Mercurial > repos > nml > assemblystats

annotate assembly_stats_txt.py @ 0:ad2b274663f8 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
author nml
date Tue, 07 Nov 2017 12:28:31 -0500
parents
children 7556309ffbaf
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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diff changeset
1 #!/usr/bin/env python
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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2 # -*- coding: utf-8 -*-
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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3
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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4 # Version 1.01 - bugs kindly corrected by Jan van Haarst
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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5 # Modified by Matthew Gopez October 13th, 2017
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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6
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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7 import logging
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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8 import os
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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9 import subprocess
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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10 import sys
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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13 log = logging.getLogger(__name__)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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14
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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15 assert sys.version_info[:2] >= (2, 4)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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17
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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18 def stop_err(msg):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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19 sys.stderr.write('%s\n' % msg)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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20 sys.exit()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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23 def __main__():
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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25 # Parse Command Line
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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27 working_dir = sys.argv[2]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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28 type = sys.argv[3]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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29 bucket = sys.argv[4]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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30 input = sys.argv[5]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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31 stats = sys.argv[6]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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32 sortedcontigs = sys.argv[7]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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33 histogrampng = sys.argv[8]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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34 summedcontigspng = sys.argv[9]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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35 histogramdata = sys.argv[10]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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36 summedcontigdata = sys.argv[11]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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37 try: # for test - needs this done
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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38 os.makedirs(working_dir)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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39 except Exception, e:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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40 stop_err('Error running assembly_stats_txt.py ' + str(e))
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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41
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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42 cmdline = '%s/fasta_summary.pl -i %s -t %s %s -o %s > /dev/null' \
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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43 % (os.path.dirname(sys.argv[0]), input, type, bucket,
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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44 working_dir)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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45 try:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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46 proc = subprocess.Popen(args=cmdline, shell=True,
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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47 stderr=subprocess.PIPE)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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48 returncode = proc.wait()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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49
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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50 # get stderr, allowing for case where it's very large
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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51
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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52 stderr = ''
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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53 buffsize = 1048576
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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54 try:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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55 while True:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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56 stderr += proc.stderr.read(buffsize)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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57 if not stderr or len(stderr) % buffsize != 0:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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58 break
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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59 except OverflowError:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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60 pass
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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61 if returncode != 0:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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62 raise Exception
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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63 except Exception, e:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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64 stop_err('Error running assembly_stats.py ' + str(e))
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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65
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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66 stats_path = os.path.join(working_dir, 'stats.txt')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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67 sorted_contigs_path = os.path.join(working_dir, 'sorted_contigs.fa')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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68 histogram_png_path = os.path.join(working_dir,
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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69 'histogram_bins.dat.png')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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70 summed_contigs_path = os.path.join(working_dir,
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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71 'summed_contig_lengths.dat.png')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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72 histogram_data_path = os.path.join(working_dir, 'histogram_bins.dat')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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73 summed_contigs_data_path = os.path.join(working_dir,
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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74 'summed_contig_lengths.dat')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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75
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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76 out = open(stats, 'w')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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77 for line in open(stats_path):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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78 out.write('%s' % line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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79 out.close()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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80
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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81 out = open(sortedcontigs, 'w')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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82 for line in open(sorted_contigs_path):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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83 out.write('%s' % line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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84 out.close()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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85
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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86 out = open(histogrampng, 'w')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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87 for line in open(histogram_png_path):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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88 out.write('%s' % line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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89 out.close()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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90
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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91 out = open(summedcontigspng, 'w')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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92 for line in open(summed_contigs_path):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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93 out.write('%s' % line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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94 out.close()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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95
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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96 out = open(histogramdata, 'w')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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97 for line in open(histogram_data_path):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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98 out.write('%s' % line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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99 out.close()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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100
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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101 out = open(summedcontigdata, 'w')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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102 for line in open(summed_contigs_data_path):
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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103 out.write('%s' % line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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104 out.close()
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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105
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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106
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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107 if __name__ == '__main__':
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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108 __main__()