Mercurial > repos > bebatut > format_cd_hit_output

annotate format_cd_hit_output.py @ 0:bbd903996900 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
author bebatut
date Wed, 27 Jan 2016 03:28:42 -0500
parents
children 4ba41bcee051
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0
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
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diff changeset
1 #!/usr/bin/env python
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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2 # -*- coding: utf-8 -*-
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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3
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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4 import sys
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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5 import os
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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6 import argparse
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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7 import copy
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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8 import operator
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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9 from sets import Set
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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10
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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11 def extract_mapping_info(input_mapping_filepath):
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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12 mapping_info = {}
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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13 categories = Set([])
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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14
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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15 with open(input_mapping_filepath,'r') as mapping_file:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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16 for line in mapping_file.readlines():
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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17 split_line = line[:-1].split('\t')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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18 mapping_info.setdefault(split_line[0],split_line[1])
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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19 categories.add(split_line[1])
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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21 return mapping_info, categories
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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23 def init_category_distribution(categories = None):
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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24 cluster_category_distribution = {}
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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25 if categories != None:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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26 for category in categories:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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27 cluster_category_distribution[category] = 0
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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28 return cluster_category_distribution
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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29
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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30 def flush_cluster_info(cluster_name, cluster_ref_seq, ref_seq_cluster,
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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31 cluster_category_distribution, categories, output_category_distribution_file,
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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32 cluster_seq_number):
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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33 if cluster_name != '':
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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34 if categories != None:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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35 output_category_distribution_file.write(cluster_name)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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36 output_category_distribution_file.write('\t' + str(cluster_seq_number))
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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37 for category in categories:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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38 output_category_distribution_file.write('\t')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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39 output_category_distribution_file.write(str(cluster_category_distribution[category]))
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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40 output_category_distribution_file.write('\n')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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41
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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42 if cluster_ref_seq == '':
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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43 string = "No reference sequence found for "
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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44 string += cluster_name
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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45 raise ValueError(string)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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46
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47 ref_seq_cluster.setdefault(cluster_ref_seq, cluster_name)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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48
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49 def extract_cluster_info(args, mapping_info = None, categories = None):
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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50 ref_seq_cluster = {}
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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51
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52 if args.output_category_distribution != None:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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53 if mapping_info == None or categories == None:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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54 string = "A file with category distribution is expected but "
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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55 string += "no mapping information are available"
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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56 raise ValueError(string)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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57 output_category_distribution_file = open(
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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58 args.output_category_distribution, 'w')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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59 output_category_distribution_file.write('Cluster\tSequence_number')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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60 for category in categories:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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61 output_category_distribution_file.write('\t' + category)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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62
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63 output_category_distribution_file.write('\n')
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64
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65 with open(args.input_cluster_info,'r') as cluster_info_file:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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66 cluster_name = ''
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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67 cluster_category_distribution = init_category_distribution(categories)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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68 cluster_ref_seq = ''
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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69 cluster_seq_number = 0
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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70 for line in cluster_info_file.readlines():
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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71 if line[0] == '>':
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72 flush_cluster_info(cluster_name, cluster_ref_seq, ref_seq_cluster,
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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73 cluster_category_distribution, categories,
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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74 output_category_distribution_file, cluster_seq_number)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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75 cluster_name = line[1:-1]
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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76 cluster_name = cluster_name.replace(' ','_')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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77 cluster_category_distribution = init_category_distribution(categories)
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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78 cluster_ref_seq = ''
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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79 cluster_seq_number = 0
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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80 else:
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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81 seq_info = line[:-1].split('\t')[1].split(' ')
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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82 seq_name = seq_info[1][1:-3]
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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83 cluster_seq_number += 1
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84
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85 if categories != None:
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86 seq_count = 1
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87 if args.number_sum == 'false':
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88 if seq_name.find('size') != -1:
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89 substring = seq_name[seq_name.find('size'):-1]
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90 seq_count = int(substring.split('=')[1])
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91 if not mapping_info.has_key(seq_name):
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92 string = seq_name + " not found in mapping"
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93 raise ValueError(string)
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94 category = mapping_info[seq_name]
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95 cluster_category_distribution[category] += seq_count
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96
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97
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98 if seq_info[-1] == '*':
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99 if cluster_ref_seq != '':
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100 string = "A reference sequence (" + cluster_ref_seq
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101 string += ") already found for cluster " + cluster_name
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102 string += " (" + seq_name + ")"
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103 raise ValueError(string)
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104 cluster_ref_seq = seq_name
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105
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106 flush_cluster_info(cluster_name, cluster_ref_seq, ref_seq_cluster,
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107 cluster_category_distribution, categories,
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108 output_category_distribution_file, cluster_seq_number)
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109
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110 if args.output_category_distribution != None:
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111 output_category_distribution_file.close()
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112
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113 return ref_seq_cluster
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114
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115 def rename_representative_sequences(args, ref_seq_cluster):
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116 with open(args.input_representative_sequences,'r') as input_sequences:
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117 with open(args.output_representative_sequences,'w') as output_sequences:
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118 for line in input_sequences.readlines():
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119 if line[0] == '>':
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120 seq_name = line[1:-1]
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121 if not ref_seq_cluster.has_key(seq_name):
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122 string = seq_name + " not found as reference sequence"
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123 raise ValueError(string)
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124 output_sequences.write('>' + ref_seq_cluster[seq_name] + '\n')
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125 else:
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126 output_sequences.write(line)
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127
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128 def format_cd_hit_outputs(args):
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129 if args.input_mapping != None:
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130 mapping_info, categories = extract_mapping_info(args.input_mapping)
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131 else:
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132 mapping_info = None
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133 categories = None
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134
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135 ref_seq_cluster = extract_cluster_info(args, mapping_info, categories)
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136
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137 if args.input_representative_sequences != None:
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138 rename_representative_sequences(args, ref_seq_cluster)
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139
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140 if __name__ == "__main__":
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141 parser = argparse.ArgumentParser()
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142 parser.add_argument('--input_cluster_info', required=True)
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143 parser.add_argument('--input_representative_sequences')
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144 parser.add_argument('--output_representative_sequences')
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145 parser.add_argument('--input_mapping')
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146 parser.add_argument('--output_category_distribution')
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147 parser.add_argument('--number_sum')
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148 args = parser.parse_args()
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149
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150 format_cd_hit_outputs(args)