FEAT: eggnog mapper functionality (#25)

* FEAT: started work on eggnog annotation stuff.

* IMP: linting....next to move dependencies

* IMP: just adding eggnog stuff

* IMP: just getting started on adding mapper.

* FEAT: initial pass at reference db downloader.

* IMP: more work on ancillary database downloader

* IMP: getting closer.

TODO: binarytextfile format to store reference database. Rewire.
Possibly multifile directory format and chose between name based on the
type of reference being created. Change subprocess stdout and stderr to
PIPE so that errors from there are captured by QIIME 2's logging
machinery.

* IMP: clean up trying to get tests passing.

TODO next time, figure out why not downloader not raising errror when
given mixed taxa types

* BUG: downloader functional/tests passing

* TEST: Tests for taxa checker utility.

* TEST: fixing failure from incorrect setup....

* TEST: skipping tests with actual downloads

* BUG: fixing linting

* BUG: fixing linting

* IMP: cleaning somethings up....

* YEP: getting there

* IMP: Formats & Types updated and sorted, started combining the
downloaders.

* FEAT: diamond_search method

* IMP: implementing functionality for search_diamond

* FEAT: eggnog_diamond_search now working?

* FEAT: diamond seed ortholog search for eggnogmapper

* LINT: cleaning up first draft

* FEAT: add eggnog_annotate_seed_orthologs

* FEAT: eggnog annotation working!

* FEAT: starting to add usage examples

* FEAT: added multi-cpu utilization

* IMP: linting

* FEAT: add read eggnog database into memory.

* GETTING q2-types-genomics and moshpit on same page

* reorganizing for just eggnog stuff

* IMP: dependency specification update.

* FEAT: Generate FT on eggnog diamond search

* EOD MONDAY

* BACKUP before cleanup

* IMP: fixing linting issues

* BUG: remove artifacts from merge

* TEST: added test data/reference artifacts and a basic test for eggnog
diamond mapper.

* LINT: cleanup test commit

* ONLY LOCAL FAILING are not eggnog related

* lint setup

* added dependency on q2_types_genomics

* make types genomics available?

* TEST: added general test to eggnog annotater.

* add --dbmem parameter to address issue with very long runtime

* TEST: revert imports and fix test_small_good_hits

* fixes incomplete extraction of sample ids from filenames

addresses #27

* IMP: preparing for merge, lint, etc

* BUG: linting errors in metabat2

* TEST: Updating metabat2 tests to be compatible w/ @greg-caporaso 's
suffix based sample name extraction pr

* linting and fixing more test bugs, maybe one left 🤷‍♂️

* more test fixes

* IMP: adding `.DS_Store` to .gitignore

* IMP: removing `.DS_Store` files

* addresses @ebolyen's comments, removed qza test data in favor of raw inputs

* lint

* small test file issue

* squash

* squash

* run tests on ubuntu only

* sta gitus

* Update ci/recipe/meta.yaml

* test OS X again

* Update ci/recipe/meta.yaml

* Update ci/recipe/meta.yaml

---------

Co-authored-by: Greg Caporaso <[email protected]>
Co-authored-by: Greg Caporaso <[email protected]>
Co-authored-by: Colin Vickers Wood <[email protected]>
Co-authored-by: colinvwood <[email protected]>
Co-authored-by: Evan Bolyen <[email protected]>
Co-authored-by: Evan Bolyen <[email protected]>

.github/workflows/ci.yml

@@ -40,16 +40,6 @@ jobs:
         # necessary for versioneer
         fetch-depth: 0
 
-    - name: Update missing libs
-      if: matrix.os == 'macos-latest'
-      run: |
-        brew install gsl
-        ln -s $HOME/homebrew/Cellar/gsl/2.7.1/lib/libgsl.27.dylib /usr/local/lib/libgsl.0.dylib
-        if [[ ! -f /usr/local/lib/libgslcblas.0.dylib ]]
-        then
-          ln -s $HOME/homebrew/Cellar/gsl/2.7.1/lib/libgslcblas.0.dylib /usr/local/lib/libgslcblas.0.dylib
-        fi
-
     - name: hack - template coverage output path
       run: echo "COV=coverage xml -o $GITHUB_WORKSPACE/coverage.xml" >> $GITHUB_ENV
 

.gitignore

@@ -130,3 +130,6 @@ dmypy.json
 
 # PyCharm configuration
 .idea/
+
+# Mac OS
+.DS_Store

ci/recipe/meta.yaml

@@ -23,6 +23,8 @@ requirements:
     - samtools
     - qiime2 {{ qiime2_epoch }}.*
     - q2-types-genomics {{ qiime2_epoch }}.*
+    - eggnog-mapper >=2.1.10
+    - diamond
     - tqdm
     - xmltodict
 

q2_moshpit/__init__.py

@@ -8,9 +8,11 @@
 
 from .kraken2 import classification, database
 from .metabat2 import metabat2
+from . import eggnog
+
 
