def test_parse_kraken_report_taxonomy(self):
manual = {"1304": ["k__Bacteria", "p__Firmicutes", "c__Bacilli",
"o__Lactobacillales", "f__Streptococcaceae",
"g__Streptococcus", "s__salivarius"],
"29288": ["k__Archaea", "p__Euryarchaeota", "c__Halobacteria",
"o__Natrialbales", "f__Natrialbaceae",
"g__Natronococcus", "s__occultus"],
"45617": ["k__Viruses", "p__", "c__", "o__", "f__Retroviridae",
"g__", "s__Human endogenous retrovirus K"],
"1301": ["k__Bacteria", "p__Firmicutes", "c__Bacilli",
"o__Lactobacillales", "f__Streptococcaceae",
"g__Streptococcus", "s__"],
"135622":["k__Bacteria", "p__Proteobacteria",
"c__Gammaproteobacteria", "o__Alteromonadales",
"f__", "g__", "s__"],
"543": ["k__Bacteria", "p__Proteobacteria",
"c__Gammaproteobacteria", "o__Enterobacteriales",
"f__Enterobacteriaceae", "g__", "s__"],
"265522":["k__Viruses", "p__", "c__", "o__",
"f__Polydnaviridae", "g__Ichnovirus",
"s__Hyposoter fugitivus ichnovirus"],
"374840":["k__Viruses", "p__", "c__", "o__",
"f__Microviridae", "g__Microvirus",
"s__Enterobacteria phage phiX174 sensu lato"],
"5693":["k__Eukaryota", "p__", "c__", "o__Kinetoplastida",
"f__Trypanosomatidae", "g__Trypanosoma", "s__cruzi"]
}
_, taxa = kb.parse_kraken_report(self.sample_kraken_rep,
max_rank="O",
min_rank="S")
# Check that the manually assigned taxa are eqivalent to the parsed
self.assertTrue(all([manual[tax_id] == taxa[tax_id] for tax_id in manual]))
def run_parse_kraken_report(self, manual, max_rank, min_rank):
counts, _ = kb.parse_kraken_report(self.sample_kraken_rep,
max_rank=max_rank,
min_rank=min_rank)
# Check that there are no differences in taxonomy IDs
self.assertTrue(len(set(counts).symmetric_difference(set(manual))) == 0)
# Check that the counts are equivalent
self.assertTrue(all([manual[tax_id] == counts[tax_id] for tax_id in counts]))
def setUp(self):
self.krepA = prep_kraken_input(io.StringIO(twdd(u"""\
100.00 6783846 6783846 U 0 unclassified
0.00 130 18 - 1 root
0.00 105 0 - 131567 cellular organisms
0.00 105 0 D 2 Bacteria
0.00 62 30 P 1239 Firmicutes
0.00 29 0 C 91061 Bacilli
0.00 29 0 O 186826 Lactobacillales
0.00 20 0 F 1300 Streptococcaceae
0.00 20 8 G 1301 Streptococcus
0.00 5 4 S 1304 Streptococcus salivarius
0.00 1 1 - 1048332 Streptococcus salivarius CCHSS3
0.00 3 0 S 1303 Streptococcus oralis
0.00 3 3 - 927666 Streptococcus oralis Uo5
0.00 2 2 S 1318 Streptococcus parasanguinis
0.00 1 0 S 1305 Streptococcus sanguinis
0.00 1 1 - 388919 Streptococcus sanguinis SK36
0.00 1 1 S 1308 Streptococcus thermophilus
0.00 9 0 F 81852 Enterococcaceae
0.00 9 0 G 1350 Enterococcus
