revisit MorF-EggNOG overlap (Table 3)

30b67fc7 · Niko Papadopoulos · c29d13de · 30b67fc7 · 30b67fc7
Commit 30b67fc7 authored 2 years ago by Niko Papadopoulos
--- a/analysis/revision-table3-revisit.ipynb
+++ b/analysis/revision-table3-revisit.ipynb
@@ -3,11 +3,260 @@
  {
   "cell_type": "markdown",
   "id": "2ab498a2-bfa8-49c7-93ee-e5d37054a460",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
   "source": [
    "# Structure-sequence agreement in model species\n",
    "\n",
-    "In an effort to get a feeling for how often morphologs were orthologs, we searched with AlphaFoldDB against itself. In Table 3 of the manuscript we reported that proteins that had non-species morphologs (very) often were also orthologs. The reviewers pointed out that these orthologs might plausibly come from very closely related species, thus weakening our claim that structural similarity might detect functional similarity or orthology over longer evolutionary distances. Here we are revisiting this analysis and looking to exclude "
+    "In an effort to get a feeling for how often morphologs were orthologs, we searched with AlphaFoldDB against itself. In Table 3 of the manuscript we reported that proteins that had non-species morphologs (very) often were also orthologs. The reviewers pointed out that these orthologs might plausibly come from very closely related species, thus weakening our claim that structural similarity might detect functional similarity or orthology over longer evolutionary distances. Here we are revisiting this analysis and looking to exclude closely related species for the current query (e.g. exclude all vertebrates when looking at human/mouse/rat/zebrafish)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "9e515cdc-8372-42aa-b993-0f9a21d4ce86",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "\n",
+    "from matplotlib import pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "48771bad-b5d8-4f81-ae39-d0955f120201",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "afdb = pd.read_csv('/Users/npapadop/Documents/data/coffe/self_score.tsv', sep='\\t', header=None)\n",
+    "\n",
+    "afdb.columns = ['query', 'target', 'perc_id', 'ali_length', 'no_mismatch', 'no_gapopen',\n",
+    "                'q_start', 'q_end', 't_start', 't_end', 'eval', 'bit']\n",
+    "\n",
+    "afdb['query'] = afdb['query'].str.split('-').str[1]\n",
+    "afdb['target'] = afdb['target'].str.split('-').str[1]\n",
+    "afdb.drop(columns=[\"no_mismatch\", \"no_gapopen\", \"q_start\", \"q_end\", \"t_start\", \"t_end\"], inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "e795b8d5-8986-46b2-97f5-43b8dae21c05",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "uniprot_to_eggnog = pd.read_csv('/Users/npapadop/Documents/data/coffe/uni2egg_euk.Nov2018.tsv', sep='\\t', header=None)\n",
+    "uniprot_to_eggnog.columns = ['uniprot', 'orthogroup']\n",
+    "uniprot_to_eggnog.set_index(\"uniprot\", inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "06265422-c6e6-4180-bef8-908ca806a894",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annot = pd.read_csv('/Users/npapadop/Documents/data/coffe/afdb_proteomes_species.tsv', sep='\\t', index_col=0)\n",
+    "annot.set_index(\"id\", inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "892a05c7-35f4-4f92-b379-f0b17551177c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "taxonomy = {\n",
+    "   \"Zea mays\": \"Monocots\",\n",
+    "   \"Glycine max\": \"Eudicots\",\n",
+    "   \"Trypanosoma brucei brucei (strain 927/4 GUTat10.1)\": \"Trypanosomatida\",\n",
+    "   \"Staphylococcus aureus (strain NCTC 8325 / PS 47)\": \"Staphylococcales\",\n",
+    "   \"Leishmania infantum\": \"Trypanosomatida\",\n",
+    "   \"Madurella mycetomatis\": \"Sordariomycetes\",\n",
+    "   \"Cladophialophora carrionii\": \"Chaetothyriales\",\n",
