Loading unaligned sequence data

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"

We can load unaligned sequence data using the load_unaligned app, this will return a SequenceCollection.

Loading unaligned DNA sequences from a single fasta file

In this example, we load unaligned DNA sequences from a single fasta file using the load_unaligned app. We specify the molecular type (moltype="protein") and the file format (format="fasta").

from cogent3 import get_app

load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein")
seqs = load_unaligned_app("data/inseqs_protein.fasta")
seqs

	0
1091044_fragment	IPLDFDKEFRDKTVVIVAIPGAFTPT
13541053_fragment	KKKNTEVISVSEDTVYVHKAWVQYD
15605725_fragment	FEILAINMDPENLTGFLKNNP

3 x {min=21, median=25.0, max=26} protein sequence collection

Loading unaligned DNA sequences from multiple fasta files

To load unaligned DNA sequences from multiple fasta files, we need two things, a data store that identifies the files we are interested in and a process composed of our apps of interest.

1. A data store that identifies the files we are interested in

Here we open a read-only (mode="r") data store that identifies all fasta files in the data directory, limiting the data store to two members as a minimum example.

from cogent3 import get_app, open_data_store

fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2)

2. A composed process that defines our workflow

In this example, our process loads the unaligned sequences using load_unaligned, then applies jaccard_dist to estimate a kmer-based genetic distance, which we write out to a data store using write_tabular.

Note

Apps that are “writers” require a data store to write to, learn more about writers here!.

out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w")

load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna")
jdist = get_app("jaccard_dist")
writer = get_app("write_tabular", out_dstore, format="tsv")

process = load_unaligned_app + jdist + writer

Tip

When running this code on your machine, remember to replace path_to_dir with an actual directory path.

Now we’re good to go! We can apply process to our data store of fasta sequences. result is a data store, which you can index to see individual data members. We can inspect a given data member using the .read() on data members.

result = process.apply_to(fasta_seq_dstore)
print(result[1].read())