0.00 9 0 S 37734 Enterococcus casseliflavus
0.00 9 9 - 565655 Enterococcus casseliflavus EC20
0.00 1 0 C 186801 Clostridia
0.00 1 1 O 186802 Clostridiales
0.00 40 0 P 1224 Proteobacteria
0.00 20 2 C 1236 Gammaproteobacteria
0.00 11 1 O 135622 Alteromonadales
0.00 10 0 F 72275 Alteromonadaceae
0.00 10 0 G 226 Alteromonas
0.00 10 0 S 28108 Alteromonas macleodii
0.00 10 10 - 1300257 Alteromonas macleodii str. 'Ionian Sea U8'
0.00 7 0 O 91347 Enterobacteriales
0.00 7 6 F 543 Enterobacteriaceae
0.00 1 0 G 561 Escherichia
0.00 1 1 S 562 Escherichia coli
0.00 20 5 C 28216 Betaproteobacteria
0.00 15 0 O 80840 Burkholderiales
0.00 11 0 F 119060 Burkholderiaceae
0.00 11 0 G 48736 Ralstonia
0.00 11 10 S 329 Ralstonia pickettii
0.00 1 1 - 428406 Ralstonia pickettii 12D
0.00 4 0 F 80864 Comamonadaceae
0.00 2 2 G 12916 Acidovorax
0.00 2 0 G 201096 Alicycliphilus
0.00 2 0 S 179636 Alicycliphilus denitrificans
0.00 2 2 - 596154 Alicycliphilus denitrificans K601
0.00 3 0 P 201174 Actinobacteria
0.00 3 0 C 1760 Actinobacteria
0.00 2 0 - 84998 Coriobacteridae
0.00 2 0 O 84999 Coriobacteriales
0.00 2 0 - 255727 Coriobacterineae
0.00 2 0 F 84107 Coriobacteriaceae
0.00 2 0 G 1380 Atopobium
0.00 2 0 S 1382 Atopobium parvulum
0.00 2 2 - 521095 Atopobium parvulum DSM 20469
0.00 1 0 - 85003 Actinobacteridae
0.00 1 0 O 2037 Actinomycetales
0.00 1 0 - 85009 Propionibacterineae
0.00 1 0 F 31957 Propionibacteriaceae
0.00 1 0 G 1743 Propionibacterium
0.00 1 1 S 1747 Propionibacterium acnes
0.00 20 0 D 2157 Archaea
0.00 20 7 P 28890 Euryarchaeota
0.00 8 0 C 183963 Halobacteria
0.00 8 0 O 1644060 Natrialbales
0.00 8 0 F 1644061 Natrialbaceae
0.00 8 0 G 29287 Natronococcus
0.00 8 0 S 29288 Natronococcus occultus
0.00 8 8 - 694430 Natronococcus occultus SP4
0.00 4 0 C 224756 Methanomicrobia
0.00 4 0 O 94695 Methanosarcinales
0.00 4 0 F 2206 Methanosarcinaceae
0.00 3 0 G 101191 Methanomethylovorans
0.00 3 0 S 101192 Methanomethylovorans hollandica
0.00 3 3 - 867904 Methanomethylovorans hollandica DSM 15978
0.00 1 0 G 2207 Methanosarcina
0.00 1 0 S 2214 Methanosarcina acetivorans
0.00 1 1 - 188937 Methanosarcina acetivorans C2A
0.00 1 0 C 183939 Methanococci
0.00 1 0 O 2182 Methanococcales
0.00 1 0 F 2183 Methanococcaceae
0.00 1 0 G 2184 Methanococcus
0.00 1 0 S 2188 Methanococcus voltae
0.00 1 1 - 456320 Methanococcus voltae A3
0.00 7 0 D 10239 Viruses
0.00 2 0 - 29258 ssDNA viruses
0.00 2 0 F 10841 Microviridae
0.00 2 0 G 10842 Microvirus
0.00 2 2 S 374840 Enterobacteria phage phiX174 sensu lato
0.00 2 0 - 35237 dsDNA viruses, no RNA stage