+    "   \"Drosophila melanogaster\": \"Arthropoda\",\n",
+    "   \"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)\": \"Methanocaldococcales\",\n",
+    "   \"Mycobacterium leprae (strain TN)\": \"Mycobacteriales\",\n",
+    "   \"Mus musculus\": \"Vertebrata\",\n",
+    "   \"Escherichia coli (strain K12)\": \"Enterobacteriales\",\n",
+    "   \"Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)\": \"Campylobacterales\",\n",
+    "   \"Wuchereria bancrofti\": \"Nematoda\",\n",
+    "   \"Dracunculus medinensis\": \"Nematoda\",\n",
+    "   \"Homo sapiens\": \"Vertebrata\",\n",
+    "   \"Sporothrix schenckii (strain ATCC 58251 / de Perez 2211183)\": \"Sordariomycetes\",\n",
+    "   \"Mycobacterium ulcerans str. Harvey\": \"Mycobacteriales\",\n",
+    "   \"Dictyostelium discoideum\": \"Amoebozoa\",\n",
+    "   \"Arabidopsis thaliana\": \"Eudicots\",\n",
+    "   \"Caenorhabditis elegans\": \"Nematoda\",\n",
+    "   \"Oryza sativa subsp. japonica\": \"Monocots\",\n",
+    "   \"Saccharomyces cerevisiae (strain ATCC 204508 / S288c)\": \"Saccharomycetales\",\n",
+    "   \"Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)\": \"Pseudomonadales\",\n",
+    "   \"Schizosaccharomyces pombe (strain 972 / ATCC 24843)\": \"Schizosaccharomycetes\",\n",
+    "   \"Strongyloides stercoralis\": \"Nematoda\",\n",
+    "   \"Fonsecaea pedrosoi CBS 271.37\": \"Chaetothyriales\",\n",
+    "   \"Brugia malayi\": \"Nematoda\",\n",
+    "   \"Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)\": \"Enterobacteriales\",\n",
+    "   \"Onchocerca volvulus\": \"Nematoda\",\n",
+    "   \"Danio rerio\": \"Vertebrata\",\n",
+    "   \"Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)\": \"Eurotiomycetes\",\n",
+    "   \"Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)\": \"Enterobacteriales\",\n",
+    "   \"Trichuris trichiura\": \"Nematoda\",\n",
+    "   \"Schistosoma mansoni\": \"Platyhelminthes\",\n",
+    "   \"Candida albicans (strain SC5314 / ATCC MYA-2876)\": \"Saccharomycetales\",\n",
+    "   \"Trypanosoma cruzi (strain CL Brener)\": \"Trypanosomatida\",\n",
+    "   \"Enterococcus faecium\": \"Lactobacillales\",\n",
+    "   \"Helicobacter pylori (strain ATCC 700392 / 26695)\": \"Campylobacterales\",\n",
+    "   \"Plasmodium falciparum (isolate 3D7)\": \"Aconoidasida\",\n",
+    "   \"Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)\": \"Mycobacteriales\",\n",
+    "   \"Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)\": \"Neisseriales\",\n",
+    "   \"Streptococcus pneumoniae (strain ATCC BAA-255 / R6)\": \"Lactobacillales\",\n",
+    "   \"Nocardia brasiliensis ATCC 700358\": \"Mycobacteriales\",\n",
+    "   \"Paracoccidioides lutzii (strain ATCC MYA-826 / Pb01)\": \"Eurotiomycetes\",\n",
+    "   \"Rattus norvegicus\": \"Vertebrata\",\n",
+    "   \"Shigella dysenteriae serotype 1 (strain Sd197)\": \"Enterobacteriales\",\n",
+    "   \"Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)\": \"Pasteurallales\"\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "b35c269b-0a48-470e-8f5d-6dd02373826a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annot.columns = [\"query species\"]\n",
+    "afdb = afdb.join(annot, on=\"query\")\n",
+    "annot.columns = [\"target species\"]\n",
+    "afdb = afdb.join(annot, on=\"target\")\n",
+    "afdb[\"target taxonomy\"] = afdb[\"target species\"].replace(taxonomy)\n",
+    "# reset annot columns\n",
+    "annot.columns = [\"species\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "58daa91d-ec2b-47cb-b007-6621b50e5576",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "uniprot_to_eggnog.columns = [\"query euk OG\"]\n",
+    "afdb = afdb.join(uniprot_to_eggnog, on=\"query\")\n",
+    "uniprot_to_eggnog.columns = [\"target euk OG\"]\n",
