Author: Bradley T. Martin, University of Arkansas; E-mail: btm002@email.uark.edu
Python package to make a population map from STRUCTURE, PHYLIP, and .ped (PLINK) files. You can alternatively add the popmap as the second column for any of the file types.
Uses Python 2 or 3
The program reads STRUCTURE files by default; use the -a option if you want to use a .ped file commonly used in the ADMIXTURE program. Use the -t option to read in a PHYLIP file.
By default, str2popmap.py uses the first four letters of each sample name to delimit population IDs.
However, the user can specify a range of characters for the popID search pattern (e.g., 2-5).
The popID REGEX search range can be changed with the -s (start) and -e (end) command-line arguments (first character=1)
NEW OPTION: You can now use the first occurrence of an underscore character as the popID delimiter by using the -u option.
-u option (Boolean; default = off) Delimits popIDs from first occurence of an underscore in sampleID.
Using the -u option overrides the -s and -e options.
example: ./str2popmap.py -f example_input.str -s 2 -e 5 -o output.str # Uses characters 2-5 as pattern to make PopIDs
-p option (Boolean; default = off) only writes two-column sample IDs and popIDs (POPMAP) separated by tabs
# -p option output
ind1\tpop1\n
ind2\tpop1\n
ind3\tpop2\n
ind4\tpop2\n
If you want the POPMAP to be inserted between sampleIDs and sequences in a PHYLIP file while keeping the sequences, use the -t option without -p.
Default File Format = STRUCTURE.
Default popID format = integer.
But you can use other formats instead by doing as shown below:
-t option (Boolean; default = off) Uses PHYLIP format for input/output files
-a option (Boolean; default = off) Uses .ped format for input/output files (commonly used in ADMIXTURE)
-c option (Boolean; default = off) Outputs character string as popID instead of integer
[-o OUTFILE (string); default = out.txt]
[-s STARTCHAR (integer); default = 1]
[-e ENDCHAR (integer); default = 4]
[-p POPMAP (Boolean); default = False]
[-t PHYLIP (Boolean); default = False]
[-a ADMIXTURE (Boolean); default = False]
[-c CHARREGEX (Boolean); default = False]
[-u UNDERSCORE (Boolean); default = False]