0.00 2 0 F 10482 Polydnaviridae
0.00 2 0 G 10483 Ichnovirus
0.00 2 2 S 265522 Hyposoter fugitivus ichnovirus
0.00 2 0 - 439488 ssRNA viruses
0.00 2 0 - 35278 ssRNA positive-strand viruses, no DNA stage
0.00 2 0 F 11018 Togaviridae
0.00 2 0 G 11019 Alphavirus
0.00 2 0 - 177872 VEEV complex
0.00 2 2 S 11036 Venezuelan equine encephalitis virus
0.00 1 0 - 35268 Retro-transcribing viruses
0.00 1 0 F 11632 Retroviridae
0.00 1 0 - 35276 unclassified Retroviridae
0.00 1 0 - 206037 Human endogenous retroviruses
0.00 1 0 S 45617 Human endogenous retrovirus K
0.00 1 1 - 166122 Human endogenous retrovirus K113
""")))
self.krepB = prep_kraken_input(io.StringIO(twdd(u"""\
100.00 6783846 6783846 U 0 unclassified
0.00 130 18 - 1 root
0.00 105 0 - 131567 cellular organisms
0.00 105 0 D 2 Bacteria
0.00 62 30 P 1239 Firmicutes
0.00 29 0 C 91061 Bacilli
0.00 29 0 O 186826 Lactobacillales
0.00 20 0 F 1300 Streptococcaceae
0.00 20 8 G 1301 Streptococcus
0.00 5 4 S 1304 Streptococcus salivarius
0.00 1 1 - 1048332 Streptococcus salivarius CCHSS3
0.00 3 0 S 1303 Streptococcus oralis
0.00 3 3 - 927666 Streptococcus oralis Uo5
0.00 2 2 S 1318 Streptococcus parasanguinis
0.00 1 0 S 1305 Streptococcus sanguinis
0.00 1 1 - 388919 Streptococcus sanguinis SK36
0.00 1 1 S 1308 Streptococcus thermophilus
0.00 9 0 F 81852 Enterococcaceae
0.00 9 0 G 1350 Enterococcus
0.00 9 0 S 37734 Enterococcus casseliflavus
0.00 9 9 - 565655 Enterococcus casseliflavus EC20
0.00 2 0 C 909932 Negativicutes
0.00 2 0 O 909929 Selenomonadales
0.00 2 0 F 31977 Veillonellaceae
0.00 2 0 G 29465 Veillonella
0.00 2 0 S 29466 Veillonella parvula
0.00 2 2 - 479436 Veillonella parvula DSM 2008
0.00 20 0 D 2157 Archaea
0.00 20 7 P 28890 Euryarchaeota
0.00 8 0 C 183963 Halobacteria
0.00 8 0 O 1644060 Natrialbales
0.00 8 0 F 1644061 Natrialbaceae
0.00 8 0 G 29287 Natronococcus
0.00 8 0 S 29288 Natronococcus occultus
0.00 8 8 - 694430 Natronococcus occultus SP4
0.00 7 0 D 10239 Viruses
0.00 2 0 - 29258 ssDNA viruses
0.00 2 0 F 10841 Microviridae
0.00 2 0 G 10842 Microvirus
0.00 2 2 S 374840 Enterobacteria phage phiX174 sensu lato
0.00 2 0 - 35237 dsDNA viruses, no RNA stage
0.00 2 0 F 10482 Polydnaviridae
0.00 2 0 G 10483 Ichnovirus
0.00 2 2 S 265522 Hyposoter fugitivus ichnovirus
""")))
# parse the sample reports
self.taxa = OrderedDict()
self.sample_counts = OrderedDict()
countsA, taxaA = kb.parse_kraken_report(self.krepA, max_rank="O",
min_rank="S")
countsB, taxaB = kb.parse_kraken_report(self.krepB, max_rank="O",
min_rank="S")
self.taxa.update(taxaA)
self.taxa.update(taxaB)
