Mercurial > repos > bebatut > format_cd_hit_output

annotate format_cd_hit_output.py @ 1:64da677bcee2 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
author bgruening
date Wed, 19 Oct 2022 14:42:33 +0000
parents 4015e9d6d277
children
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
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1 #!/usr/bin/env python
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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2 # -*- coding: utf-8 -*-
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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4 import argparse
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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7 def extract_mapping_info(input_mapping_filepath):
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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8 mapping_info = {}
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
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9 categories = set([])
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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11 with open(input_mapping_filepath, 'r') as mapping_file:
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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12 for line in mapping_file.readlines():
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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13 split_line = line[:-1].split('\t')
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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14 mapping_info.setdefault(split_line[0], split_line[1])
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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15 categories.add(split_line[1])
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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17 return mapping_info, categories
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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20 def init_category_distribution(categories=None):
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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21 cluster_categ_distri = {}
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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22 if categories is not None:
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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23 for category in categories:
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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24 cluster_categ_distri[category] = 0
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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25 return cluster_categ_distri
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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28 def flush_cluster_info(cluster_name, cluster_ref_seq, ref_seq_cluster,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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29 cluster_categ_distri, categories,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
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30 output_category_distribution_file, cluster_seq_number):
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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31 if cluster_name != '':
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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32 if categories is not None:
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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33 string = cluster_name
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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34 string += '\t' + str(cluster_seq_number)
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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35 for category in categories:
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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36 string += '\t'
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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37 string += str(cluster_categ_distri[category])
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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38 string += '\n'
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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39 output_category_distribution_file.write(string)
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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41 if cluster_ref_seq == '':
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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42 string = "No reference sequence found for "
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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43 string += cluster_name
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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44 raise ValueError(string)
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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45
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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46 ref_seq_cluster.setdefault(cluster_ref_seq, cluster_name)
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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47
1
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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49 def extract_cluster_info(args, mapping_info=None, categories=None):
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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50 ref_seq_cluster = {}
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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51
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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52 if args.output_category_distribution is not None:
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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53 if mapping_info is None or categories is None:
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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54 string = "A file with category distribution is expected but "
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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55 string += "no mapping information are available"
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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56 raise ValueError(string)
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57 output_cat_distri_file = open(args.output_category_distribution, 'w')
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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58 output_cat_distri_file.write('Cluster\tSequence_number')
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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59 for category in categories:
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60 output_cat_distri_file.write('\t' + category)
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61
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62 output_cat_distri_file.write('\n')
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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63 else:
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64 output_cat_distri_file = None
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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65
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
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66 with open(args.input_cluster_info, 'r') as cluster_info_file:
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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67 cluster_name = ''
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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68 cluster_categ_distri = init_category_distribution(categories)
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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69 cluster_ref_seq = ''
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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70 cluster_seq_number = 0
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71 for line in cluster_info_file.readlines():
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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72 if line[0] == '>':
1
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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73 flush_cluster_info(
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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74 cluster_name,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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75 cluster_ref_seq,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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76 ref_seq_cluster,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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77 cluster_categ_distri,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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78 categories,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
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79 output_cat_distri_file,
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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80 cluster_seq_number)
0
4015e9d6d277 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
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81 cluster_name = line[1:-1]
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64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
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82 cluster_name = cluster_name.replace(' ', '_')
64da677bcee2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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83 cluster_categ_distri = init_category_distribution(categories)
0
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84 cluster_ref_seq = ''
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85 cluster_seq_number = 0
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86 else:
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87 seq_info = line[:-1].split('\t')[1].split(' ')
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88 seq_name = seq_info[1][1:-3]
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89 cluster_seq_number += 1
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90
1
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91 if categories is not None:
0
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92 seq_count = 1
1
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93 if args.number_sum is not None:
0
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94 if seq_name.find('size') != -1:
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95 substring = seq_name[seq_name.find('size'):-1]
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96 seq_count = int(substring.split('=')[1])
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97 if seq_name not in mapping_info:
0
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98 string = seq_name + " not found in mapping"
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99 raise ValueError(string)
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100 category = mapping_info[seq_name]
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101 cluster_categ_distri[category] += seq_count
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102
0
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103 if seq_info[-1] == '*':
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104 if cluster_ref_seq != '':
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105 string = "A reference sequence (" + cluster_ref_seq
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106 string += ") already found for cluster " + cluster_name
0
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107 string += " (" + seq_name + ")"
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108 raise ValueError(string)
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109 cluster_ref_seq = seq_name
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110
1
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111 flush_cluster_info(
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112 cluster_name,
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113 cluster_ref_seq,
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114 ref_seq_cluster,
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115 cluster_categ_distri,
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116 categories,
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117 output_cat_distri_file,
0
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118 cluster_seq_number)
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119
1
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120 if args.output_category_distribution is not None:
0
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121 output_cat_distri_file.close()
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122
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123 return ref_seq_cluster
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124
1
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125
0
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126 def rename_representative_sequences(args, ref_seq_cluster):
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127 with open(args.input_representative_sequences, 'r') as input_sequences:
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128 with open(args.output_representative_sequences, 'w') as output_seq:
0
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129 for line in input_sequences.readlines():
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130 if line[0] == '>':
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131 seq_name = line[1:-1]
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132 if seq_name not in ref_seq_cluster:
0
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133 string = seq_name + " not found as reference sequence"
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134 raise ValueError(string)
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135 string = '>' + ref_seq_cluster[seq_name] + '\n'
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136 output_seq.write(string)
0
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137 else:
1
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138 output_seq.write(line)
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139
0
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140
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141 def format_cd_hit_outputs(args):
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142 if args.input_mapping is not None:
0
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143 mapping_info, categories = extract_mapping_info(args.input_mapping)
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144 else:
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145 mapping_info = None
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146 categories = None
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147
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148 ref_seq_cluster = extract_cluster_info(args, mapping_info, categories)
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149
1
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150 if args.input_representative_sequences is not None:
0
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151 rename_representative_sequences(args, ref_seq_cluster)
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152
1
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153
0
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154 if __name__ == "__main__":
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155 parser = argparse.ArgumentParser()
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156 parser.add_argument('--input_cluster_info', required=True)
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157 parser.add_argument('--input_representative_sequences')
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158 parser.add_argument('--output_representative_sequences')
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159 parser.add_argument('--input_mapping')
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160 parser.add_argument('--output_category_distribution')
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161 parser.add_argument('--number_sum')
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162 args = parser.parse_args()
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163
1
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164 format_cd_hit_outputs(args)