eutils fasta xml

Custom COI BLAST -- downloading FASTA.ipynb

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  "cells": [
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2020-03-31T12:55:13.914098Z",
          "end_time": "2020-03-31T12:55:15.114831Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "import pandas as pd\n\nimport requests\nfrom lxml import objectify\n\nimport time\nfrom tenacity import retry\nfrom tenacity.stop import stop_after_attempt\nfrom tenacity.wait import wait_fixed\n",
      "execution_count": 1,
      "outputs": []
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2020-03-31T12:55:15.116276Z",
          "end_time": "2020-03-31T12:55:15.326057Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "search_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'\nsearch_term = \"coi[Gene] OR cox1[Gene] OR co1[Gene]\"\n\nsearch_params = {'term': search_term,\n                 'db': 'nuccore',\n                 'retmode': 'json',\n                 'retmax': 10,\n                 'idtype':'acc',\n                 'usehistory': 'y'}\n\nr = requests.post(search_url, data=search_params)\nsearch_results = r.json()\nresult_count = int(search_results['esearchresult']['count'])\nsearch_results",
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 2,
          "data": {
            "text/plain": "{'header': {'type': 'esearch', 'version': '0.3'},\n 'esearchresult': {'count': '3542369',\n  'retmax': '10',\n  'retstart': '0',\n  'querykey': '1',\n  'webenv': 'NCID_1_87154153_130.14.18.48_9001_1585659315_335741641_0MetA0_S_MegaStore',\n  'idlist': ['KY430860.2',\n   'KY430858.2',\n   'KY430816.2',\n   'MN317567.1',\n   'NC_046603.1',\n   'NC_046596.1',\n   'NC_046595.1',\n   'NC_046594.1',\n   'NC_046592.1',\n   'NC_046591.1'],\n  'translationset': [],\n  'translationstack': [{'term': 'coi[Gene]',\n    'field': 'Gene',\n    'count': '3270152',\n    'explode': 'N'},\n   {'term': 'cox1[Gene]', 'field': 'Gene', 'count': '221561', 'explode': 'N'},\n   'OR',\n   {'term': 'co1[Gene]', 'field': 'Gene', 'count': '56118', 'explode': 'N'},\n   'OR'],\n  'querytranslation': 'coi[Gene] OR cox1[Gene] OR co1[Gene]'}}"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2020-03-31T12:55:15.327879Z",
          "end_time": "2020-03-31T12:55:15.331651Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "query_key = search_results['esearchresult']['querykey']\nweb_env = search_results['esearchresult']['webenv']\nprint(query_key, web_env)",
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "text": "1 NCID_1_87154153_130.14.18.48_9001_1585659315_335741641_0MetA0_S_MegaStore\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2020-03-31T12:55:15.333739Z",
          "end_time": "2020-03-31T12:55:15.470108Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "efetch = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi\"\nparams = {'db': 'nuccore',\n          'rettype': 'fasta',\n          'retmode': 'xml',\n          'query_key': query_key,\n          'WebEnv': web_env,\n          'retmax':3}\nr = requests.post(efetch, data=params)\nxml_results = objectify.fromstring(r.content)",
      "execution_count": 4,
      "outputs": []
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2020-03-31T12:55:15.472228Z",
          "end_time": "2020-03-31T12:55:15.477416Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "print(objectify.dump(xml_results))",