+    "afdb = afdb.join(uniprot_to_eggnog, on=\"target\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "02448ebd-05d4-47a0-90a5-3f579e3a5fff",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "query_OG_present = ~afdb[\"query euk OG\"].isnull()\n",
+    "target_OG_present = ~afdb[\"target euk OG\"].isnull()\n",
+    "\n",
+    "OGs_available = query_OG_present & target_OG_present"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "ae403d3f-ed80-4b03-b408-c7f00cceb86b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def best_match(df, sort_by='bit', tiebreak='ali_length'):\n",
+    "    have_max = df[sort_by] == np.max(df[sort_by])\n",
+    "    max_ali = df[have_max][tiebreak] == np.max(df[have_max][tiebreak])\n",
+    "    return df[have_max][max_ali].index.values[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "6bcc92ad-84f9-4b17-a886-fdcf306410a0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)\t0\t0\t0.00%\n",
+      "Arabidopsis thaliana\t27357\t19800\t 83.78%\n",
+      "Brugia malayi\t0\t0\t0.00%\n",
+      "Caenorhabditis elegans\t19599\t11177\t 67.29%\n",
+      "Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)\t0\t0\t0.00%\n",
+      "Candida albicans (strain SC5314 / ATCC MYA-2876)\t5973\t4118\t 84.41%\n",
+      "Cladophialophora carrionii\t11169\t7040\t 81.29%\n",
+      "Danio rerio\t24626\t13303\t 75.36%\n",
+      "Dictyostelium discoideum\t12584\t6312\t 63.96%\n",
+      "Dracunculus medinensis\t0\t0\t0.00%\n",
+      "Drosophila melanogaster\t13418\t8828\t 79.69%\n",
+      "Enterococcus faecium\t0\t0\t0.00%\n",
+      "Escherichia coli (strain K12)\t0\t0\t0.00%\n",
+      "Fonsecaea pedrosoi CBS 271.37\t0\t0\t0.00%\n",
+      "Glycine max\t55759\t32239\t 85.40%\n",
+      "Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)\t0\t0\t0.00%\n",
+      "Helicobacter pylori (strain ATCC 700392 / 26695)\t0\t0\t0.00%\n",
+      "Homo sapiens\t20392\t13838\t 74.30%\n",
+      "Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)\t0\t0\t0.00%\n",
+      "Leishmania infantum\t7914\t4423\t 56.14%\n",
+      "Madurella mycetomatis\t0\t0\t0.00%\n",
+      "Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)\t0\t0\t0.00%\n",
+      "Mus musculus\t21507\t15084\t 75.05%\n",
+      "Mycobacterium leprae (strain TN)\t0\t0\t0.00%\n",
+      "Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)\t0\t0\t0.00%\n",
+      "Mycobacterium ulcerans str. Harvey\t0\t0\t0.00%\n",
+      "Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)\t0\t0\t0.00%\n",
+      "Nocardia brasiliensis ATCC 700358\t0\t0\t0.00%\n",
+      "Onchocerca volvulus\t0\t0\t0.00%\n",
+      "Oryza sativa subsp. japonica\t41794\t20306\t 86.51%\n",
+      "Paracoccidioides lutzii (strain ATCC MYA-826 / Pb01)\t8791\t5086\t 84.19%\n",
+      "Plasmodium falciparum (isolate 3D7)\t0\t0\t0.00%\n",
+      "Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)\t0\t0\t0.00%\n",
+      "Rattus norvegicus\t19246\t13180\t 74.60%\n",
+      "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)\t6013\t4347\t 83.41%\n",
+      "Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)\t0\t0\t0.00%\n",
+      "Schistosoma mansoni\t13845\t1730\t 91.85%\n",
+      "Schizosaccharomyces pombe (strain 972 / ATCC 24843)\t5104\t3982\t 90.51%\n",
+      "Shigella dysenteriae serotype 1 (strain Sd197)\t0\t0\t0.00%\n",
+      "Sporothrix schenckii (strain ATCC 58251 / de Perez 2211183)\t8652\t6349\t 78.41%\n",
+      "Staphylococcus aureus (strain NCTC 8325 / PS 47)\t0\t0\t0.00%\n",
+      "Streptococcus pneumoniae (strain ATCC BAA-255 / R6)\t0\t0\t0.00%\n",
+      "Strongyloides stercoralis\t0\t0\t0.00%\n",
+      "Trichuris trichiura\t0\t0\t0.00%\n",
+      "Trypanosoma brucei brucei (strain 927/4 GUTat10.1)\t8476\t4303\t 60.26%\n",