self.sample_counts["A"] = countsA
self.sample_counts["B"] = countsB
# Make the dummy metadata for the samples.
self.metadata =kb.process_metadata(self.sample_counts ,None)
# create the BIOM table from the sample counts and taxa
self.biomT = kb.create_biom_table(self.sample_counts, self.taxa,self.metadata)
def setUp(self):
self.krepA = prep_kraken_input(io.StringIO(twdd(u"""\
100.00 6783846 6783846 U 0 unclassified
0.00 130 18 - 1 root
0.00 105 0 - 131567 cellular organisms
0.00 105 0 D 2 Bacteria
0.00 62 30 P 1239 Firmicutes
0.00 29 0 C 91061 Bacilli
0.00 29 0 O 186826 Lactobacillales
0.00 20 0 F 1300 Streptococcaceae
0.00 20 8 G 1301 Streptococcus
0.00 5 4 S 1304 Streptococcus salivarius
0.00 1 1 - 1048332 Streptococcus salivarius CCHSS3
0.00 3 0 S 1303 Streptococcus oralis
0.00 3 3 - 927666 Streptococcus oralis Uo5
0.00 2 2 S 1318 Streptococcus parasanguinis
0.00 1 0 S 1305 Streptococcus sanguinis
0.00 1 1 - 388919 Streptococcus sanguinis SK36
0.00 1 1 S 1308 Streptococcus thermophilus
0.00 9 0 F 81852 Enterococcaceae
0.00 9 0 G 1350 Enterococcus
0.00 9 0 S 37734 Enterococcus casseliflavus
0.00 9 9 - 565655 Enterococcus casseliflavus EC20
0.00 1 0 C 186801 Clostridia
0.00 1 1 O 186802 Clostridiales
0.00 40 0 P 1224 Proteobacteria
0.00 20 2 C 1236 Gammaproteobacteria
0.00 11 1 O 135622 Alteromonadales
0.00 10 0 F 72275 Alteromonadaceae
0.00 10 0 G 226 Alteromonas
0.00 10 0 S 28108 Alteromonas macleodii
0.00 10 10 - 1300257 Alteromonas macleodii str. 'Ionian Sea U8'
0.00 7 0 O 91347 Enterobacteriales
0.00 7 6 F 543 Enterobacteriaceae
0.00 1 0 G 561 Escherichia
0.00 1 1 S 562 Escherichia coli
0.00 20 5 C 28216 Betaproteobacteria
0.00 15 0 O 80840 Burkholderiales
0.00 11 0 F 119060 Burkholderiaceae
0.00 11 0 G 48736 Ralstonia
0.00 11 10 S 329 Ralstonia pickettii
0.00 1 1 - 428406 Ralstonia pickettii 12D
0.00 4 0 F 80864 Comamonadaceae
0.00 2 2 G 12916 Acidovorax
0.00 2 0 G 201096 Alicycliphilus
0.00 2 0 S 179636 Alicycliphilus denitrificans
0.00 2 2 - 596154 Alicycliphilus denitrificans K601
0.00 3 0 P 201174 Actinobacteria
0.00 3 0 C 1760 Actinobacteria
0.00 2 0 - 84998 Coriobacteridae
0.00 2 0 O 84999 Coriobacteriales
0.00 2 0 - 255727 Coriobacterineae
0.00 2 0 F 84107 Coriobacteriaceae
0.00 2 0 G 1380 Atopobium
0.00 2 0 S 1382 Atopobium parvulum
0.00 2 2 - 521095 Atopobium parvulum DSM 20469
0.00 1 0 - 85003 Actinobacteridae
0.00 1 0 O 2037 Actinomycetales
0.00 1 0 - 85009 Propionibacterineae
0.00 1 0 F 31957 Propionibacteriaceae
0.00 1 0 G 1743 Propionibacterium
0.00 1 1 S 1747 Propionibacterium acnes
0.00 20 0 D 2157 Archaea
0.00 20 7 P 28890 Euryarchaeota
0.00 8 0 C 183963 Halobacteria
0.00 8 0 O 1644060 Natrialbales
0.00 8 0 F 1644061 Natrialbaceae
0.00 8 0 G 29287 Natronococcus
0.00 8 0 S 29288 Natronococcus occultus
0.00 8 8 - 694430 Natronococcus occultus SP4
0.00 4 0 C 224756 Methanomicrobia
0.00 4 0 O 94695 Methanosarcinales
0.00 4 0 F 2206 Methanosarcinaceae
0.00 3 0 G 101191 Methanomethylovorans
0.00 3 0 S 101192 Methanomethylovorans hollandica
0.00 3 3 - 867904 Methanomethylovorans hollandica DSM 15978
0.00 1 0 G 2207 Methanosarcina
0.00 1 0 S 2214 Methanosarcina acetivorans
0.00 1 1 - 188937 Methanosarcina acetivorans C2A