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
 
-__all__ = ['metabat2', 'classification', 'database']
+__all__ = ['metabat2', 'classification', 'database', 'eggnog']

q2_moshpit/eggnog/__init__.py

@@ -0,0 +1,12 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2022, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+
+from ._method import (eggnog_diamond_search, eggnog_annotate)
+
+__all__ = ['eggnog_diamond_search', 'eggnog_annotate']

q2_moshpit/eggnog/_method.py

@@ -0,0 +1,122 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2022, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import subprocess
+import os
+import tempfile
+import re
+import pandas as pd
+
+from q2_types_genomics.per_sample_data import ContigSequencesDirFmt
+from q2_types_genomics.genome_data import SeedOrthologDirFmt, OrthologFileFmt
+from q2_types_genomics.feature_data import OrthologAnnotationDirFmt
+from q2_types_genomics.reference_db import EggnogRefDirFmt
+from q2_types.feature_data import DNAFASTAFormat
+from q2_types_genomics.reference_db import DiamondDatabaseDirFmt
+import qiime2.util
+
+
+def eggnog_diamond_search(input_sequences: ContigSequencesDirFmt,
+                          diamond_db: DiamondDatabaseDirFmt,
+                          num_cpus: int = 1, db_in_memory: bool = False
+                          ) -> (SeedOrthologDirFmt, pd.DataFrame):
+
+    diamond_db_fp = os.path.join(str(diamond_db), 'ref_db.dmnd')
+    temp = tempfile.TemporaryDirectory()
+
+    # run analysis
+    for relpath, obj_path in input_sequences.sequences.iter_views(
+            DNAFASTAFormat):
+        sample_label = str(relpath).rsplit(r'_', 1)[0]
+
+        _diamond_search_runner(input_path=obj_path,
+                               diamond_db=diamond_db_fp,
+                               sample_label=sample_label,
+                               output_loc=temp.name,
+                               num_cpus=num_cpus,
+                               db_in_memory=db_in_memory)
+
+    result = SeedOrthologDirFmt()
+
+    for item in os.listdir(temp.name):
+        if re.match(r".*\.seed_orthologs", item):
+            qiime2.util.duplicate(os.path.join(temp.name, item),
+                                  os.path.join(result.path, item))
+
+    ft = _eggnog_feature_table(result)
+
+    return (result, ft)
+
+
+def _eggnog_feature_table(seed_orthologs: SeedOrthologDirFmt) -> pd.DataFrame:
+
+    per_sample_counts = []
+
+    for sample_path, obj in seed_orthologs.seed_orthologs.iter_views(
+            OrthologFileFmt):
+        # TODO: put filename to sample name logic on OrthologFileFmt object
+        sample_name = str(sample_path).replace('.emapper.seed_orthologs', '')
+        sample_df = obj.view(pd.DataFrame)
+        sample_feature_counts = sample_df.value_counts('sseqid')
+        sample_feature_counts.name = str(sample_name)
+        per_sample_counts.append(sample_feature_counts)
+    df = pd.DataFrame(per_sample_counts)
+    df.fillna(0, inplace=True)
+    df.columns = df.columns.astype('str')
+
+    return df
+
+
+def _diamond_search_runner(input_path, diamond_db, sample_label, output_loc,
+                           num_cpus, db_in_memory):
+
+    cmds = ['emapper.py', '-i', str(input_path), '-o', sample_label,
+            '-m', 'diamond', '--no_annot', '--dmnd_db', str(diamond_db),
+            '--itype', 'metagenome', '--output_dir', output_loc, '--cpu',
+            str(num_cpus)]
+    if db_in_memory:
+        cmds.append('--dbmem')
+
+    subprocess.run(cmds, check=True)
+
+
+def eggnog_annotate(hits_table: SeedOrthologDirFmt,
+                    eggnog_db: EggnogRefDirFmt,
+                    db_in_memory: bool = False) -> OrthologAnnotationDirFmt:
+
+    eggnog_db_fp = eggnog_db.path
+
+    result = OrthologAnnotationDirFmt()
+
+    # run analysis
+    for relpath, obj_path in hits_table.seed_orthologs.iter_views(
+            OrthologFileFmt):
+        sample_label = str(relpath).rsplit(r'.', 2)[0]
+
+        _annotate_seed_orthologs_runner(seed_ortholog=obj_path,
+                                        eggnog_db=eggnog_db_fp,
+                                        sample_label=sample_label,
+                                        output_loc=result,
+                                        db_in_memory=db_in_memory)
+
+    return result
+
+
+def _annotate_seed_orthologs_runner(seed_ortholog, eggnog_db, sample_label,
+                                    output_loc, db_in_memory):
+
+    # at this point instead of being able to specify the type of target
+    # orthologs, we want to annotate _all_.
+
+    cmds = ['emapper.py', '-m', 'no_search', '--annotate_hits_table',
+            str(seed_ortholog), '--data_dir', str(eggnog_db),
+            '-o', str(sample_label), '--output_dir', str(output_loc)]
+    if db_in_memory:
+        cmds.append('--dbmem')
+
+    subprocess.run(cmds, check=True)

