --RowTags
• --StacksTags, --StacksSNPs, and --StacksAlleles
• --TASSELSAM
• --pyRADalleles

Example:

python tagdigger_script.py -e PstI -w C:\Users\lvclark\Documents\bestSeqProject\ -b mybarcodes.csv -o mycounts.csv -k markerstokeep.txt --UNEAKtags HapMap.fas.txt