0.00 1 0 C 183939 Methanococci
0.00 1 0 O 2182 Methanococcales
0.00 1 0 F 2183 Methanococcaceae
0.00 1 0 G 2184 Methanococcus
0.00 1 0 S 2188 Methanococcus voltae
0.00 1 1 - 456320 Methanococcus voltae A3
0.00 7 0 D 10239 Viruses
0.00 2 0 - 29258 ssDNA viruses
0.00 2 0 F 10841 Microviridae
0.00 2 0 G 10842 Microvirus
0.00 2 2 S 374840 Enterobacteria phage phiX174 sensu lato
0.00 2 0 - 35237 dsDNA viruses, no RNA stage
0.00 2 0 F 10482 Polydnaviridae
0.00 2 0 G 10483 Ichnovirus
0.00 2 2 S 265522 Hyposoter fugitivus ichnovirus
0.00 2 0 - 439488 ssRNA viruses
0.00 2 0 - 35278 ssRNA positive-strand viruses, no DNA stage
0.00 2 0 F 11018 Togaviridae
0.00 2 0 G 11019 Alphavirus
0.00 2 0 - 177872 VEEV complex
0.00 2 2 S 11036 Venezuelan equine encephalitis virus
0.00 1 0 - 35268 Retro-transcribing viruses
0.00 1 0 F 11632 Retroviridae
0.00 1 0 - 35276 unclassified Retroviridae
0.00 1 0 - 206037 Human endogenous retroviruses
0.00 1 0 S 45617 Human endogenous retrovirus K
0.00 1 1 - 166122 Human endogenous retrovirus K113
""")))
self.krepB = prep_kraken_input(io.StringIO(twdd(u"""\
100.00 6783846 6783846 U 0 unclassified
0.00 130 18 - 1 root
0.00 105 0 - 131567 cellular organisms
0.00 105 0 D 2 Bacteria
0.00 62 30 P 1239 Firmicutes
0.00 29 0 C 91061 Bacilli
0.00 29 0 O 186826 Lactobacillales
0.00 20 0 F 1300 Streptococcaceae
0.00 20 8 G 1301 Streptococcus
0.00 5 4 S 1304 Streptococcus salivarius
0.00 1 1 - 1048332 Streptococcus salivarius CCHSS3
0.00 3 0 S 1303 Streptococcus oralis
0.00 3 3 - 927666 Streptococcus oralis Uo5
0.00 2 2 S 1318 Streptococcus parasanguinis
0.00 1 0 S 1305 Streptococcus sanguinis
0.00 1 1 - 388919 Streptococcus sanguinis SK36
0.00 1 1 S 1308 Streptococcus thermophilus
0.00 9 0 F 81852 Enterococcaceae
0.00 9 0 G 1350 Enterococcus
0.00 9 0 S 37734 Enterococcus casseliflavus
0.00 9 9 - 565655 Enterococcus casseliflavus EC20
0.00 2 0 C 909932 Negativicutes
0.00 2 0 O 909929 Selenomonadales
0.00 2 0 F 31977 Veillonellaceae
0.00 2 0 G 29465 Veillonella
0.00 2 0 S 29466 Veillonella parvula
0.00 2 2 - 479436 Veillonella parvula DSM 2008
0.00 20 0 D 2157 Archaea
0.00 20 7 P 28890 Euryarchaeota
0.00 8 0 C 183963 Halobacteria
0.00 8 0 O 1644060 Natrialbales
0.00 8 0 F 1644061 Natrialbaceae
0.00 8 0 G 29287 Natronococcus
0.00 8 0 S 29288 Natronococcus occultus
0.00 8 8 - 694430 Natronococcus occultus SP4
0.00 7 0 D 10239 Viruses
0.00 2 0 - 29258 ssDNA viruses
0.00 2 0 F 10841 Microviridae
0.00 2 0 G 10842 Microvirus
0.00 2 2 S 374840 Enterobacteria phage phiX174 sensu lato
0.00 2 0 - 35237 dsDNA viruses, no RNA stage
0.00 2 0 F 10482 Polydnaviridae
0.00 2 0 G 10483 Ichnovirus
0.00 2 2 S 265522 Hyposoter fugitivus ichnovirus
""")))
# parse the sample reports
self.taxa = OrderedDict()
self.sample_counts = OrderedDict()
countsA, taxaA = kb.parse_kraken_report(self.krepA, max_rank="O",
min_rank="S")
countsB, taxaB = kb.parse_kraken_report(self.krepB, max_rank="O",
min_rank="S")
self.taxa.update(taxaA)
self.taxa.update(taxaB)
self.sample_counts["A"] = countsA
self.sample_counts["B"] = countsB
# create the BIOM table from the sample counts and taxa
self.biomT = kb.create_biom_table(self.sample_counts, self.taxa)