q2_moshpit/eggnog/tests/__init__.py

@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2022, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------

q2_moshpit/eggnog/tests/data/README.md

@@ -0,0 +1,5 @@
+The `random-db-1.fa` file in this directory is the source for `random-db-1/ref_db.dmnd`. Construction of the database was performed using diamond version 2.1.7 with the following command.
+
+```
+diamond makedb --in random-db-1.fa --db random-db1
+```

q2_moshpit/eggnog/tests/data/contig-sequences-1/s1_contigs.fa

@@ -0,0 +1,6 @@
+>should-hit-seq-0
+AACGATACCGAAGCGGTGATTGCGCATAAAAACAGCCTGAACATGGCGATTCTGATTATGTTTGATGATGCGGTGGCGATTTTTGTGTATAGCAACCTGGTGTGCATTCGCTTTGATGAACATTATGGCTGGGGCAACGAAGCGAACCGCATTCCGCATATTCTGCCGGATATTCGCCGCTGCATGCCGTGGAGCCATAAAGGCGATCATAACCCGATGGGCAACATGAGCGCGCTGTGCAAATGGGCGACCTATCGCCCGATTAAAAGCTGGTGGAGCCCGTATAAAATTGCGCGCGTGTTTTTTTGCATTGTGCATTTTGTGAACACCCCGAAACCGAAATGGGGCATGGAATTTGATAAACGCGAAGGCATGGTGATTACCATGCGCATTTGGAAAAACTGCCTGGGCATGTGCCTGGAAAAAGCGAACATTTGCGAAGGCACCCGCAACTGGCGCATTAAAATGAGCATGTGGGCGGGCAGCTTTATTGCGCTGATGGATT
+>should-hit-seq-2
+CTGGAAAGCGCGATGGGCGGCCCGCATATGAGCATTACCCCGGAAGAAAACGCGTTTGGCGGCTTTAACTTTTGCACCGGCGTGGTGACCGAACATATTCCGATGGATATTGTGGCGATTTGCTGGGCGCTGTTTAGCTGGGAAAACACCAAATTTGGCACCGTGAAAGATAACTGGCTGTATCGCTGGACCATTTGGTGGTGGTTTACCCTGGATACCGGCGCGAGCGTGGATTGCAAATGGGGCTGCAACCGCCGCGAACGCGCGATTTGGGTGTGCTGGAACCGCTTTATTACCATTAGCTTTCATAAACCGCGCGATTGCAAAACCAGCGCGTATCATACCGGCAAACCGGAAATGTATCTGGATCTGATGTGGATTTTTGTGAGCGTGCATGTGTTTATTATGACCCATCTGGCGGGCGATCATTTTCTGGGCCGCGTGCTGCTGCATCATAACAACGATGAAGATTATGATCGCAACTTTCCGATGCTGGATTTTAACTGCCATTGCTGGATTGCGATTTGGCATCGCGTGTGGTATCCGAGCAAAGTGCATGGCAGCGTGGATGCGCTGTTTGAATGGATTCCGCGCAACGGCGATTTTACCCTGCGCCGCAACGCGGGCGATCCGCGCTATACCAGCGCGAGCATGCGCTTTTTTGCGATGTGCGCGATGGAAATTATGCTGGCGCTGATGGGCGAAAGCATGAAACATGCGCTGGAAAGCGCGATGGGCGGCCCGCATATGAGCATTACCCCGGAAGAAAACGCGTTTGGCGGCTTTAACTTTTGCACCGGCGTGGTGACCGAACATATTCCGATGGATATTGTGGCGATTTGCTGGGCGCTGTTTAGCTGGGAAAACACCAAATTTGGCACCGTGAAAGATAACTGGCTGTATCGCTGGACCATTTGGTGGTGGTTTACCCTGGATACCGGCGCGAGCGTGGATTGCAAATGGGGCTGCAACCGCCGCGAACGCGCGATTTGGGTGTGCTGGAACCGCTTTATTACCATTAGCTTTCATAAACCGCGCGATTGCAAAACCAGCGCGTATCATACCGGCAAACCGGAAATGTATCTGGATCTGATGTGGATTTTTGTGAGCGTGCATGTGTTTATTATGACCCATCTGGCGGGCGATCATTTTCTGGGCCGCGTGCTGCTGCATCATAACAACGATGAAGATTATGATCGCAACTTTCCGATGCTGGATTTTAACTGCCATTGCTGGATTGCGATTTGGCATCGCGTGTGGTATCCGAGCAAAGTGCATGGCAGCGTGGATGCGCTGTTTGAATGGATTCCGCGCAACGGCGATTTTACCCTGCGCCGCAACGCGGGCGATCCGCGCTATACCAGCGCGAGCATGCGCTTTTTTGCGATGTGCGCGATGGAAATTATGCTGGCGCTGATGGGCGAAAGCATGAAACATGCGCATGGC
+>shouldnt-hit
+GCATTGAAGCTTTCTGACTGTTAAATAGTGTAGGCCCCAGCTGTTGATTTTTTAGACTAGAGGTGGGGCACTGTCCCGACACTTCTGGGTGTCCGCCACTGAGATGAACCCCACCGGGTCAAAGGATGTCAACGAAGTTCATTCAAGCTCACACGTCCAAGACCAGTGGTCAGGCTCTCTGTCATGCACCGTCCGCTTTGCAGCCGCGTCTCAGCGCCTCCCTACGCTCGAGATTGTCTGGCGCTCGGGTCATGGC