+      "Trypanosoma cruzi (strain CL Brener)\t19026\t8782\t 56.56%\n",
+      "Wuchereria bancrofti\t0\t0\t0.00%\n",
+      "Zea mays\t38818\t18644\t 85.47%\n"
+     ]
+    }
+   ],
+   "source": [
+    "for species in np.unique(annot['species']):\n",
+    "    taxon = taxonomy[species]\n",
+    "    query_is_species = afdb[\"query species\"] == species\n",
+    "    target_is_diff_taxon = afdb[\"target taxonomy\"] != taxon\n",
+    "\n",
+    "    keep = query_is_species & target_is_diff_taxon & OGs_available\n",
+    "    if np.sum(keep) == 0:\n",
+    "        print(f'{species}\\t{0}\\t{0}\\t0.00%')\n",
+    "        continue\n",
+    "    \n",
+    "    best_indices = afdb[keep].groupby(\"query\").apply(best_match)\n",
+    "    species_best = afdb.loc[best_indices]\n",
+    "    total_proteins = len(afdb[query_is_species][\"query\"].unique())\n",
+    "    have_og = len(species_best)\n",
+    "    og_agreement = np.sum(species_best[\"query euk OG\"] == species_best[\"target euk OG\"]) / have_og\n",
+    "    print(f'{species}\\t{total_proteins}\\t{have_og}\\t{og_agreement * 100: .2f}%')"
   ]
  }
 ],

 %% Cell type:markdown id:2ab498a2-bfa8-49c7-93ee-e5d37054a460 tags:

 # Structure-sequence agreement in model species

-In an effort to get a feeling for how often morphologs were orthologs, we searched with AlphaFoldDB against itself. In Table 3 of the manuscript we reported that proteins that had non-species morphologs (very) often were also orthologs. The reviewers pointed out that these orthologs might plausibly come from very closely related species, thus weakening our claim that structural similarity might detect functional similarity or orthology over longer evolutionary distances. Here we are revisiting this analysis and looking to exclude
+In an effort to get a feeling for how often morphologs were orthologs, we searched with AlphaFoldDB against itself. In Table 3 of the manuscript we reported that proteins that had non-species morphologs (very) often were also orthologs. The reviewers pointed out that these orthologs might plausibly come from very closely related species, thus weakening our claim that structural similarity might detect functional similarity or orthology over longer evolutionary distances. Here we are revisiting this analysis and looking to exclude closely related species for the current query (e.g. exclude all vertebrates when looking at human/mouse/rat/zebrafish).
+
+%% Cell type:code id:9e515cdc-8372-42aa-b993-0f9a21d4ce86 tags:
+
+``` python
+import numpy as np
+import pandas as pd
+
+from matplotlib import pyplot as plt
+```
+
+%% Cell type:code id:48771bad-b5d8-4f81-ae39-d0955f120201 tags:
+
+``` python
+afdb = pd.read_csv('/Users/npapadop/Documents/data/coffe/self_score.tsv', sep='\t', header=None)
+
+afdb.columns = ['query', 'target', 'perc_id', 'ali_length', 'no_mismatch', 'no_gapopen',
+                'q_start', 'q_end', 't_start', 't_end', 'eval', 'bit']
+
+afdb['query'] = afdb['query'].str.split('-').str[1]
+afdb['target'] = afdb['target'].str.split('-').str[1]
+afdb.drop(columns=["no_mismatch", "no_gapopen", "q_start", "q_end", "t_start", "t_end"], inplace=True)
+```
+
+%% Cell type:code id:e795b8d5-8986-46b2-97f5-43b8dae21c05 tags:
+
+``` python
+uniprot_to_eggnog = pd.read_csv('/Users/npapadop/Documents/data/coffe/uni2egg_euk.Nov2018.tsv', sep='\t', header=None)
+uniprot_to_eggnog.columns = ['uniprot', 'orthogroup']
+uniprot_to_eggnog.set_index("uniprot", inplace=True)
+```
+
+%% Cell type:code id:06265422-c6e6-4180-bef8-908ca806a894 tags:
+
+``` python
+annot = pd.read_csv('/Users/npapadop/Documents/data/coffe/afdb_proteomes_species.tsv', sep='\t', index_col=0)
+annot.set_index("id", inplace=True)
+```
+
+%% Cell type:code id:892a05c7-35f4-4f92-b379-f0b17551177c tags:
+
+``` python
+taxonomy = {
+   "Zea mays": "Monocots",