dim-1	dim-2	value
seq_104_Tropheryma_whipplei	seq_105_Xylella_fastidiosa	0.9770992366412213
seq_104_Tropheryma_whipplei	seq_117_Pseudomonas_syringae_pv._Tomato	1.0
seq_104_Tropheryma_whipplei	seq_119_Bacillus_anthracis	0.9770992366412213
seq_104_Tropheryma_whipplei	seq_129_Bacillus_anthracis	0.9770992366412213
seq_104_Tropheryma_whipplei	seq_130_Geobacter_sulfurreducens	0.9848484848484849
seq_104_Tropheryma_whipplei	seq_135_Yersinia_pestis_biovar_Medievalis	1.0
seq_104_Tropheryma_whipplei	seq_138_Bacillus_cereus	0.9770992366412213
seq_104_Tropheryma_whipplei	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.9770992366412213
seq_104_Tropheryma_whipplei	seq_148_Bartonella_quintana	0.9105691056910569
seq_104_Tropheryma_whipplei	seq_23_Haemophilus_influenzae	1.0
seq_104_Tropheryma_whipplei	seq_24_Campylobacter_jejuni	0.9848484848484849
seq_104_Tropheryma_whipplei	seq_31_Pseudomonas_aeruginosa	0.9193548387096774
seq_104_Tropheryma_whipplei	seq_46_Salmonella_enterica	1.0
seq_104_Tropheryma_whipplei	seq_48_Aeropyrum_pernix	1.0
seq_104_Tropheryma_whipplei	seq_50_Halobacterium_sp.	1.0
seq_104_Tropheryma_whipplei	seq_59_Thermoplasma_acidophilum	0.9689922480620154
seq_104_Tropheryma_whipplei	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.9770992366412213
seq_104_Tropheryma_whipplei	seq_86_Xanthomonas_axonopodis_pv._citri.	0.9193548387096774
seq_104_Tropheryma_whipplei	seq_95_Shewanella_oneidensis	1.0
seq_105_Xylella_fastidiosa	seq_104_Tropheryma_whipplei	0.9770992366412213
seq_105_Xylella_fastidiosa	seq_117_Pseudomonas_syringae_pv._Tomato	0.7592592592592593
seq_105_Xylella_fastidiosa	seq_119_Bacillus_anthracis	0.8347826086956522
seq_105_Xylella_fastidiosa	seq_129_Bacillus_anthracis	0.8347826086956522
seq_105_Xylella_fastidiosa	seq_130_Geobacter_sulfurreducens	0.9448818897637795
seq_105_Xylella_fastidiosa	seq_135_Yersinia_pestis_biovar_Medievalis	0.7818181818181819
seq_105_Xylella_fastidiosa	seq_138_Bacillus_cereus	0.8347826086956522
seq_105_Xylella_fastidiosa	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8347826086956522
seq_105_Xylella_fastidiosa	seq_148_Bartonella_quintana	0.9612403100775194
seq_105_Xylella_fastidiosa	seq_23_Haemophilus_influenzae	0.7592592592592593
seq_105_Xylella_fastidiosa	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_105_Xylella_fastidiosa	seq_31_Pseudomonas_aeruginosa	0.8448275862068966
seq_105_Xylella_fastidiosa	seq_46_Salmonella_enterica	0.7818181818181819
seq_105_Xylella_fastidiosa	seq_48_Aeropyrum_pernix	1.0
seq_105_Xylella_fastidiosa	seq_50_Halobacterium_sp.	1.0
seq_105_Xylella_fastidiosa	seq_59_Thermoplasma_acidophilum	0.9847328244274809
seq_105_Xylella_fastidiosa	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_105_Xylella_fastidiosa	seq_86_Xanthomonas_axonopodis_pv._citri.	0.8547008547008547
seq_105_Xylella_fastidiosa	seq_95_Shewanella_oneidensis	0.8925619834710744
seq_117_Pseudomonas_syringae_pv._Tomato	seq_104_Tropheryma_whipplei	1.0
seq_117_Pseudomonas_syringae_pv._Tomato	seq_105_Xylella_fastidiosa	0.7592592592592593
seq_117_Pseudomonas_syringae_pv._Tomato	seq_119_Bacillus_anthracis	0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato	seq_129_Bacillus_anthracis	0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato	seq_130_Geobacter_sulfurreducens	0.6862745098039216
seq_117_Pseudomonas_syringae_pv._Tomato	seq_135_Yersinia_pestis_biovar_Medievalis	0.6185567010309279
seq_117_Pseudomonas_syringae_pv._Tomato	seq_138_Bacillus_cereus	0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato	seq_148_Bartonella_quintana	0.9193548387096774
seq_117_Pseudomonas_syringae_pv._Tomato	seq_23_Haemophilus_influenzae	0.5894736842105264
seq_117_Pseudomonas_syringae_pv._Tomato	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_117_Pseudomonas_syringae_pv._Tomato	seq_31_Pseudomonas_aeruginosa	0.574468085106383
seq_117_Pseudomonas_syringae_pv._Tomato	seq_46_Salmonella_enterica	0.6185567010309279
seq_117_Pseudomonas_syringae_pv._Tomato	seq_48_Aeropyrum_pernix	1.0
seq_117_Pseudomonas_syringae_pv._Tomato	seq_50_Halobacterium_sp.	1.0
seq_117_Pseudomonas_syringae_pv._Tomato	seq_59_Thermoplasma_acidophilum	1.0