q2_moshpit/eggnog/tests/data/contig-sequences-1/s2_contigs.fa

@@ -0,0 +1,10 @@
+>shouldnt-hit-0
+ATAAATTAGTTACACTCTCCGTGACTCGAGCTAACCTGAACTCGTAAGAGGGTCCCTTAGCTAGAGACTTGTCTTGACCCAAACTAGTAGTAACTGCAAAACGGAATCTTAACAAAGGTTGCTACTAATGGCACGTCGTCACTTTTCTGAATTCGCATATGGATCCACGAGGGGAAATTGGCTTTGGAGAGATACACATCTGCCGACCAGACGCGGAATCTCAGTGAGTGTCATTCATGGCCCCTACCCT
+>shouldnt-hit-1
+ATGCGTTCGTCACGAGGTTGCAACGGGCCGCCTTGCTTCTTAGCTCGAGAGATAGTTACGGGTTTTAGTAGTAGGAGCGTATTCCATACCCACAATTCGGAACTGCCCATGAGCCGCCTAGTAAGGATAACCTTATGATAGCTATATGCTCTTCCTACTATCTAGCGGTGCTCAATTTGCCAATTTCCGGGTCCGACTACGAGGCCGGATCGCTGAGGAGTGACAACCCCTGTGCTATACATTACGGTCA
+>should-hit-seq8a
+TGCAAATGGAGCATGTGCACCTTTTGGAACTATCGCTTTTTTAGCCTGATTCTGTATTTTCGCACCACCAACGCGCTGACCGCGTGGACCTTTGTGTTTTGCTGGCCGAACCTGATTGGCCGCAGCATGAAACATGATGGCCTGTGCCATCATAGCGCGACCTATGTGTTTCATGCGATGATGGCGGAAATGGCGAAAGTGATGGATTTTTGCAGCGCGTGGGTGGAAGATGTGATGATGCCGATGCTGGGCTTTTATCATAACCTGTTTAACCCGCGCACCGGCAACGAAAACATTTGGAACGATAACTGCGAAGTGAACTGGACCGTGGTGATGAACGGCGGCATGATGTTTTTTGTGCTGTGGGATAAACTGATTATGGTGAGCGCGGAATGGAACAACTGGGCGCGCAAAATTGTGAAAGTGTATCGCGATAAAGATAACAAAATTGTGAGCCGCTGGTTTAGCTATCGCGATGGCGTGAGCTTTAACTTTAAAGGCTGCCTGCCGTGCTTTAAAAGCGGCATTATTCATCATTGGAACCATGATTTTGCGGCGTATAAAAACTGCGGCATGCCGGAAACCCGCCCGGATCTGTATTATGGCATGAGCTATGCGCTGTTTTATAGCCTGAAAGAAACCTTTGATGGCTTTCATATTGTGAACCCGGGCGAACTGAACGTGTGGCGCATTAAAAAACGCAAAGAAATGAACATGACCCTGGAACTGCATCATATGCATTGGTATGCGTGCAAATTTCTGGATCCGATTGGCAACGGCAAAATTGCGTGCAAATGCATTGATTATGTGTATCGCGTGCATGAAAGCTGCTGCGTGCGCCATCTGAGCCTGTGGGATTATTATTGCGAAGCGGATAACGAAGAAATGCTGGCGGCGACCGCGCCGAAAAACAAACGCCTGAGCGCGGCGCTGTATGATCGCTGCGGCTTTGATATGGATAAAGGCAGCGAACATGAATGCGAATTTAAACGCAAAGATATTGTGAAATATTTTATGATGATTGAAATGTATACCGGCACCCCGGTGCGCCCGTTTCGCCGCAAATGGCGCCTGTGCCATTGCCATAAAGAAAGCCGCTGGTGGTTTGTGTGCAGCCCGGGCCCGTTTTTTGGCTAT
