Mercurial > repos > bebatut > combine_metaphlan2_humann2

annotate combine_metaphlan_humann.py @ 4:662a334004b4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sat, 04 Nov 2023 18:59:48 +0000
parents 01ac9954c27f
children
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01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
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1 #!/usr/bin/env python
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
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2 # -*- coding: utf-8 -*-
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
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4 import argparse
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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7 def extract_clade_abundance(metaphlan_fp):
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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8 clade_abund = {}
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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9 with open(metaphlan_fp, "r") as metaphlan_f:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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10 is_metaphlan_v4 = False
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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11 for line in metaphlan_f.readlines():
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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12 if 'SGB' in line:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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13 # New versions of metaphlan against a recent DB contain a header line with DB name, which contains SGB
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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14 is_metaphlan_v4 = True
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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15 if line.find("g__") == -1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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16 continue
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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18 split_line = line[:-1].split("\t")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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19 taxo = split_line[0]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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20 if is_metaphlan_v4:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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21 # Column order in new metaphlan versions:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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22 # clade_name NCBI_tax_id relative_abundance additional_species
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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23 abundance = split_line[2]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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24 else:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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25 # Column order in the old metaphlan versions:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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26 # clade_name relative_abundance coverage average_genome_length_in_the_clade estimated_number_of_reads_from_the_clade
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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27 abundance = split_line[1]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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28
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29 genus = taxo[(taxo.find("g__") + 3):]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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30 if genus.find("|") != -1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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31 genus = genus[: (genus.find("|"))]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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32 clade_abund.setdefault(genus, {"abundance": 0, "species": {}})
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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33 if taxo.find("t__") != -1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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34 continue
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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35 elif taxo.find("s__") != -1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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36 species = taxo[(taxo.find("s__") + 3):]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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37 clade_abund[genus]["species"].setdefault(species, abundance)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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38 else:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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39 clade_abund[genus]["abundance"] = abundance
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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40 return clade_abund
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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41
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42
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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43 def compute_overall_abundance(humann_fp):
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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44 overall_abundance = 0
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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45 with open(humann_fp, "r") as humann_f:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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46 for line in humann_f.readlines():
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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47 if line.find("|") != -1 or line.startswith("#"):
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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48 continue
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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49 split_line = line[:-1].split("\t")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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50 overall_abundance += float(split_line[1])
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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51 return overall_abundance
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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52
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54 def format_characteristic_name(name):
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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55 formatted_n = name
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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56 formatted_n = formatted_n.replace("/", " ")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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57 formatted_n = formatted_n.replace("-", " ")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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58 formatted_n = formatted_n.replace("'", "")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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59 if formatted_n.find("(") != -1 and formatted_n.find(")") != -1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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60 open_bracket = formatted_n.find("(")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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61 close_bracket = formatted_n.find(")") + 1
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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62 formatted_n = formatted_n[:open_bracket] + formatted_n[close_bracket:]
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63 return formatted_n
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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64
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66 def combine_metaphlan_humann(args):
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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67 clade_abund = extract_clade_abundance(args.metaphlan_fp)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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68 overall_abund = compute_overall_abundance(args.humann_fp)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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69
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70 with open(args.output_fp, "w") as output_f:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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71 s = "genus\tgenus_abundance\tspecies\tspecies_abundance\t"
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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72 s = "%s\t%s_id\t%s_name\t%s_abundance\n" % (s, args.type, args.type, args.type)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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73 output_f.write(s)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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74 with open(args.humann_fp, "r") as humann_f:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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75 for line in humann_f.readlines():
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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76 if line.find("|") == -1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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77 continue
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78
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79 split_line = line[:-1].split("\t")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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80 abundance = 100 * float(split_line[1]) / overall_abund
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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81 annotation = split_line[0].split("|")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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82 charact = annotation[0].split(":")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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83 charact_id = charact[0]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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84 char_name = ""
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
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85 if len(charact) > 1:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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86 char_name = format_characteristic_name(charact[-1])
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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parents:
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87 taxo = annotation[1].split(".")
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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88
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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89 if taxo[0] == "unclassified":
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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90 continue
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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91 genus = taxo[0][3:]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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92 species = taxo[1][3:]
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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93
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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94 if genus not in clade_abund:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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95 print("no %s found in %s" % (genus, args.metaphlan_fp))
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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96 continue
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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97 if species not in clade_abund[genus]["species"]:
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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98 print(
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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99 "No %s found in %s for % s"
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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100 % (species, args.metaphlan_fp, genus)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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parents:
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101 )
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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102 continue
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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parents:
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103
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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104 s = "%s\t%s\t" % (genus, clade_abund[genus]["abundance"])
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
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105 s += "%s\t%s\t" % (species, clade_abund[genus]["species"][species])
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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106 s += "%s\t%s\t%s\n" % (charact_id, char_name, abundance)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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parents:
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107 output_f.write(s)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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108
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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109
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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parents:
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110 if __name__ == "__main__":
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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111 parser = argparse.ArgumentParser()
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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112 parser.add_argument("--humann_fp", required=True)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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113 parser.add_argument("--metaphlan_fp", required=True)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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114 parser.add_argument("--output_fp", required=True)
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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115 parser.add_argument("--type", required=True, choices=["gene_families", "pathways"])
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
bgruening
parents:
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116 args = parser.parse_args()
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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117
01ac9954c27f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
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118 combine_metaphlan_humann(args)