seq_117_Pseudomonas_syringae_pv._Tomato	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_117_Pseudomonas_syringae_pv._Tomato	seq_86_Xanthomonas_axonopodis_pv._citri.	0.5894736842105264
seq_117_Pseudomonas_syringae_pv._Tomato	seq_95_Shewanella_oneidensis	0.8347826086956522
seq_119_Bacillus_anthracis	seq_104_Tropheryma_whipplei	0.9770992366412213
seq_119_Bacillus_anthracis	seq_105_Xylella_fastidiosa	0.8347826086956522
seq_119_Bacillus_anthracis	seq_117_Pseudomonas_syringae_pv._Tomato	0.7706422018348624
seq_119_Bacillus_anthracis	seq_129_Bacillus_anthracis	0.05797101449275366
seq_119_Bacillus_anthracis	seq_130_Geobacter_sulfurreducens	0.5894736842105264
seq_119_Bacillus_anthracis	seq_135_Yersinia_pestis_biovar_Medievalis	0.8833333333333333
seq_119_Bacillus_anthracis	seq_138_Bacillus_cereus	0.0
seq_119_Bacillus_anthracis	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.0
seq_119_Bacillus_anthracis	seq_148_Bartonella_quintana	0.9612403100775194
seq_119_Bacillus_anthracis	seq_23_Haemophilus_influenzae	0.8833333333333333
seq_119_Bacillus_anthracis	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_119_Bacillus_anthracis	seq_31_Pseudomonas_aeruginosa	0.8347826086956522
seq_119_Bacillus_anthracis	seq_46_Salmonella_enterica	0.8833333333333333
seq_119_Bacillus_anthracis	seq_48_Aeropyrum_pernix	1.0
seq_119_Bacillus_anthracis	seq_50_Halobacterium_sp.	1.0
seq_119_Bacillus_anthracis	seq_59_Thermoplasma_acidophilum	0.9847328244274809
seq_119_Bacillus_anthracis	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_119_Bacillus_anthracis	seq_86_Xanthomonas_axonopodis_pv._citri.	0.8547008547008547
seq_119_Bacillus_anthracis	seq_95_Shewanella_oneidensis	0.7706422018348624
seq_129_Bacillus_anthracis	seq_104_Tropheryma_whipplei	0.9770992366412213
seq_129_Bacillus_anthracis	seq_105_Xylella_fastidiosa	0.8347826086956522
seq_129_Bacillus_anthracis	seq_117_Pseudomonas_syringae_pv._Tomato	0.7706422018348624
seq_129_Bacillus_anthracis	seq_119_Bacillus_anthracis	0.05797101449275366
seq_129_Bacillus_anthracis	seq_130_Geobacter_sulfurreducens	0.5894736842105264
seq_129_Bacillus_anthracis	seq_135_Yersinia_pestis_biovar_Medievalis	0.8833333333333333
seq_129_Bacillus_anthracis	seq_138_Bacillus_cereus	0.05797101449275366
seq_129_Bacillus_anthracis	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.05797101449275366
seq_129_Bacillus_anthracis	seq_148_Bartonella_quintana	0.9612403100775194
seq_129_Bacillus_anthracis	seq_23_Haemophilus_influenzae	0.8833333333333333
seq_129_Bacillus_anthracis	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_129_Bacillus_anthracis	seq_31_Pseudomonas_aeruginosa	0.8347826086956522
seq_129_Bacillus_anthracis	seq_46_Salmonella_enterica	0.8833333333333333
seq_129_Bacillus_anthracis	seq_48_Aeropyrum_pernix	1.0
seq_129_Bacillus_anthracis	seq_50_Halobacterium_sp.	1.0
seq_129_Bacillus_anthracis	seq_59_Thermoplasma_acidophilum	0.9847328244274809
seq_129_Bacillus_anthracis	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_129_Bacillus_anthracis	seq_86_Xanthomonas_axonopodis_pv._citri.	0.8547008547008547
seq_129_Bacillus_anthracis	seq_95_Shewanella_oneidensis	0.7706422018348624
seq_130_Geobacter_sulfurreducens	seq_104_Tropheryma_whipplei	0.9848484848484849
seq_130_Geobacter_sulfurreducens	seq_105_Xylella_fastidiosa	0.9448818897637795
seq_130_Geobacter_sulfurreducens	seq_117_Pseudomonas_syringae_pv._Tomato	0.6862745098039216
seq_130_Geobacter_sulfurreducens	seq_119_Bacillus_anthracis	0.5894736842105264
seq_130_Geobacter_sulfurreducens	seq_129_Bacillus_anthracis	0.5894736842105264
seq_130_Geobacter_sulfurreducens	seq_135_Yersinia_pestis_biovar_Medievalis	0.9612403100775194
seq_130_Geobacter_sulfurreducens	seq_138_Bacillus_cereus	0.5894736842105264
seq_130_Geobacter_sulfurreducens	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.5894736842105264
seq_130_Geobacter_sulfurreducens	seq_148_Bartonella_quintana	0.8833333333333333
seq_130_Geobacter_sulfurreducens	seq_23_Haemophilus_influenzae	0.9612403100775194
seq_130_Geobacter_sulfurreducens	seq_24_Campylobacter_jejuni	0.9692307692307692
seq_130_Geobacter_sulfurreducens	seq_31_Pseudomonas_aeruginosa	0.8547008547008547
seq_130_Geobacter_sulfurreducens	seq_46_Salmonella_enterica	0.9612403100775194