+   "Glycine max": "Eudicots",
+   "Trypanosoma brucei brucei (strain 927/4 GUTat10.1)": "Trypanosomatida",
+   "Staphylococcus aureus (strain NCTC 8325 / PS 47)": "Staphylococcales",
+   "Leishmania infantum": "Trypanosomatida",
+   "Madurella mycetomatis": "Sordariomycetes",
+   "Cladophialophora carrionii": "Chaetothyriales",
+   "Drosophila melanogaster": "Arthropoda",
+   "Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)": "Methanocaldococcales",
+   "Mycobacterium leprae (strain TN)": "Mycobacteriales",
+   "Mus musculus": "Vertebrata",
+   "Escherichia coli (strain K12)": "Enterobacteriales",
+   "Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)": "Campylobacterales",
+   "Wuchereria bancrofti": "Nematoda",
+   "Dracunculus medinensis": "Nematoda",
+   "Homo sapiens": "Vertebrata",
+   "Sporothrix schenckii (strain ATCC 58251 / de Perez 2211183)": "Sordariomycetes",
+   "Mycobacterium ulcerans str. Harvey": "Mycobacteriales",
+   "Dictyostelium discoideum": "Amoebozoa",
+   "Arabidopsis thaliana": "Eudicots",
+   "Caenorhabditis elegans": "Nematoda",
+   "Oryza sativa subsp. japonica": "Monocots",
+   "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)": "Saccharomycetales",
+   "Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)": "Pseudomonadales",
+   "Schizosaccharomyces pombe (strain 972 / ATCC 24843)": "Schizosaccharomycetes",
+   "Strongyloides stercoralis": "Nematoda",
+   "Fonsecaea pedrosoi CBS 271.37": "Chaetothyriales",
+   "Brugia malayi": "Nematoda",
+   "Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)": "Enterobacteriales",
+   "Onchocerca volvulus": "Nematoda",
+   "Danio rerio": "Vertebrata",
+   "Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)": "Eurotiomycetes",
+   "Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)": "Enterobacteriales",
+   "Trichuris trichiura": "Nematoda",
+   "Schistosoma mansoni": "Platyhelminthes",
+   "Candida albicans (strain SC5314 / ATCC MYA-2876)": "Saccharomycetales",
+   "Trypanosoma cruzi (strain CL Brener)": "Trypanosomatida",
+   "Enterococcus faecium": "Lactobacillales",
+   "Helicobacter pylori (strain ATCC 700392 / 26695)": "Campylobacterales",
+   "Plasmodium falciparum (isolate 3D7)": "Aconoidasida",
+   "Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)": "Mycobacteriales",
+   "Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)": "Neisseriales",
+   "Streptococcus pneumoniae (strain ATCC BAA-255 / R6)": "Lactobacillales",
+   "Nocardia brasiliensis ATCC 700358": "Mycobacteriales",
+   "Paracoccidioides lutzii (strain ATCC MYA-826 / Pb01)": "Eurotiomycetes",
+   "Rattus norvegicus": "Vertebrata",
+   "Shigella dysenteriae serotype 1 (strain Sd197)": "Enterobacteriales",
+   "Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)": "Pasteurallales"
+}
+```
+
+%% Cell type:code id:b35c269b-0a48-470e-8f5d-6dd02373826a tags:
+
+``` python
+annot.columns = ["query species"]
+afdb = afdb.join(annot, on="query")
+annot.columns = ["target species"]
+afdb = afdb.join(annot, on="target")
+afdb["target taxonomy"] = afdb["target species"].replace(taxonomy)
+# reset annot columns
+annot.columns = ["species"]
+```
+
+%% Cell type:code id:58daa91d-ec2b-47cb-b007-6621b50e5576 tags:
+
+``` python
+uniprot_to_eggnog.columns = ["query euk OG"]
+afdb = afdb.join(uniprot_to_eggnog, on="query")
+uniprot_to_eggnog.columns = ["target euk OG"]
+afdb = afdb.join(uniprot_to_eggnog, on="target")
+```
+
+%% Cell type:code id:02448ebd-05d4-47a0-90a5-3f579e3a5fff tags:
+
+``` python
+query_OG_present = ~afdb["query euk OG"].isnull()
+target_OG_present = ~afdb["target euk OG"].isnull()
+
+OGs_available = query_OG_present & target_OG_present
+```
+
+%% Cell type:code id:ae403d3f-ed80-4b03-b408-c7f00cceb86b tags:
+
+``` python
+def best_match(df, sort_by='bit', tiebreak='ali_length'):
