add script to convert pwm to bamm

.gitignore

@@ -121,3 +121,4 @@ cmake-build-debug/
 # python
 ##############
 */*/__pycache__/
+*/__pycache__/

py/pwm2bamm.py

@@ -0,0 +1,38 @@
+'''
+This is a script to convert PWMs from a MEME-formated file to BaMM-formated files.
+The only input is a MEME-formated file (version 4)
+Written by Wanwan Ge
+'''
+
+import argparse
+import os
+
+from utils import parse_meme, write_bamm
+
+def create_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('meme_file')
+
+    return parser
+
+def main():
+    parser = create_parser()
+    args = parser.parse_args()
+
+    ipath = args.meme_file
+    dir = os.path.dirname(ipath)
+    basename = os.path.splitext(os.path.basename(ipath))[0]
+    motifset = parse_meme(ipath)
+    models = motifset['models']
+
+    for num in range(len(models)):
+        filepath_v = dir + '/' + basename + "_motif_" + str(num+1) + ".ihbcp"
+        filepath_p = dir + '/' + basename + "_motif_" + str(num+1) + ".ihbp"
+        write_bamm(models[num]['pwm'], filepath_v )
+        write_bamm(models[num]['pwm'], filepath_p )
+
+
+if __name__ == '__main__':
+    main()
+
+

py/utils.py

@@ -279,5 +279,12 @@ def write_meme(dataset, meme_output_file):
                 print(" ".join(['{:.4f}'.format(x) for x in line]), file=fh)
             print(file=fh)
 
+def write_bamm(pwm, ofile):
+    eps = 1e-16
+    with open(ofile, "w") as fh:
+        for i in range(len(pwm)):
+            print(' '.join(['{:.4e}'.format(x+eps) for x in pwm[i]]) + ' \n', file=fh)
+
+
 class MalformattedMemeError(ValueError):
     pass