Fix incomplete read (#47)

* added logging, bumped version * fixed logging in container * implemented new parser for ncbi * added abstract parser ABC * added chunk loading * added examples
PyEED · Mar 7, 2024 · 49345df · 49345df
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diff --git a/examples/alignments/test_pairwise.ipynb b/examples/alignments/test_pairwise.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,14 +28,42 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
     "ald1 = ProteinInfo.from_ncbi(\"NP_001287541.1\")\n",
     "ald2 = ProteinInfo.from_ncbi(\"AAN14384.1\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/max/miniconda3/envs/pye/lib/python3.10/site-packages/sdRDM/base/datamodel.py:322: UserWarning: No 'URL' and 'Commit' specified. This model might not be re-usable.\n",
+      "  warnings.warn(\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'{\\n  \"id\": \"proteininfo0\",\\n  \"source_id\": \"NP_001287541.1\",\\n  \"name\": \"aldolase 1, isoform M\",\\n  \"sequence\": \"MTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVILFHETLYQKADDGTPFAEILKKKGIILGIKVDKGVVPLFGSEDEVTTQGLDDLAARCAQYKKDGCDFAKWRCVLKIGKNTPSYQSILENANVLARYASICQSQRIVPIVEPEVLPDGDHDLDRAQKVTETVLAAVYKALSDHHVYLEGTLLKPNMVTAGQSAKKNTPEEIALATVQALRRTVPAAVTGVTFLSGGQSEEEATVNLSAINNVPLIRPWALTFSYGRALQASVLRAWAGKKENIAAGQNELLKRAKANGDAAQGKYVAGSAGAGSGSLFVANHAY\",\\n  \"organism\": {\\n    \"id\": \"organism0\",\\n    \"name\": \"Drosophila melanogaster\",\\n    \"taxonomy_id\": \"taxon:7227\",\\n    \"domain\": \"Eukaryota\",\\n    \"kingdom\": \"Metazoa\",\\n    \"phylum\": \"Arthropoda\",\\n    \"tax_class\": \"Insecta\",\\n    \"order\": \"Diptera\",\\n    \"family\": \"Drosophilidae\",\\n    \"genus\": \"Drosophila\",\\n    \"species\": \"melanogaster\"\\n  },\\n  \"regions\": [\\n    {\\n      \"id\": \"proteinregion0\",\\n      \"name\": \"Glycolytic\",\\n      \"spans\": [\\n        {\\n          \"id\": \"span0\",\\n          \"start\": 14,\\n          \"end\": 361\\n        }\\n      ],\\n      \"note\": \"Fructose-bisphosphate aldolase class-I; pfam00274\",\\n      \"cross_reference\": \"CDD:425574\"\\n    }\\n  ],\\n  \"sites\": [\\n    {\\n      \"id\": \"site0\",\\n      \"name\": \"active\",\\n      \"type\": \"active\",\\n      \"positions\": [\\n        33,\\n        34,\\n        35,\\n        38,\\n        107,\\n        146,\\n        148,\\n        187,\\n        229,\\n        269,\\n        270,\\n        271,\\n        299,\\n        301,\\n        302\\n      ],\\n      \"cross_ref\": \"CDD:188635\"\\n    },\\n    {\\n      \"id\": \"site1\",\\n      \"name\": \"intersubunit interface [polypeptide binding]\",\\n      \"type\": \"unannotated\",\\n      \"positions\": [\\n        110,\\n        161,\\n        164,\\n        165,\\n        168,\\n        172,\\n        175,\\n        203,\\n        207,\\n        210,\\n        217,\\n        218,\\n        220,\\n        224,\\n        256,\\n        257,\\n        259\\n      ],\\n      \"cross_ref\": \"CDD:188635\"\\n    },\\n    {\\n      \"id\": \"site2\",\\n      \"name\": \"catalytic residue [active]\",\\n      \"type\": \"active\",\\n      \"positions\": [\\n        229\\n      ],\\n      \"cross_ref\": \"CDD:188635\"\\n    }\\n  ],\\n  \"coding_sequence_ref\": {\\n    \"id\": \"NM_001300612.1\",\\n    \"spans\": [\\n      {\\n        \"id\": \"span1\",\\n        \"start\": 278,\\n        \"end\": 1363\\n      }\\n    ],\\n    \"type\": \"coding sequence\"\\n  },\\n  \"ec_number\": \"4.1.2.13\",\\n  \"mol_weight\": 38916.0\\n}'"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ald1.json()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 8,
@@ -66,6 +94,44 @@
    "source": [
