Write the comments in for the work to be done

Comment first, write code later! Also I fixed an erroneous space that
really didn't need to be there. Laid down the import for biopyton.

Created the basic iteration through our fasta files and added
loading of fasta file titles through biopython

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):