seq_130_Geobacter_sulfurreducens	seq_48_Aeropyrum_pernix	1.0
seq_130_Geobacter_sulfurreducens	seq_50_Halobacterium_sp.	1.0
seq_130_Geobacter_sulfurreducens	seq_59_Thermoplasma_acidophilum	1.0
seq_130_Geobacter_sulfurreducens	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_130_Geobacter_sulfurreducens	seq_86_Xanthomonas_axonopodis_pv._citri.	0.864406779661017
seq_130_Geobacter_sulfurreducens	seq_95_Shewanella_oneidensis	0.8739495798319328
seq_135_Yersinia_pestis_biovar_Medievalis	seq_104_Tropheryma_whipplei	1.0
seq_135_Yersinia_pestis_biovar_Medievalis	seq_105_Xylella_fastidiosa	0.7818181818181819
seq_135_Yersinia_pestis_biovar_Medievalis	seq_117_Pseudomonas_syringae_pv._Tomato	0.6185567010309279
seq_135_Yersinia_pestis_biovar_Medievalis	seq_119_Bacillus_anthracis	0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis	seq_129_Bacillus_anthracis	0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis	seq_130_Geobacter_sulfurreducens	0.9612403100775194
seq_135_Yersinia_pestis_biovar_Medievalis	seq_138_Bacillus_cereus	0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis	seq_148_Bartonella_quintana	0.9770992366412213
seq_135_Yersinia_pestis_biovar_Medievalis	seq_23_Haemophilus_influenzae	0.6041666666666667
seq_135_Yersinia_pestis_biovar_Medievalis	seq_24_Campylobacter_jejuni	0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis	seq_31_Pseudomonas_aeruginosa	0.7706422018348624
seq_135_Yersinia_pestis_biovar_Medievalis	seq_46_Salmonella_enterica	0.0
seq_135_Yersinia_pestis_biovar_Medievalis	seq_48_Aeropyrum_pernix	1.0
seq_135_Yersinia_pestis_biovar_Medievalis	seq_50_Halobacterium_sp.	1.0
seq_135_Yersinia_pestis_biovar_Medievalis	seq_59_Thermoplasma_acidophilum	1.0
seq_135_Yersinia_pestis_biovar_Medievalis	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_135_Yersinia_pestis_biovar_Medievalis	seq_86_Xanthomonas_axonopodis_pv._citri.	0.7706422018348624
seq_135_Yersinia_pestis_biovar_Medievalis	seq_95_Shewanella_oneidensis	0.8245614035087719
seq_138_Bacillus_cereus	seq_104_Tropheryma_whipplei	0.9770992366412213
seq_138_Bacillus_cereus	seq_105_Xylella_fastidiosa	0.8347826086956522
seq_138_Bacillus_cereus	seq_117_Pseudomonas_syringae_pv._Tomato	0.7706422018348624
seq_138_Bacillus_cereus	seq_119_Bacillus_anthracis	0.0
seq_138_Bacillus_cereus	seq_129_Bacillus_anthracis	0.05797101449275366
seq_138_Bacillus_cereus	seq_130_Geobacter_sulfurreducens	0.5894736842105264
seq_138_Bacillus_cereus	seq_135_Yersinia_pestis_biovar_Medievalis	0.8833333333333333
seq_138_Bacillus_cereus	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.0
seq_138_Bacillus_cereus	seq_148_Bartonella_quintana	0.9612403100775194
seq_138_Bacillus_cereus	seq_23_Haemophilus_influenzae	0.8833333333333333
seq_138_Bacillus_cereus	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_138_Bacillus_cereus	seq_31_Pseudomonas_aeruginosa	0.8347826086956522
seq_138_Bacillus_cereus	seq_46_Salmonella_enterica	0.8833333333333333
seq_138_Bacillus_cereus	seq_48_Aeropyrum_pernix	1.0
seq_138_Bacillus_cereus	seq_50_Halobacterium_sp.	1.0
seq_138_Bacillus_cereus	seq_59_Thermoplasma_acidophilum	0.9847328244274809
seq_138_Bacillus_cereus	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_138_Bacillus_cereus	seq_86_Xanthomonas_axonopodis_pv._citri.	0.8547008547008547
seq_138_Bacillus_cereus	seq_95_Shewanella_oneidensis	0.7706422018348624
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_104_Tropheryma_whipplei	0.9770992366412213
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_105_Xylella_fastidiosa	0.8347826086956522
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_117_Pseudomonas_syringae_pv._Tomato	0.7706422018348624
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_119_Bacillus_anthracis	0.0
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_129_Bacillus_anthracis	0.05797101449275366
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_130_Geobacter_sulfurreducens	0.5894736842105264
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_135_Yersinia_pestis_biovar_Medievalis	0.8833333333333333
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_138_Bacillus_cereus	0.0