     "## BLASTP"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'TaxId': '9606', 'ScientificName': 'Homo sapiens', 'OtherNames': {'Misnomer': [], 'CommonName': [], 'Synonym': [], 'Misspelling': [], 'EquivalentName': [], 'Anamorph': [], 'GenbankAnamorph': [], 'Name': [{'ClassCDE': 'authority', 'DispName': 'Homo sapiens Linnaeus, 1758'}, {'ClassCDE': 'misspelling', 'DispName': 'Home sapiens'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sampiens'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapeins'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapian'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapians'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapien'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapience'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapiense'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapients'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo sapines'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo spaiens'}, {'ClassCDE': 'misspelling', 'DispName': 'Homo spiens'}, {'ClassCDE': 'misspelling', 'DispName': 'Humo sapiens'}], 'Teleomorph': [], 'GenbankSynonym': [], 'Inpart': [], 'Acronym': [], 'Includes': [], 'GenbankCommonName': 'human'}, 'ParentTaxId': '9605', 'Rank': 'species', 'Division': 'Primates', 'GeneticCode': {'GCId': '1', 'GCName': 'Standard'}, 'MitoGeneticCode': {'MGCId': '2', 'MGCName': 'Vertebrate Mitochondrial'}, 'Lineage': 'cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo', 'LineageEx': [{'TaxId': '131567', 'ScientificName': 'cellular organisms', 'Rank': 'no rank'}, {'TaxId': '2759', 'ScientificName': 'Eukaryota', 'Rank': 'superkingdom'}, {'TaxId': '33154', 'ScientificName': 'Opisthokonta', 'Rank': 'clade'}, {'TaxId': '33208', 'ScientificName': 'Metazoa', 'Rank': 'kingdom'}, {'TaxId': '6072', 'ScientificName': 'Eumetazoa', 'Rank': 'clade'}, {'TaxId': '33213', 'ScientificName': 'Bilateria', 'Rank': 'clade'}, {'TaxId': '33511', 'ScientificName': 'Deuterostomia', 'Rank': 'clade'}, {'TaxId': '7711', 'ScientificName': 'Chordata', 'Rank': 'phylum'}, {'TaxId': '89593', 'ScientificName': 'Craniata', 'Rank': 'subphylum'}, {'TaxId': '7742', 'ScientificName': 'Vertebrata', 'Rank': 'clade'}, {'TaxId': '7776', 'ScientificName': 'Gnathostomata', 'Rank': 'clade'}, {'TaxId': '117570', 'ScientificName': 'Teleostomi', 'Rank': 'clade'}, {'TaxId': '117571', 'ScientificName': 'Euteleostomi', 'Rank': 'clade'}, {'TaxId': '8287', 'ScientificName': 'Sarcopterygii', 'Rank': 'superclass'}, {'TaxId': '1338369', 'ScientificName': 'Dipnotetrapodomorpha', 'Rank': 'clade'}, {'TaxId': '32523', 'ScientificName': 'Tetrapoda', 'Rank': 'clade'}, {'TaxId': '32524', 'ScientificName': 'Amniota', 'Rank': 'clade'}, {'TaxId': '40674', 'ScientificName': 'Mammalia', 'Rank': 'class'}, {'TaxId': '32525', 'ScientificName': 'Theria', 'Rank': 'clade'}, {'TaxId': '9347', 'ScientificName': 'Eutheria', 'Rank': 'clade'}, {'TaxId': '1437010', 'ScientificName': 'Boreoeutheria', 'Rank': 'clade'}, {'TaxId': '314146', 'ScientificName': 'Euarchontoglires', 'Rank': 'superorder'}, {'TaxId': '9443', 'ScientificName': 'Primates', 'Rank': 'order'}, {'TaxId': '376913', 'ScientificName': 'Haplorrhini', 'Rank': 'suborder'}, {'TaxId': '314293', 'ScientificName': 'Simiiformes', 'Rank': 'infraorder'}, {'TaxId': '9526', 'ScientificName': 'Catarrhini', 'Rank': 'parvorder'}, {'TaxId': '314295', 'ScientificName': 'Hominoidea', 'Rank': 'superfamily'}, {'TaxId': '9604', 'ScientificName': 'Hominidae', 'Rank': 'family'}, {'TaxId': '207598', 'ScientificName': 'Homininae', 'Rank': 'subfamily'}, {'TaxId': '9605', 'ScientificName': 'Homo', 'Rank': 'genus'}], 'CreateDate': '1995/02/27 09:24:00', 'UpdateDate': '2021/09/24 13:17:40', 'PubDate': '1992/05/26 01:00:00'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "from Bio import Entrez\n",
+    "from numpy import rec\n",
+    "\n",
+    "# Always provide your email address to NCBI when using the Entrez API\n",
+    "Entrez.email = \"your.email@example.com\"\n",
+    "\n",
+    "\n",
+    "def get_taxonomy(tax_id):\n",
+    "    handle = Entrez.efetch(db=\"taxonomy\", id=str(tax_id), retmode=\"xml\")\n",
+    "    records = Entrez.read(handle)\n",
+    "\n",
+    "    # Close the handle after reading the data\n",
+    "    handle.close()\n",
+    "\n",
+    "    # Process and return the taxonomy information\n",
+    "    return records[0]\n",
+    "\n",
+    "\n",
+    "# Example usage\n",
+    "tax_id = \"9606\"  # Taxonomy ID for Homo sapiens\n",
+    "taxonomy_info = get_taxonomy(tax_id)\n",
+    "print(taxonomy_info)"
+   ]
   }
  ],
  "metadata": {
@@ -84,7 +150,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,