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USF-HII / snptk

USF HII SNP Toolkit - Analyze and translate SNP entries using NCBI dbSNP and related databases
GNU General Public License v3.0
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Change --output-prefix in map-using-coord and --map-using-rs-id to positional arg #15

Closed countdigi closed 4 years ago

countdigi commented 4 years ago

Since --output-prefix was mandatory, we moved this to a positional argument and also renamed it to the more accurate description of output_map_dir.

The functionality will check if a directory exists and if it is not present it will create it and output to STDERR that it is creating it. It fails if the path exists but is not a directory:

E.g.:

(base) kcounts@hii2.rc.usf.edu:~/dev/usf-hii/snptk (master + u=)
$ bin/snptk map-using-coord --help
usage: snptk map-using-coord [-h] [--bim-offset BIM_OFFSET] [-d DBSNP]
                             [--keep-multi-snp-mappings]
                             [--keep-unmapped-rsids] [--skip-rs-ids]
                             input_bim output_map_dir

positional arguments:
  input_bim
  output_map_dir