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "text": "TSeqSet = None [ObjectifiedElement]\n    TSeq = None [ObjectifiedElement]\n        TSeq_seqtype = '' [StringElement]\n          * value = 'nucleotide'\n        TSeq_accver = 'KY430860.2' [StringElement]\n        TSeq_taxid = 696725 [IntElement]\n        TSeq_orgname = 'Hedychrum nobile' [StringElement]\n        TSeq_defline = 'Hedychrum nobile voucher ZFMK-TIS-29687 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial' [StringElement]\n        TSeq_length = 675 [IntElement]\n        TSeq_sequence = 'ATATTATATTTTTTATTTGGAATATGATCAGGAGTTTTAGGTTCTTCATTAAGAATAATTATTCGATTAGAGTTGGGATTTTCAGGTTCATTAATTAAAGATGATCAATTTTATAATAGAGTAATTACAATACATGCATTTGTGATAATTTTTTTTATAGTTATACCTTTTATGATTGGTGGATTTGGAAATTGATTAATTCCTYTAATATTAGGTGCTCCTGATATAGCTTATCCTCGAATAAATAATATAAGGTTTTGATTATTACCTCCATCAATTTTATTTTTATTATTGAGTGGTTTTGTTAGATCGGGTTGTGGGACTGGGTGGACTGTATATCCTCCTCTCTCTTCATTATTAGGTCATTCAGGAATTAGGGTTGATTTAGCAATTTTTTCTTTGCATATTGCTGGGGTTTCGTCAATTATAGGGGCAGTAAATTTTATTTCTACTATTATAAATATACGTAGATTTTCATTAAAGATAGATCAATTAACTTTATTAACATGGTCAATTATTATTACTGCAATTTTATTATTACTATCTCTTCCAGTTTTAGCTGGTGCAATTACTATATTATTAACTGATCGAAATTTTAATACTTCATTTTTTGATCCTATGGGAGGTGGGGACCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCACCCA' [StringElement]\n    TSeq = None [ObjectifiedElement]\n        TSeq_seqtype = '' [StringElement]\n          * value = 'nucleotide'\n        TSeq_accver = 'KY430858.2' [StringElement]\n        TSeq_taxid = 212593 [IntElement]\n        TSeq_orgname = 'Hedychrum rutilans' [StringElement]\n        TSeq_defline = 'Hedychrum rutilans voucher ZFMK-TIS-29801 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial' [StringElement]\n        TSeq_length = 675 [IntElement]\n        TSeq_sequence = 'ATATTGTATTTTTTGTTTGGGATGTGATCAGGAATTTTAGGAGCATCTTTAAGAATAATTATTCGTTTAGAGTTGGGAAGTTCAGGGTCATTAATTAAAGATGATCAATTTTATAATAGGATTATTACTATACATGCTTTTGTAATGATTTTTTTTATAGTCATACCTTTTATGATTGGTGGATTTGGAAATTGATTAATTCCTTTAATATTAGGTGCTCCTGATATAGCTTATCCTCGAATAAATAATATGAGATTTTGATTATTACCTCCTTCTATTTTATTTTTATTACTTAGAGGATTTGTGAGATCTGGATGTGGAACTGGATGAACTGTTTACCCTCCTTTATCCTCATTACTTGGTCACTCAGGGATGAGGGTTGATTTAGCAATTTTTTCTTTGCATATTGCTGGGGCTTCTTCAATTATAGGTGCTGTAAATTTTATTTCTACAATTATAAATATACGAAGGGTTTCACTAAAAATAGATCAGTTAACATTATTGATTTGATCAATTATAATTACTGCAATTTTATTATTATTATCTCTTCCTGTATTGGCTGGTGCAATTACTATATTACTGACTGATCGAAATTTTAATACTTCATTTTTTGATCCAATAGGAGGGGGTGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCA' [StringElement]\n    TSeq = None [ObjectifiedElement]\n        TSeq_seqtype = '' [StringElement]\n          * value = 'nucleotide'\n        TSeq_accver = 'KY430816.2' [StringElement]\n        TSeq_taxid = 212606 [IntElement]\n        TSeq_orgname = 'Parnopes grandior' [StringElement]\n        TSeq_defline = 'Parnopes grandior voucher ZFMK-TIS-29757 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial' [StringElement]\n        TSeq_length = 444 [IntElement]\n        TSeq_sequence = 'TATCCTCGAATAAATAATATGAGATTTTGACTTTTACCACCTTCTTTATTAATATTGTTATTAAGAAGAATTGTAGGGGGAGGGGTAGGAACAGGGTGAACAGTGTATCCTCCTTTATCATTATTAAGAGGCCACTCAAGAATAAGTGTGGATTTTGGAATTTTTTCTCTTCATATTGCGGGAGTATCTTCTATTATAGGAGCAATTAACTTTATTTCAACAGTTGGGAATATTAAAAGTAAAAGATTAAAAACTGAACAATTAACTTTATTAGTATGATCAATTTTTATTACAGCAATTTTATTACTTTTGTCATTACCAGTTTTGGCAGGAGCTATTACTATATTATTAAGAGATCGAAATTTAAATACTTCATTTTTTGATCCTGTGGGAGGGGGAGATCCAGTTTTATATCAGCATTTATTTTGATTTTTTGGTCATCCT' [StringElement]\n",
          "name": "stdout"
        }
      ]
    },
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      "data": {
        "description": "eutils fasta xml",
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