+>should-hit-seq8b
+ACCGGCAACGAAAACATTTGGAACGATAACTGCGAAGTGAACTGGACCGTGGTGATGAACGGCGGCATGATGTTTTTTGTGCTGTGGGATAAACTGATTATGGTGAGCGCGGAATGGAACAACTGGGCGCGCAAAATTGTGAAAGTGTATCGCGATAAAGATAACAAAATTGTGAGCCGCTGGTTTAGCTATCGCGATGGCGTGAGCTTTAACTTTAAAGGCTGCCTGCCGTGCTTTAAAAGCGGCATTATTCATCATTGGAACCATGATTTTGCGGCGTATAAAAACTGCGGCATGCCGGAAACCCGCCCGGATCTGTATTATGGCATGAGCTATGCGCTGTTTTATAGCCTGAAAGAAACCTTTGATGGCTTTCATATTGTGAACCCGGGCGAACTGAACGTGTGGCGCATTAAAAAACGCAAAGAAATGAACATGACCCTGGAACTGCATCATATGCATTGGTATGCGTGCAAATTTCTGGATCCGATTGGCAACGGCAAAATTGCGTGCAAATGCATTGATTATGTGTATCGCGTGCATGAAAGCTGCTGCGTGCGCCATCTGAGCCTGTGGGATTATTATTGCGAAGCGGATAACGAAGAAATGCTGGCGGCGACCGCGCCGAAAAACAAACGCCTGAGCGCGGCGCTGTATGATCGCTGCGGCTTTGATATGGATAAAGGCAGCGAACATGAATGCGAATTTAAACGCAAAGATATTGTGAAATATTTTATGATGATTGAAATGTATACCGGCACCCCGGTGCGCCCGTTTCGCCGCAAATGGCGCCTGTGCCATTGCCATAAAGAAAGCCGCTGGTGGTTTGTGTGCAGCCCGGGCCCGTTTTTTGGCTAT
+>should-hit-seq8c
+TGCAAATGGAGCATGTGCACCTTTTGGAACTATCGCTTTTTTAGCCTGATTCTGTATTTTCGCACCACCAACGCGCTGACCGCGTGGACCTTTGTGTTTTGCTGGCCGAACCTGATTGGCCGCAGGAAACATGATGGCCTGTGCCATCATAGCGCGACCTATGTGTTTCATGCGATGATGGCGGAAATGGCGAAAGTGATGGATTTTTGCAGCGCGTGGGTGGAAGATGTGATGATGCCGATGCTGGGCTTTTATCATAACCTGTTTAACCCGCGCACCGGCAACGAAAACATTTGGAACGATAACTGCGAAGTGAACTGGACCGTGGTGATGAACGGCGGCATGATGTTTTTTGTGCTGTGGGATAAACTGATTATGGTGAGCGCGGAATGGAACAACTGGGCGCGCAAAATTGTGAAAGTGTATCGCGATAAAGATAACAAAATTGTGAGCCGCTGGTTTAGCTATCGCGATGGCGTGAGCTTTAACTTTAAAGGCTGCCTGCCGTGCTTTAAAAGCGGCATTATTCATCATTGGAACCATGATTTTGCGGCGTATAAAAACTGCGGCATGCCGGAAACCCGCCCGGATCTGTATTATGGCATGAGCTATGCGCTGTTTTATAGCCTGAAAGAAACCTTTGATGGCTTTCATATTGTGAACCCGGGCGAACTGAACGTGTGGCGCATTAAAAAACGCAAAGAAATGAACATGACCCTGGAACTGCATCATATGCATTGGTATGCGTGCAAATTTCTGGATCCGATTGGCAAC

