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| author | Arthur Centeno | 2021-10-25 21:04:23 +0000 |
|---|---|---|
| committer | Arthur Centeno | 2021-10-25 21:04:23 +0000 |
| commit | 499a80f138030c4de1629c043c8f9401a99894ea (patch) | |
| tree | 449dcae965d13f966fb6d52625fbc86661c8c6a0 /wqflask/maintenance/convert_dryad_to_bimbam.py | |
| parent | 6151faa9ea67af4bf4ea95fb681a9dc4319474b6 (diff) | |
| parent | 700802303e5e8221a9d591ba985d6607aa61e1ce (diff) | |
| download | genenetwork2-499a80f138030c4de1629c043c8f9401a99894ea.tar.gz | |
Merge github.com:genenetwork/genenetwork2 into acenteno
Diffstat (limited to 'wqflask/maintenance/convert_dryad_to_bimbam.py')
| -rw-r--r-- | wqflask/maintenance/convert_dryad_to_bimbam.py | 14 |
1 files changed, 8 insertions, 6 deletions
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py index e833b395..18fbb8a1 100644 --- a/wqflask/maintenance/convert_dryad_to_bimbam.py +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") @@ -42,7 +41,7 @@ def read_dryad_file(filename): return geno_rows - #for i, marker in enumerate(marker_list): + # for i, marker in enumerate(marker_list): # this_row = [] # this_row.append(marker) # this_row.append("X") @@ -53,18 +52,21 @@ def read_dryad_file(filename): # this_row.append(line.split(" ")[i+2]) # print("row: " + str(i)) # geno_rows.append(this_row) - # - #return geno_rows + # + # return geno_rows + def write_bimbam_files(geno_rows): with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh: for row in geno_rows: geno_fh.write(", ".join(row) + "\n") + def convert_dryad_to_bimbam(filename): geno_file_rows = read_dryad_file(filename) write_bimbam_files(geno_file_rows) -if __name__=="__main__": + +if __name__ == "__main__": input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" - convert_dryad_to_bimbam(input_filename)
\ No newline at end of file + convert_dryad_to_bimbam(input_filename) |