--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assembly_stats_txt.py	Tue Nov 07 12:28:31 2017 -0500
@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Version 1.01 - bugs kindly corrected by Jan van Haarst
+# Modified by Matthew Gopez October 13th, 2017
+
+import logging
+import os
+import subprocess
+import sys
+
+
+log = logging.getLogger(__name__)
+
+assert sys.version_info[:2] >= (2, 4)
+
+
+def stop_err(msg):
+    sys.stderr.write('%s\n' % msg)
+    sys.exit()
+
+
+def __main__():
+
+    # Parse Command Line
+
+    working_dir = sys.argv[2]
+    type = sys.argv[3]
+    bucket = sys.argv[4]
+    input = sys.argv[5]
+    stats = sys.argv[6]
+    sortedcontigs = sys.argv[7]
+    histogrampng = sys.argv[8]
+    summedcontigspng = sys.argv[9]
+    histogramdata = sys.argv[10]
+    summedcontigdata = sys.argv[11]
+    try:  # for test - needs this done
+        os.makedirs(working_dir)
+    except Exception, e:
+        stop_err('Error running assembly_stats_txt.py ' + str(e))
+
+    cmdline = '%s/fasta_summary.pl -i %s -t %s %s -o %s > /dev/null' \
+        % (os.path.dirname(sys.argv[0]), input, type, bucket,
+           working_dir)
+    try:
+        proc = subprocess.Popen(args=cmdline, shell=True,
+                                stderr=subprocess.PIPE)
+        returncode = proc.wait()
+
+        # get stderr, allowing for case where it's very large
+
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += proc.stderr.read(buffsize)
+                if not stderr or len(stderr) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        if returncode != 0:
+            raise Exception
+    except Exception, e:
+        stop_err('Error running assembly_stats.py ' + str(e))
+
+    stats_path = os.path.join(working_dir, 'stats.txt')
+    sorted_contigs_path = os.path.join(working_dir, 'sorted_contigs.fa')
+    histogram_png_path = os.path.join(working_dir,
+                                      'histogram_bins.dat.png')
+    summed_contigs_path = os.path.join(working_dir,
+                                       'summed_contig_lengths.dat.png')
+    histogram_data_path = os.path.join(working_dir, 'histogram_bins.dat')
+    summed_contigs_data_path = os.path.join(working_dir,
+                                            'summed_contig_lengths.dat')
+
+    out = open(stats, 'w')
+    for line in open(stats_path):
+        out.write('%s' % line)
+    out.close()
+
+    out = open(sortedcontigs, 'w')
+    for line in open(sorted_contigs_path):
+        out.write('%s' % line)
+    out.close()
+
+    out = open(histogrampng, 'w')
+    for line in open(histogram_png_path):
+        out.write('%s' % line)
+    out.close()
+
+    out = open(summedcontigspng, 'w')
+    for line in open(summed_contigs_path):
+        out.write('%s' % line)
+    out.close()
+
+    out = open(histogramdata, 'w')
+    for line in open(histogram_data_path):
+        out.write('%s' % line)
+    out.close()
+
+    out = open(summedcontigdata, 'w')
+    for line in open(summed_contigs_data_path):
+        out.write('%s' % line)
+    out.close()
+
+
+if __name__ == '__main__':
+    __main__()