diff options
| -rwxr-xr-x | multifasta_to_otu.py | 16 |
1 files changed, 15 insertions, 1 deletions
diff --git a/multifasta_to_otu.py b/multifasta_to_otu.py index 3e14fcf..e313e4a 100755 --- a/multifasta_to_otu.py +++ b/multifasta_to_otu.py @@ -1,5 +1,6 @@ #!/usr/bin/python from multiprocessing import Pool +from Bio import SeqIO import multiprocessing import os import quikr_train as qt @@ -54,7 +55,7 @@ def main(): if not os.path.isfile(args.trained_matrix): parser.error("custom trained matrix not found") - # use alternative lambda + # use alternative lambda if args.lamb is not None: lamb = args.lamb @@ -67,11 +68,24 @@ def main(): # Load trained matrix trained_matrix = np.load(args.trained_matrix); + # Return a list of the input directory fasta_list = os.listdir(args.input_directory) + # Queue up and run our quikr functions. pool = Pool(processes=jobs) results = pool.map(quikr_call, fasta_list) + # Create a dictionary and load up our keys + + + for fasta in fasta_list: + fasta_file = open(input_directory + fasta, "rU") + + for record in SeqIO.parse(fasta_file, "fasta") : + + # load the keys with values from each fasta result + + # Write the otu table return 0 def quikr_call(fasta_file): |