removed multifasta's py extension, modified the --help argument output for quikr_train

1 files changed, 154 insertions, 0 deletions

diff --git a/src/python/multifasta_to_otu b/src/python/multifasta_to_otu
new file mode 100755
index 0000000..c6fb562
--- /dev/null
+++ b/src/python/multifasta_to_otu
@@ -0,0 +1,154 @@
+#!/usr/bin/python
+
+from multiprocessing import Pool
+from Bio import SeqIO
+import multiprocessing
+from subprocess import *
+import os
+import gzip
+import quikr as q
+import sys
+import numpy as np
+import argparse
+import platform
+import csv
+
+# our defaults
+kmer = 6
+lamb = 10000
+output_directory = ""
+input_directory = ""
+
+
+def main():
+
+  global kmer
+  global input_directory 
+  global output_directory 
+  global lamb
+  global trained_matrix 
+
+  parser = argparse.ArgumentParser(description="MultifastaOTU")
+
+  parser.add_argument("-i", "--input-directory", help="directory containing fasta files", required=True)
+  parser.add_argument("-o", "--otu-table", help="otu_table", required=True)
+  parser.add_argument("-t", "--trained-matrix", help="your trained matrix ", required=True)
+  parser.add_argument("-f", "--trained-fasta", help="the fasta file used to train your matrix", required=True)
+  parser.add_argument("-d", "--output-directory", help="quikr output directory", required=True)
+  parser.add_argument("-l", "--lamb", type=int, help="the default lambda value is 10,000")
+  parser.add_argument("-k", "--kmer", type=int, help="specifies which kmer to use, default=6")
+  parser.add_argument("-j", "--jobs", type=int, help="specifies how many jobs to run at once, default=number of CPUs")
+  args = parser.parse_args()
+    
+  # our defaults
+  jobs=multiprocessing.cpu_count()
+  trained_matrix = args.trained_matrix
+  input_directory = args.input_directory
+  output_directory = args.output_directory
+
+  # Make sure our input exist
+  if not os.path.isdir(args.input_directory):
+    parser.error("Input directory not found")
+
+  if not os.path.isdir(args.output_directory):
+    print "Output directory not found, creating directory"
+    os.path.mkdir(args, output_directory)
+
+  if not os.path.isfile(args.trained_matrix):
+    parser.error("Custom trained matrix not found")
+    
+  if not os.path.isfile(args.trained_fasta):
+    parser.error("Fasta file of trained matrix not found")
+
+  # use alternative lambda
+  if args.lamb is not None:
+    lamb = args.lamb
+    
+  if args.jobs is not None:
+    jobs = args.jobs
+
+  if args.kmer is not None:
+    kmer = args.kmer
+
+  # Load trained matrix
+  if qu.isCompressed(args.trained_matrix):
+    trained_matrix_file = gzip.open(args.trained_matrix, "rb")
+  else:
+    trained_matrix_file = open(args.trained_matrix, "rb")
+  
+  trained_matrix = np.load(trained_matrix_file)
+
+  # 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 an array of headers
+  headers = []
+  trained_matrix_headers = open(args.trained_fasta, "rU")
+  for header in SeqIO.parse(trained_matrix_headers, "fasta"):
+    headers.append(header.id)
+  trained_matrix_headers.close()
+
+  # create our number of reads matrix
+  number_of_reads = np.zeros((len(headers), len(fasta_list)))
+
+  # load the keys with values from each fasta result
+  for fasta, fasta_it in map(None, fasta_list, range(len(fasta_list))):
+
+    count_sequences = Popen(["grep", "-c" , "^>", args.input_directory + fasta], stdout=PIPE) 
+    number_of_sequences = int(count_sequences.stdout.readline())
+
+    proportions = np.loadtxt(output_directory + fasta);
+    
+    for proportion, proportion_it in map(None, proportions, range(len(proportions))):
+      number_of_reads[proportion_it, fasta_it] = round(proportion * number_of_sequences)
+
+  # remove empty rows from our matrix
+  final_headers = list()
+  final_data = list()
+  for row, header in map(None, number_of_reads, headers):
+    if row.sum() != 0:
+      final_headers.append(header)
+      final_data.append(row)
+
+  # convert from a list back into a numpy array
+  final_data = np.array(final_data, dtype=int)
+
+  # stack our final header and our number_of_reads matrix
+  number_of_reads = np.column_stack((final_headers, final_data))
+
+  # write our OTU table
+  output_file = open(args.otu_table, "wb") 
+  writer = csv.writer(output_file, delimiter="\t")
+
+  #write out our fasta file row
+  writer.writerow(['# QIIME vGail OTU table'])
+
+  fasta_row = ['#OTU_ID']
+  fasta_row.append(' '.join(fasta_list))
+  fasta_row = [' '.join(fasta_row)]
+  writer.writerow(fasta_row)
+
+  # write out our results
+  for i in range(0, np.shape(number_of_reads)[0]):
+      writer.writerow(list(number_of_reads[i]))
+
+  output_file.close()
+
+  return 0
+
+
+def quikr_call(fasta_file):
+  input_location = input_directory + fasta_file
+  output_location = output_directory + os.path.basename(fasta_file)
+
+  xstar = q.quikr(input_location, trained_matrix, kmer, lamb)
+  np.savetxt(output_location, xstar, delimiter=",", fmt="%f")
+  return xstar
+
+if __name__ == "__main__":
+  sys.exit(main())
+