q2_moshpit/eggnog/tests/data/expected/test_output.emapper.annotations

@@ -0,0 +1,2 @@
+1000565.METUNv1_03812	1000565.METUNv1_03812	4.71e-264	714.0	COG0012@1|root,COG0012@2|Bacteria,1MVM4@1224|Proteobacteria,2VJ1W@28216|Betaproteobacteria,2KUD2@206389|Rhodocyclales	206389|Rhodocyclales	J	ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner	ychF	-	-	ko:K06942	-	-	-	-	ko00000,ko03009	-	-	-	MMR_HSR1,YchF-GTPase_C
+362663.ECP_0061	362663.ECP_0061	0.0	1624.0	COG0417@1|root,COG0417@2|Bacteria,1MVY9@1224|Proteobacteria,1RMQ1@1236|Gammaproteobacteria,3XPER@561|Escherichia	1236|Gammaproteobacteria	L	DNA polymerase	polB	GO:0003674,GO:0003824,GO:0003887,GO:0004518,GO:0004527,GO:0004529,GO:0004536,GO:0006139,GO:0006259,GO:0006260,GO:0006261,GO:0006281,GO:0006725,GO:0006807,GO:0006950,GO:0006974,GO:0007154,GO:0008150,GO:0008152,GO:0008296,GO:0008408,GO:0009058,GO:0009059,GO:0009432,GO:0009605,GO:0009987,GO:0009991,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0016796,GO:0016895,GO:0018130,GO:0019438,GO:0031668,GO:0033554,GO:0034061,GO:0034641,GO:0034645,GO:0034654,GO:0043170,GO:0044237,GO:0044238,GO:0044249,GO:0044260,GO:0044271,GO:0045004,GO:0045005,GO:0046483,GO:0050896,GO:0051716,GO:0071496,GO:0071704,GO:0071897,GO:0090304,GO:0090305,GO:0140097,GO:1901360,GO:1901362,GO:1901576	2.7.7.7	ko:K02336	-	-	-	-	ko00000,ko01000,ko03400	-	-	-	DNA_pol_B,DNA_pol_B_exo1

q2_moshpit/eggnog/tests/data/good_hits/test_tiny.emappper.seed_orthologs

@@ -0,0 +1,2 @@
+1000565.METUNv1_03812	1000565.METUNv1_03812	4.71e-264	714.0	1	363	1	363	100.0	100.0	100.0
+362663.ECP_0061	362663.ECP_0061	0.0	1624.0	1	783	1	783	100.0	100.0	100.0

