ddrad_scripts

Random scripts for dealing with ddRAD data, including output from pyRAD

snps2phylip.py - converts a .snps file from pyRAD to Phylip format

Usage:
snps2phylip -f [input.snps] -o [output.phy; optional, default="out.phy"]

getbadpyrad.py - Writes samples with high missing data from pyRAD .stats file to CSV so they can be input into a pyRAD params file

Usage:
getbadpyrad.py -f [input.stats] -o [output_filename] -p [minimum proportion of loci for inclusion; float]

I.e., -p 0.15 excludes samples with more than 85% missing data

filterUninformative.py - Uses .log file from IQ-TREE to blacklist uninformative loci from a directory of loci files.

Usage:
filterUninformative -l [input.log (must be in working directory)] -d [path/to/directoryWithLociFiles/ (must be subdirectory)]

Optional arguments: -b [/path/to/blacklistDIR]
-h Displays help menu

The log file must be in the current working directory, and the loci directory must be a subdirectory within the working directory.

popmap2exDFOIL.py

Dependencies

Python3
pandas
numpy

General Instructions

Takes two-column tab-separated map files to make the mysampleinfo.txt file used in the ExDFOIL pipeline

Each map file must have two columns: One with individual IDs, and another with either popIDs, batch#, speciesID, or subspeciesID. The map files should not contain a header. If you want to include all five columns in the output, five files need to be specified. The map file columns should not contain spaces.

Example Files

Example popmap file:

sample1\tpop1
sample2\tpop1
sample3\tpop2
sample4\tpop2

Example speciesID file:

sample1\tGorilla_gorilla
sample2\tGorilla_gorilla
sample3\tPan_troglodytes
sample4\tPan_troglodytes

At least one map file is required. Only the ones the user specify as commmand-line arguments will be included in the output file.

Example Output:

Individual batch popID speciesID subspeciesID
oberon10_JJW683p1 1 oberon10 oberon oberon_black
oberon10_JJW684p1 1 oberon10 oberon oberon_black
oberon10_JJW685 2 oberon10 oberon oberon_black

Usage and Options:

Required arguments:  
-p [POPMAP_FILENAME]  Specifies popID filename  

Optional arguments:  
-b [BATCH_FILENAME]  Specifies batch filename  
-S [SPECIES_FILENAME]  Specifies speciesID filename  
-s [SUBSPECIES_FILENAME]  specifies subspeciesID filename  
-o [OUTFILE]  Specifies output filename. Default = "mysampleinfo.txt"  
-h Displays help menu