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_148_Bartonella_quintana	0.9612403100775194
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_23_Haemophilus_influenzae	0.8833333333333333
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_31_Pseudomonas_aeruginosa	0.8347826086956522
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_46_Salmonella_enterica	0.8833333333333333
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_48_Aeropyrum_pernix	1.0
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_50_Halobacterium_sp.	1.0
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_59_Thermoplasma_acidophilum	0.9847328244274809
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_86_Xanthomonas_axonopodis_pv._citri.	0.8547008547008547
seq_146_Bacillus_thuringiensis_serovar_konkukian	seq_95_Shewanella_oneidensis	0.7706422018348624
seq_148_Bartonella_quintana	seq_104_Tropheryma_whipplei	0.9105691056910569
seq_148_Bartonella_quintana	seq_105_Xylella_fastidiosa	0.9612403100775194
seq_148_Bartonella_quintana	seq_117_Pseudomonas_syringae_pv._Tomato	0.9193548387096774
seq_148_Bartonella_quintana	seq_119_Bacillus_anthracis	0.9612403100775194
seq_148_Bartonella_quintana	seq_129_Bacillus_anthracis	0.9612403100775194
seq_148_Bartonella_quintana	seq_130_Geobacter_sulfurreducens	0.8833333333333333
seq_148_Bartonella_quintana	seq_135_Yersinia_pestis_biovar_Medievalis	0.9770992366412213
seq_148_Bartonella_quintana	seq_138_Bacillus_cereus	0.9612403100775194
seq_148_Bartonella_quintana	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.9612403100775194
seq_148_Bartonella_quintana	seq_23_Haemophilus_influenzae	0.9770992366412213
seq_148_Bartonella_quintana	seq_24_Campylobacter_jejuni	0.953125
seq_148_Bartonella_quintana	seq_31_Pseudomonas_aeruginosa	0.9016393442622951
seq_148_Bartonella_quintana	seq_46_Salmonella_enterica	0.9770992366412213
seq_148_Bartonella_quintana	seq_48_Aeropyrum_pernix	0.9847328244274809
seq_148_Bartonella_quintana	seq_50_Halobacterium_sp.	1.0
seq_148_Bartonella_quintana	seq_59_Thermoplasma_acidophilum	0.9769230769230769
seq_148_Bartonella_quintana	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.9770992366412213
seq_148_Bartonella_quintana	seq_86_Xanthomonas_axonopodis_pv._citri.	0.9105691056910569
seq_148_Bartonella_quintana	seq_95_Shewanella_oneidensis	0.9848484848484849
seq_23_Haemophilus_influenzae	seq_104_Tropheryma_whipplei	1.0
seq_23_Haemophilus_influenzae	seq_105_Xylella_fastidiosa	0.7592592592592593
seq_23_Haemophilus_influenzae	seq_117_Pseudomonas_syringae_pv._Tomato	0.5894736842105264
seq_23_Haemophilus_influenzae	seq_119_Bacillus_anthracis	0.8833333333333333
seq_23_Haemophilus_influenzae	seq_129_Bacillus_anthracis	0.8833333333333333
seq_23_Haemophilus_influenzae	seq_130_Geobacter_sulfurreducens	0.9612403100775194
seq_23_Haemophilus_influenzae	seq_135_Yersinia_pestis_biovar_Medievalis	0.6041666666666667
seq_23_Haemophilus_influenzae	seq_138_Bacillus_cereus	0.8833333333333333
seq_23_Haemophilus_influenzae	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8833333333333333
seq_23_Haemophilus_influenzae	seq_148_Bartonella_quintana	0.9770992366412213
seq_23_Haemophilus_influenzae	seq_24_Campylobacter_jejuni	0.8925619834710744
seq_23_Haemophilus_influenzae	seq_31_Pseudomonas_aeruginosa	0.7476635514018692
seq_23_Haemophilus_influenzae	seq_46_Salmonella_enterica	0.6041666666666667
seq_23_Haemophilus_influenzae	seq_48_Aeropyrum_pernix	1.0
seq_23_Haemophilus_influenzae	seq_50_Halobacterium_sp.	1.0
seq_23_Haemophilus_influenzae	seq_59_Thermoplasma_acidophilum	1.0
seq_23_Haemophilus_influenzae	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_23_Haemophilus_influenzae	seq_86_Xanthomonas_axonopodis_pv._citri.	0.7476635514018692
seq_23_Haemophilus_influenzae	seq_95_Shewanella_oneidensis	0.8245614035087719
seq_24_Campylobacter_jejuni	seq_104_Tropheryma_whipplei	0.9848484848484849
seq_24_Campylobacter_jejuni	seq_105_Xylella_fastidiosa	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_117_Pseudomonas_syringae_pv._Tomato	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_119_Bacillus_anthracis	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_129_Bacillus_anthracis	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_130_Geobacter_sulfurreducens	0.9692307692307692