q2_moshpit/eggnog/tests/data/random-db-1.fa

@@ -0,0 +1,20 @@
+>0
+WDHEEAWAYDNCVSMGKHYGPVAISAKCASCPKNLFGMYSYECHHTRVDNMGMKIEDMNHCCDCGGPYKTCRCARYTPEIEMTPTSVVVYDGAVENRIFARHFCEVMNDTEAVIAHKNSLNMAILIMFDDAVAIFVYSNLVCIRFDEHYGWGNEANRIPHILPDIRRCMPWSHKGDHNPMGNMSALCKWATYRPIKSWWSPYKIARVFFCIVHFVNTPKPKWGMEFDKREGMVITMRIWKNCLGMCLEKANICEGTRNWRIKMSMWAGSFIALMDCRMWDVEIINPVWGRMHWATVRGVGEWVVGPLIYSEFKSHHVIIWLWGYCRAPWKEACMVRDNMSDIHHLEWTVIVDHIEPWPNWHPVRNGPFEGSSPLWCPLVIKRIRWKCNPREACHGTEGGAYMGKDCNKSIKDASTMMKEIERLKHCNKHPANPAGERWGGDYPEIKYKPILSPKAIMNHSIDIMTDWLRTFKFLSWYIPHPHEAISAERFGCPTLVKGKR
+>1
+SGGIYRVYGWTTLYSYNTYHGLCRGGERNSCYYEKIHCYSGIDDIEMPMPGICWEKGWCKTWKLLIPMYWNNYKGNAELHCLFGPTWLNCWVSEGSSAENAMRFPALRPAHYCARLIYMMWAYDVPFCVCIRDHDFRRHKNPKGHEVLVPTLKIEESINNISPDAVGYAFLEKCYPNMGEWPPPEMLEFERADTKNKHMCKYLSDGKCHKFHICDNRLIAERRASRLGYTELYDPCYSVDLIEGHESCDIWVSYSPYRINDGNFHARARTHILYTSMYFGEHTKHDMVIDYADWMALKALSDVLTSAHAKGLMVFAWMMPAEDMRTKPEIFYVHPYDDTFYCKGTAVHKLKWGYSVLNNCHTGAMHGWIFPMPMGVAHAYVKRNYEYEIKKECSPHLKYCVLYSIDVYLGPCMRFEWWTRSTFPCNWGFHWGDKVVNETKYHTGCCDHNTFYIGHHFPSWPGLWRDLKMMCCHDKPENGWCERYDVEIMYIVLEIMLGMY
+>2
+WRFIIDYVRYFASCVKPEHHLWTCWGGVEVEFLVHSFKVLGFTHMFMYPPIHPDMACGVWDVRTDAYFANSFLIAVTVFKVFNLINNMHSPSRTRFFLSMWHMWEATVDGNTKIPGTDEEELVYDHKSSKLPCCEMCEMGSTLFEEVLICPHDVSYEGESEEWSGWTHKRMPKRCLNVIDVIVIDNTVHYCTNHKNMILWRWYTGIYKWYNSRSRCTLSHGHMYLRDWCDFHNTVCTVPWTGYCVANVEHHFGGIMRSLESAMGGPHMSITPEENAFGGFNFCTGVVTEHIPMDIVAICWALFSWENTKFGTVKDNWLYRWTIWWWFTLDTGASVDCKWGCNRRERAIWVCWNRFITISFHKPRDCKTSAYHTGKPEMYLDLMWIFVSVHVFIMTHLAGDHFLGRVLLHHNNDEDYDRNFPMLDFNCHCWIAIWHRVWYPSKVHGSVDALFEWIPRNGDFTLRRNAGDPRYTSASMRFFAMCAMEIMLALMGESMKHAHG
+>3
+CPENGWFKCETHWMAEDPEKKLIVWNVNRRKCGYVKGGIRFCDEDITMIKYRDLGFTNFNFFRSWCHETNILFKFYAPMTHCLPPTSNTKVKDSTPTFMHAKTCWFMTLSRNIKYYCRDMIMYYASMPMIGLKINCLGTVHRRVGEATCTMDSTNHPGFNDIMMLDAGKNLWVMHFGGNHNGVLGLRHLVTMLWPMLGWEFPDSAWSFSTWADCDCHIGLSESWWVLLPADSSPGRLMHRHRMRKLNGTANNCPYHGLCLWHNVCESHIMRRWRMYKIWRKTGFVHYAGLYIFIGGTEYMLIVTRSTIWPYWVTRCTGIHKMICKCYERHWFFDLSRPVCWMNLYVLNKPWCGKLEGKCPIHIERIACKLKMLYKVHIVESDGLVPWIAVNPMDSGTCLIKSMMCIGCHALPDTYNMAGDCNGRESAVPYRGHSSTCMWVRHFWCGVMAHFETHGCESVRNAHDRPKNAGNARTFANADHPPVLYMGHYCVRHNPWHAEG
+>4
+FCYGVNDNEWCDRPTWYPKMYKRAHRSNDMPFYCHGDPGSYDNVINYLNCFMAYLSACMHMFEPHCFGVCMGMADWLNRAGIESNGEIMDGAMRKECWGYLVERARNGHEENVMTEIATMHAIWLTWEVSTCWYAPKVWKGLPGTPYSVVHLRCPGADGNHPLMIELTCKNACSTYFLTEVWNDVDEDYKLITLLCDEFVVYWPMKRGNTCNCAYLCWRMAYRRNASDCHGAKWPWIMAEIFAKWPKSAKYYLSCMRMATNCPIDDGSTVGVHRESMMEWTIPNRSHFEESLVKTETNFGSLWCPWFCIPHKTLENGSCTYWMGCPRRPAWTGWVLWEIAEPVAWFIGCSWDWAHMTLSLLEDVWIFDSKGKLHGLWRFYFVVCKPHVMMFNFFCFLNTGCWYCVLTHWWKHLSRLFLGSPRMAVIWLNLNLTLSFWENNEVHAFKCMTACVPCFRISFVTADHNDTSNALGPLFPWPCGVNLCLWMHSKNASMFIAPRW