+    have_max = df[sort_by] == np.max(df[sort_by])
+    max_ali = df[have_max][tiebreak] == np.max(df[have_max][tiebreak])
+    return df[have_max][max_ali].index.values[0]
+```
+
+%% Cell type:code id:6bcc92ad-84f9-4b17-a886-fdcf306410a0 tags:
+
+``` python
+for species in np.unique(annot['species']):
+    taxon = taxonomy[species]
+    query_is_species = afdb["query species"] == species
+    target_is_diff_taxon = afdb["target taxonomy"] != taxon
+
+    keep = query_is_species & target_is_diff_taxon & OGs_available
+    if np.sum(keep) == 0:
+        print(f'{species}\t{0}\t{0}\t0.00%')
+        continue
+
+    best_indices = afdb[keep].groupby("query").apply(best_match)
+    species_best = afdb.loc[best_indices]
+    total_proteins = len(afdb[query_is_species]["query"].unique())
+    have_og = len(species_best)
+    og_agreement = np.sum(species_best["query euk OG"] == species_best["target euk OG"]) / have_og
+    print(f'{species}\t{total_proteins}\t{have_og}\t{og_agreement * 100: .2f}%')
+```
+
+%% Output
+
+    Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)	0	0	0.00%
+    Arabidopsis thaliana	27357	19800	 83.78%
+    Brugia malayi	0	0	0.00%
+    Caenorhabditis elegans	19599	11177	 67.29%
+    Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)	0	0	0.00%
+    Candida albicans (strain SC5314 / ATCC MYA-2876)	5973	4118	 84.41%
+    Cladophialophora carrionii	11169	7040	 81.29%
+    Danio rerio	24626	13303	 75.36%
+    Dictyostelium discoideum	12584	6312	 63.96%
+    Dracunculus medinensis	0	0	0.00%
+    Drosophila melanogaster	13418	8828	 79.69%
+    Enterococcus faecium	0	0	0.00%
+    Escherichia coli (strain K12)	0	0	0.00%
+    Fonsecaea pedrosoi CBS 271.37	0	0	0.00%
+    Glycine max	55759	32239	 85.40%
+    Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)	0	0	0.00%
+    Helicobacter pylori (strain ATCC 700392 / 26695)	0	0	0.00%
+    Homo sapiens	20392	13838	 74.30%
+    Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)	0	0	0.00%
+    Leishmania infantum	7914	4423	 56.14%
+    Madurella mycetomatis	0	0	0.00%
+    Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)	0	0	0.00%
+    Mus musculus	21507	15084	 75.05%
+    Mycobacterium leprae (strain TN)	0	0	0.00%
+    Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	0	0	0.00%
+    Mycobacterium ulcerans str. Harvey	0	0	0.00%
+    Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)	0	0	0.00%
+    Nocardia brasiliensis ATCC 700358	0	0	0.00%
+    Onchocerca volvulus	0	0	0.00%
+    Oryza sativa subsp. japonica	41794	20306	 86.51%
+    Paracoccidioides lutzii (strain ATCC MYA-826 / Pb01)	8791	5086	 84.19%
+    Plasmodium falciparum (isolate 3D7)	0	0	0.00%
+    Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)	0	0	0.00%
+    Rattus norvegicus	19246	13180	 74.60%
+    Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	6013	4347	 83.41%
+    Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)	0	0	0.00%
+    Schistosoma mansoni	13845	1730	 91.85%
+    Schizosaccharomyces pombe (strain 972 / ATCC 24843)	5104	3982	 90.51%
+    Shigella dysenteriae serotype 1 (strain Sd197)	0	0	0.00%
+    Sporothrix schenckii (strain ATCC 58251 / de Perez 2211183)	8652	6349	 78.41%
+    Staphylococcus aureus (strain NCTC 8325 / PS 47)	0	0	0.00%
+    Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	0	0	0.00%
+    Strongyloides stercoralis	0	0	0.00%
+    Trichuris trichiura	0	0	0.00%
+    Trypanosoma brucei brucei (strain 927/4 GUTat10.1)	8476	4303	 60.26%
+    Trypanosoma cruzi (strain CL Brener)	19026	8782	 56.56%
+    Wuchereria bancrofti	0	0	0.00%
+    Zea mays	38818	18644	 85.47%

--- a/analysis/suppl-get_species.ipynb
+++ b/analysis/suppl-get_species.ipynb
@@ -150,7 +150,7 @@
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.10.8"
  }
 },
 "nbformat": 4,