seq_24_Campylobacter_jejuni	seq_135_Yersinia_pestis_biovar_Medievalis	0.8833333333333333
seq_24_Campylobacter_jejuni	seq_138_Bacillus_cereus	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_148_Bartonella_quintana	0.953125
seq_24_Campylobacter_jejuni	seq_23_Haemophilus_influenzae	0.8925619834710744
seq_24_Campylobacter_jejuni	seq_31_Pseudomonas_aeruginosa	0.9924812030075187
seq_24_Campylobacter_jejuni	seq_46_Salmonella_enterica	0.8833333333333333
seq_24_Campylobacter_jejuni	seq_48_Aeropyrum_pernix	1.0
seq_24_Campylobacter_jejuni	seq_50_Halobacterium_sp.	1.0
seq_24_Campylobacter_jejuni	seq_59_Thermoplasma_acidophilum	1.0
seq_24_Campylobacter_jejuni	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_24_Campylobacter_jejuni	seq_86_Xanthomonas_axonopodis_pv._citri.	0.9924812030075187
seq_24_Campylobacter_jejuni	seq_95_Shewanella_oneidensis	0.9016393442622951
seq_31_Pseudomonas_aeruginosa	seq_104_Tropheryma_whipplei	0.9193548387096774
seq_31_Pseudomonas_aeruginosa	seq_105_Xylella_fastidiosa	0.8448275862068966
seq_31_Pseudomonas_aeruginosa	seq_117_Pseudomonas_syringae_pv._Tomato	0.574468085106383
seq_31_Pseudomonas_aeruginosa	seq_119_Bacillus_anthracis	0.8347826086956522
seq_31_Pseudomonas_aeruginosa	seq_129_Bacillus_anthracis	0.8347826086956522
seq_31_Pseudomonas_aeruginosa	seq_130_Geobacter_sulfurreducens	0.8547008547008547
seq_31_Pseudomonas_aeruginosa	seq_135_Yersinia_pestis_biovar_Medievalis	0.7706422018348624
seq_31_Pseudomonas_aeruginosa	seq_138_Bacillus_cereus	0.8347826086956522
seq_31_Pseudomonas_aeruginosa	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8347826086956522
seq_31_Pseudomonas_aeruginosa	seq_148_Bartonella_quintana	0.9016393442622951
seq_31_Pseudomonas_aeruginosa	seq_23_Haemophilus_influenzae	0.7476635514018692
seq_31_Pseudomonas_aeruginosa	seq_24_Campylobacter_jejuni	0.9924812030075187
seq_31_Pseudomonas_aeruginosa	seq_46_Salmonella_enterica	0.7706422018348624
seq_31_Pseudomonas_aeruginosa	seq_48_Aeropyrum_pernix	1.0
seq_31_Pseudomonas_aeruginosa	seq_50_Halobacterium_sp.	1.0
seq_31_Pseudomonas_aeruginosa	seq_59_Thermoplasma_acidophilum	0.9609375
seq_31_Pseudomonas_aeruginosa	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.9770992366412213
seq_31_Pseudomonas_aeruginosa	seq_86_Xanthomonas_axonopodis_pv._citri.	0.3855421686746988
seq_31_Pseudomonas_aeruginosa	seq_95_Shewanella_oneidensis	0.9365079365079365
seq_46_Salmonella_enterica	seq_104_Tropheryma_whipplei	1.0
seq_46_Salmonella_enterica	seq_105_Xylella_fastidiosa	0.7818181818181819
seq_46_Salmonella_enterica	seq_117_Pseudomonas_syringae_pv._Tomato	0.6185567010309279
seq_46_Salmonella_enterica	seq_119_Bacillus_anthracis	0.8833333333333333
seq_46_Salmonella_enterica	seq_129_Bacillus_anthracis	0.8833333333333333
seq_46_Salmonella_enterica	seq_130_Geobacter_sulfurreducens	0.9612403100775194
seq_46_Salmonella_enterica	seq_135_Yersinia_pestis_biovar_Medievalis	0.0
seq_46_Salmonella_enterica	seq_138_Bacillus_cereus	0.8833333333333333
seq_46_Salmonella_enterica	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8833333333333333
seq_46_Salmonella_enterica	seq_148_Bartonella_quintana	0.9770992366412213
seq_46_Salmonella_enterica	seq_23_Haemophilus_influenzae	0.6041666666666667
seq_46_Salmonella_enterica	seq_24_Campylobacter_jejuni	0.8833333333333333
seq_46_Salmonella_enterica	seq_31_Pseudomonas_aeruginosa	0.7706422018348624
seq_46_Salmonella_enterica	seq_48_Aeropyrum_pernix	1.0
seq_46_Salmonella_enterica	seq_50_Halobacterium_sp.	1.0
seq_46_Salmonella_enterica	seq_59_Thermoplasma_acidophilum	1.0
seq_46_Salmonella_enterica	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_46_Salmonella_enterica	seq_86_Xanthomonas_axonopodis_pv._citri.	0.7706422018348624
seq_46_Salmonella_enterica	seq_95_Shewanella_oneidensis	0.8245614035087719
seq_48_Aeropyrum_pernix	seq_104_Tropheryma_whipplei	1.0
seq_48_Aeropyrum_pernix	seq_105_Xylella_fastidiosa	1.0
seq_48_Aeropyrum_pernix	seq_117_Pseudomonas_syringae_pv._Tomato	1.0
seq_48_Aeropyrum_pernix	seq_119_Bacillus_anthracis	1.0
seq_48_Aeropyrum_pernix	seq_129_Bacillus_anthracis	1.0