+>5
+CYHKMTTPCIRPGRRGRSSFILCRKLSDCRGEFYVNKRRWYYSTWKHYWYIFATGVIESGRKCYFFVGLGHEIPTFGFNYNLCISLFLIFYKIFLSHDCATFYYKYDWLYMVSIAHGHTWDVKWWWKAFPSNRDFCMFRTCVPTTFAACGAGCEHWWEHDSVHVAVSYKRVVPHDFDWFYIAVSTCGPIEGWHEELAHFLPNHVTCKMCPKFCPENRAVCIAHIMKHEENRWDLDDCYSWSSDKNVHIGVTVGEWSYIDTYCMITVYPLHVMNEYPTMINMEMDPRPPSRDRSRNGSVFNCPEKVWMNSNCYSYGKGIYHECKNYPWDSTCFRSHWVLMIVMRIWCNCRRGRLFPEELHFVIWWEHHDWVCHAPVFWANYFRANEIFFMKHFTKYTNRTKICNPSYSRCDSHVHERSSWIAKDKGIVMCTTSRHKSMWGAAMAMSAKWVKRREWSTDHFFDVPVTDPAFPIRMRDCDESWRTVVFATPPCCEMCTLAEAW
+>6
+NDIERSISTSYFMPVLVAFWFDAEDISKGKTYERSETPIGSWTVTMKPLTDWRIFSEFWIEAGNIIKDGRILKVPREYNWWPGWEDCEVIPAPTYFVHLFETFRAHCHPHEDNPPYKAWAYPKYHWRATVCCMSDFDNNWLTEMFSRLSWIAAEEMKPCAPATINHMVLMMVAWEGWRAFPEAANEIKLTHYTWKMETIRGASHVYPLHSPICEMSGRAMNEWVGPTANHLAFCLSIDCLFGCFPHTAITSKTHEKCYEITGWYDWHCYLVMRKWHPTRWVTDGALNNGIMHFTEFYDGVKPTGLRHVMWGVIYSVSPHWEAFYLNDLDDLYNFGVDSELLVHWAYGHRYGMNIGIFAVPMGSPESGRYYYITAVIDKDCNRVNGFNSALIVRFTTEVNVGTKDLWNCNINCMVAIIRAPRRFHALEAFSHGVMEYMWECREPMWCYRKIYNNSKWAETNPDMCMWALFMKIAMPKYRPDPGFHAKFNSSYEPRMLWALH
+>7
+FMRTFHEWHITGNVHCDGKVWTYITVCEAILIHHTMNVPGIPPCSETGLWKIVTVMGEICLDFYMGAADICYMRFDGCTVILRMHWPLLAWKDIPYFVPIESPPGLVRPCLGMLTDMIKADMVRIHKWVHCEYKGLPDAPHRMKRKFWSKSKPWLHMYGIIWMGEEYRFDGHSLYEEIDSADPVHKIKFTRRKARAKEWVPSYMKKGCRFIWECCHTECLDCPMKAHDSEAEIKPNDYHFKWCCKMTGEMFTPLDRKVYLNPCFKPCFEEFTVNHTAWWNYSSVECALYWCETYNGAHWFIWTNDERGTLCFWRHCLTDMHCWVSYPRTRAASKYCYFSTWDGSHLGKHWPMNKVSCLETWYMAFYAVPGKDMFACNILPEKAWKWGHYDTSHGYLDGCSPTADIHSIEAWHEHEKAMYIKVCVEYKVERWKETLWEKKFWYMCLEESAALIIPPNRDSTVWVIMFMDDKLMAAPPVNYTEFNRRNKNLCNMSEAYIGVF
+>8
+CKWSMCTFWNYRFFSLILYFRTTNALTAWTFVFCWPNLIGRSMKHDGLCHHSATYVFHAMMAEMAKVMDFCSAWVEDVMMPMLGFYHNLFNPRTGNENIWNDNCEVNWTVVMNGGMMFFVLWDKLIMVSAEWNNWARKIVKVYRDKDNKIVSRWFSYRDGVSFNFKGCLPCFKSGIIHHWNHDFAAYKNCGMPETRPDLYYGMSYALFYSLKETFDGFHIVNPGELNVWRIKKRKEMNMTLELHHMHWYACKFLDPIGNGKIACKCIDYVYRVHESCCVRHLSLWDYYCEADNEEMLAATAPKNKRLSAALYDRCGFDMDKGSEHECEFKRKDIVKYFMMIEMYTGTPVRPFRRKWRLCHCHKESRWWFVCSPGPFFGYMGHCWTYCHAKGMRACFRLIKEMASHCFFCMPLMHHNMRIHHMHTTRTPAKDVIIDILVGAASAYNDNEVSSMKTFYHCHAYSFWMRNVCPLTWTVHRMLPGWMACHLILEGSYCNGDMAD
+>9
+FDFFKRVFIPFMETDDFMEHFYTSWHCGTIFIFRTYHILIWPGYRITNPFCIHGSPEFVAAHRAYLPAHPDDLKAWSDWFCMKEVVGKKWGYVAAKHNIHLVEKFKLDNGCDNCRRGMHSSGLKLVSGRNCNRHWSCVVLPCFCATLHHHHLWSESGPHLIFLWNYFKGGLHAFVADGMECHWIGSLTFFCMDPCVWKKDRGCWPWIFKLVVNYEKPKWMNFMVKNDCHMVRMPAMRMPKFNGYNSLAYSKCRVHHSAPVWHAVGRRMTVHPVGNLNSVIGYWDFRTNGYGTSGLLFRKFCCPHPADCFRACSFANAMHEGAEHPCDWSFYSKWEHICCSRMRRHECIREWDIRTDYDSDCEWMSVVSTLNPIKEWTHSELWSKSFWNWRVWDMFGTMYPGHRGPLECNLYDGVPRCPNTSSRSGMHEGIAYVLECESPHMAILGDAKFDLANREKYKATPHPPRTKYTRDERVRCNFEWEFSKHVGWHAGLSSVRIYCC