--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genetrack.py	Tue Dec 22 17:03:27 2015 -0500
@@ -0,0 +1,65 @@
+"""
+genetrack.py
+
+Input: either scidx or gff format of reads
+Output: Called peaks in gff format
+"""
+import optparse
+import csv
+import os
+import genetrack_util
+
+CHUNK_SIZE = 10000000
+
+
+if __name__ == '__main__':
+    parser = optparse.OptionParser()
+    parser.add_option('-t', '--input_format', dest='input_format', type='string', help='Input format')
+    parser.add_option('-i', '--input', dest='inputs', type='string', action='append', nargs=2, help='Input datasets')
+    parser.add_option('-s', '--sigma', dest='sigma', type='int', default=5, help='Sigma.')
+    parser.add_option('-e', '--exclusion', dest='exclusion', type='int', default=20, help='Exclusion zone.')
+    parser.add_option('-u', '--up_width', dest='up_width', type='int', default=10, help='Upstream width of called peaks.')
+    parser.add_option('-d', '--down_width', dest='down_width', type='int', default=10, help='Downstream width of called peaks.')
+    parser.add_option('-f', '--filter', dest='filter', type='int', default=1, help='Absolute read filter.')
+    options, args = parser.parse_args()
+
+    os.mkdir('output')
+    for (dataset_path, hid) in options.inputs:
+        if options.input_format == 'gff':
+            # Make sure the reads for each chromosome are sorted by index.
+            input_path = genetrack_util.sort_chromosome_reads_by_index(dataset_path)
+        else:
+            # We're processing scidx data.
+            input_path = dataset_path
+        output_name = 's%se%su%sd%sF%s_on_data_%s' % (options.sigma,
+                                                      options.exclusion,
+                                                      options.up_width,
+                                                      options.down_width,
+                                                      options.filter,
+                                                      hid)
+        output_path = os.path.join('output', output_name)
+        reader = csv.reader(open(input_path, 'rU'), delimiter='\t')
+        writer = csv.writer(open(output_path, 'wt'), delimiter='\t')
+        width = options.sigma * 5
+        manager = genetrack_util.ChromosomeManager(reader)
+        while not manager.done:
+            cname = manager.chromosome_name()
+            # Should we process this chromosome?
+            data = manager.load_chromosome()
+            if not data:
+                continue
+            keys = genetrack_util.make_keys(data)
+            lo, hi = genetrack_util.get_range(data)
+            for chunk in genetrack_util.get_chunks(lo, hi, size=CHUNK_SIZE, overlap=width):
+                (slice_start, slice_end), process_bounds = chunk
+                window = genetrack_util.get_window(data, slice_start, slice_end, keys)
+                genetrack_util.process_chromosome(cname,
+                                                  window,
+                                                  writer,
+                                                  process_bounds,
+                                                  width,
+                                                  options.sigma,
+                                                  options.up_width,
+                                                  options.down_width,
+                                                  options.exclusion,
+                                                  options.filter)