seq_48_Aeropyrum_pernix	seq_130_Geobacter_sulfurreducens	1.0
seq_48_Aeropyrum_pernix	seq_135_Yersinia_pestis_biovar_Medievalis	1.0
seq_48_Aeropyrum_pernix	seq_138_Bacillus_cereus	1.0
seq_48_Aeropyrum_pernix	seq_146_Bacillus_thuringiensis_serovar_konkukian	1.0
seq_48_Aeropyrum_pernix	seq_148_Bartonella_quintana	0.9847328244274809
seq_48_Aeropyrum_pernix	seq_23_Haemophilus_influenzae	1.0
seq_48_Aeropyrum_pernix	seq_24_Campylobacter_jejuni	1.0
seq_48_Aeropyrum_pernix	seq_31_Pseudomonas_aeruginosa	1.0
seq_48_Aeropyrum_pernix	seq_46_Salmonella_enterica	1.0
seq_48_Aeropyrum_pernix	seq_50_Halobacterium_sp.	1.0
seq_48_Aeropyrum_pernix	seq_59_Thermoplasma_acidophilum	0.9846153846153847
seq_48_Aeropyrum_pernix	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.9847328244274809
seq_48_Aeropyrum_pernix	seq_86_Xanthomonas_axonopodis_pv._citri.	1.0
seq_48_Aeropyrum_pernix	seq_95_Shewanella_oneidensis	1.0
seq_50_Halobacterium_sp.	seq_104_Tropheryma_whipplei	1.0
seq_50_Halobacterium_sp.	seq_105_Xylella_fastidiosa	1.0
seq_50_Halobacterium_sp.	seq_117_Pseudomonas_syringae_pv._Tomato	1.0
seq_50_Halobacterium_sp.	seq_119_Bacillus_anthracis	1.0
seq_50_Halobacterium_sp.	seq_129_Bacillus_anthracis	1.0
seq_50_Halobacterium_sp.	seq_130_Geobacter_sulfurreducens	1.0
seq_50_Halobacterium_sp.	seq_135_Yersinia_pestis_biovar_Medievalis	1.0
seq_50_Halobacterium_sp.	seq_138_Bacillus_cereus	1.0
seq_50_Halobacterium_sp.	seq_146_Bacillus_thuringiensis_serovar_konkukian	1.0
seq_50_Halobacterium_sp.	seq_148_Bartonella_quintana	1.0
seq_50_Halobacterium_sp.	seq_23_Haemophilus_influenzae	1.0
seq_50_Halobacterium_sp.	seq_24_Campylobacter_jejuni	1.0
seq_50_Halobacterium_sp.	seq_31_Pseudomonas_aeruginosa	1.0
seq_50_Halobacterium_sp.	seq_46_Salmonella_enterica	1.0
seq_50_Halobacterium_sp.	seq_48_Aeropyrum_pernix	1.0
seq_50_Halobacterium_sp.	seq_59_Thermoplasma_acidophilum	0.9847328244274809
seq_50_Halobacterium_sp.	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.9848484848484849
seq_50_Halobacterium_sp.	seq_86_Xanthomonas_axonopodis_pv._citri.	1.0
seq_50_Halobacterium_sp.	seq_95_Shewanella_oneidensis	0.9770992366412213
seq_59_Thermoplasma_acidophilum	seq_104_Tropheryma_whipplei	0.9689922480620154
seq_59_Thermoplasma_acidophilum	seq_105_Xylella_fastidiosa	0.9847328244274809
seq_59_Thermoplasma_acidophilum	seq_117_Pseudomonas_syringae_pv._Tomato	1.0
seq_59_Thermoplasma_acidophilum	seq_119_Bacillus_anthracis	0.9847328244274809
seq_59_Thermoplasma_acidophilum	seq_129_Bacillus_anthracis	0.9847328244274809
seq_59_Thermoplasma_acidophilum	seq_130_Geobacter_sulfurreducens	1.0
seq_59_Thermoplasma_acidophilum	seq_135_Yersinia_pestis_biovar_Medievalis	1.0
seq_59_Thermoplasma_acidophilum	seq_138_Bacillus_cereus	0.9847328244274809
seq_59_Thermoplasma_acidophilum	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.9847328244274809
seq_59_Thermoplasma_acidophilum	seq_148_Bartonella_quintana	0.9769230769230769
seq_59_Thermoplasma_acidophilum	seq_23_Haemophilus_influenzae	1.0
seq_59_Thermoplasma_acidophilum	seq_24_Campylobacter_jejuni	1.0
seq_59_Thermoplasma_acidophilum	seq_31_Pseudomonas_aeruginosa	0.9609375
seq_59_Thermoplasma_acidophilum	seq_46_Salmonella_enterica	1.0
seq_59_Thermoplasma_acidophilum	seq_48_Aeropyrum_pernix	0.9846153846153847
seq_59_Thermoplasma_acidophilum	seq_50_Halobacterium_sp.	0.9847328244274809
seq_59_Thermoplasma_acidophilum	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.6831683168316831
seq_59_Thermoplasma_acidophilum	seq_86_Xanthomonas_axonopodis_pv._citri.	0.9689922480620154
seq_59_Thermoplasma_acidophilum	seq_95_Shewanella_oneidensis	0.9924242424242424
