diff options
| -rw-r--r-- | kmer.py | 23 |
1 files changed, 18 insertions, 5 deletions
@@ -20,19 +20,32 @@ try: except: raise Exception("Error: could not load libkmer.so") -def load_kmer_counts_from_file(fh, kmer): +def get_counts_from_file(fn, kmer): ''' + load kmer counts from a filename (not a handle), of size kmer. + +returns an array size 4^k of counts + + >>> import kmer + >>> counts = kmer.get_counts_from_file("test.fa", 6) + ''' + + if type(fn) is not str: + raise TypeError("fn must be a str"); + if type(kmer) is not int: + raise TypeError("fn must be int"); + ret = [] - width = (kmer ** 4) + 1 + width = (kmer ** 4) libkmer.get_kmer_counts_from_filename.restype = c.POINTER(c.c_ulonglong * width ) - counts = libkmer.get_kmer_counts_from_filename(fh, kmer); + counts = libkmer.get_kmer_counts_from_filename(fn, kmer); - if counts.contents: + if counts: for i in counts.contents: ret.append(i) else: - ret = 'error' + ret = 'error could not count mers on' + str(fn) return ret |