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_104_Tropheryma_whipplei	0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_105_Xylella_fastidiosa	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_117_Pseudomonas_syringae_pv._Tomato	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_119_Bacillus_anthracis	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_129_Bacillus_anthracis	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_130_Geobacter_sulfurreducens	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_135_Yersinia_pestis_biovar_Medievalis	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_138_Bacillus_cereus	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_146_Bacillus_thuringiensis_serovar_konkukian	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_148_Bartonella_quintana	0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_23_Haemophilus_influenzae	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_24_Campylobacter_jejuni	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_31_Pseudomonas_aeruginosa	0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_46_Salmonella_enterica	1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_48_Aeropyrum_pernix	0.9847328244274809
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_50_Halobacterium_sp.	0.9848484848484849
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_59_Thermoplasma_acidophilum	0.6831683168316831
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_86_Xanthomonas_axonopodis_pv._citri.	0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	seq_95_Shewanella_oneidensis	1.0
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_104_Tropheryma_whipplei	0.9193548387096774
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_105_Xylella_fastidiosa	0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_117_Pseudomonas_syringae_pv._Tomato	0.5894736842105264
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_119_Bacillus_anthracis	0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_129_Bacillus_anthracis	0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_130_Geobacter_sulfurreducens	0.864406779661017
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_135_Yersinia_pestis_biovar_Medievalis	0.7706422018348624
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_138_Bacillus_cereus	0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_148_Bartonella_quintana	0.9105691056910569
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_23_Haemophilus_influenzae	0.7476635514018692
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_24_Campylobacter_jejuni	0.9924812030075187
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_31_Pseudomonas_aeruginosa	0.3855421686746988
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_46_Salmonella_enterica	0.7706422018348624
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_48_Aeropyrum_pernix	1.0
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_50_Halobacterium_sp.	1.0
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_59_Thermoplasma_acidophilum	0.9689922480620154
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	0.9770992366412213
seq_86_Xanthomonas_axonopodis_pv._citri.	seq_95_Shewanella_oneidensis	0.9365079365079365
seq_95_Shewanella_oneidensis	seq_104_Tropheryma_whipplei	1.0
seq_95_Shewanella_oneidensis	seq_105_Xylella_fastidiosa	0.8925619834710744
seq_95_Shewanella_oneidensis	seq_117_Pseudomonas_syringae_pv._Tomato	0.8347826086956522
seq_95_Shewanella_oneidensis	seq_119_Bacillus_anthracis	0.7706422018348624
seq_95_Shewanella_oneidensis	seq_129_Bacillus_anthracis	0.7706422018348624
seq_95_Shewanella_oneidensis	seq_130_Geobacter_sulfurreducens	0.8739495798319328
seq_95_Shewanella_oneidensis	seq_135_Yersinia_pestis_biovar_Medievalis	0.8245614035087719
seq_95_Shewanella_oneidensis	seq_138_Bacillus_cereus	0.7706422018348624
seq_95_Shewanella_oneidensis	seq_146_Bacillus_thuringiensis_serovar_konkukian	0.7706422018348624
seq_95_Shewanella_oneidensis	seq_148_Bartonella_quintana	0.9848484848484849
seq_95_Shewanella_oneidensis	seq_23_Haemophilus_influenzae	0.8245614035087719
seq_95_Shewanella_oneidensis	seq_24_Campylobacter_jejuni	0.9016393442622951
seq_95_Shewanella_oneidensis	seq_31_Pseudomonas_aeruginosa	0.9365079365079365
seq_95_Shewanella_oneidensis	seq_46_Salmonella_enterica	0.8245614035087719
seq_95_Shewanella_oneidensis	seq_48_Aeropyrum_pernix	1.0
seq_95_Shewanella_oneidensis	seq_50_Halobacterium_sp.	0.9770992366412213
seq_95_Shewanella_oneidensis	seq_59_Thermoplasma_acidophilum	0.9924242424242424
seq_95_Shewanella_oneidensis	seq_70_Saccharomyces_cerevisiae_(baker's_yeast)	1.0
seq_95_Shewanella_oneidensis	seq_86_Xanthomonas_axonopodis_pv._citri.	0.9365079365079365