677 lines
43 KiB
XML
677 lines
43 KiB
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<div class="res_logo"><h1 class="res_name"><a href="/dbvar/" title="dbVar home">dbVar</a></h1><h2 class="res_tagline">Database of genomic structural variation</h2></div>
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<div class="search"><form method="get" action="/dbvar/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="dbvar" selected="selected">dbVar</option><option value="gap">dbGaP</option><option value="clinvar">ClinVar</option><option value="medgen" class="last">MedGen</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search dbVar" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div><input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="PAFAppLayout" /><input type="hidden" name="p$st" id="p$st" value="dbvar" /><input name="SessionId" id="SessionId" value="CE8B5AF87C7FFCB1_0191SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/dbVar/dbVar@9.7" disabled="disabled" type="hidden" /></form><ul class="inline_list searchlinks"><li>
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<a href="/dbvar/advanced">Advanced</a>
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</li><li>
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<a class="help" href="/dbvar/content/help">Help</a>
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</li></ul></div>
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</div>
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<div class="nav_and_browser">
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<h1 id="use-entrez-and-python-to-search-">Use Entrez and Python to search, retrieve, and parse dbVar records.</h1>
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<h4 id="objectives">Objectives:</h4>
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<h5 id="1-search-dbvar-using-entrez-esea">1. Search dbVar using Entrez eSearch</h5>
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<h5 id="2-retrieve-results-using-esummar">2. Retrieve results using eSummary</h5>
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<h5 id="3-parse-esummary-xml-results-and">3. Parse eSummary XML results and print tab delimited output</h5>
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<pre><code>#### General details on eUtils tools and options along with tutorials and examples
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#### are available on NCBI bookshelf. https://www.ncbi.nlm.nih.gov/books/NBK25499/
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</code></pre>
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<h4 id="first-part-of-python-script">first part of Python script:</h4>
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<pre><code># You should test that your search return results first on the web
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# https://www.ncbi.nlm.nih.gov/dbvar before using them
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# in your python script. Available dbVar search terms are on the help page
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# (https://www.ncbi.nlm.nih.gov/dbvar/content/help/#entrezsearch).
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# For general Entrez help and boolean search see the online book
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# (https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options)
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# This example will make use of these eUtils History Server parameters
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# usehistory, WebEnv, and query_key. It is highly recommended you use them in
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# your pipeline and script.
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# /usehistory=/
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# When usehistory is set to 'y', ESearch will post the UIDs resulting from the
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# search operation onto the History server so that they can be used directly in
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# a subsequent E-utility call. Also, usehistory must be set to 'y' for ESearch
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# to interpret query key values included in term or to accept a WebEnv as input.
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# /WebEnv=/
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# Web environment string returned from a previous ESearch, EPost or ELink call.
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# When provided, ESearch will post the results of the search operation to this
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# pre-existing WebEnv, thereby appending the results to the existing
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# environment. In addition, providing WebEnv allows query keys to be used in
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# term so that previous search sets can be combined or limited. As described
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# above, if WebEnv is used, usehistory must be set to 'y' (ie.
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# esearch.fcgi?db=dbvar&term=asthma&WebEnv=<webenv string>&usehistory=y)
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# /query_key=/
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# Integer query key returned by a previous ESearch, EPost or ELink call. When
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# provided, ESearch will find the intersection of the set specified by query_key
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# and the set retrieved by the query in term (i.e. joins the two with AND). For
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# query_key to function, WebEnv must be assigned an existing WebEnv string and
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# usehistory must be set to 'y'.
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# load python modules
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# May require one time install of biopython and xml2dict.
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from Bio import Entrez
|
||
import xmltodict
|
||
|
||
# initialize some default parameters
|
||
Entrez.email = 'myemail@ncbi.nlm.nih.gov' # provide your email address
|
||
db = 'dbvar' # set search to dbVar database
|
||
paramEutils = { 'usehistory':'Y' } # Use Entrez search history to cache results
|
||
|
||
# generate query to Entrez eSearch
|
||
eSearch = Entrez.esearch(db=db, term='("variant"[Object Type] AND estd214)', **paramEutils)
|
||
|
||
# get eSearch result as dict object
|
||
res = Entrez.read(eSearch)
|
||
|
||
# take a peek of what's in the result (ie. WebEnv, Count, etc.)
|
||
for k in res:
|
||
print (k, "=", res[k])
|
||
|
||
paramEutils['WebEnv'] = res['WebEnv'] #add WebEnv and query_key to eUtils parameters to request esummary using
|
||
paramEutils['query_key'] = res['QueryKey'] #search history (cache results) instead of using IdList
|
||
paramEutils['rettype'] = 'xml' #get report as xml
|
||
paramEutils['retstart'] = 0 #get result starting at 0, top of IdList
|
||
paramEutils['retmax'] = 5 #get next five results
|
||
|
||
# generate request to Entrez eSummary
|
||
result = Entrez.esummary(db=db, **paramEutils)
|
||
# get xml result
|
||
xml = result.read()
|
||
# take a peek at xml
|
||
print(xml)
|
||
</code></pre>
|
||
|
||
|
||
<h4 id="peek-at-xml">peek at xml:</h4>
|
||
|
||
|
||
<pre><code><?xml version="1.0" encoding="UTF-8" ?>
|
||
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary dbvar 20170523//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20170523/esummary_dbvar.dtd">
|
||
<eSummaryResult>
|
||
<DocumentSummarySet status="OK">
|
||
<DbBuild>Build190602-0830.1</DbBuild>
|
||
|
||
<DocumentSummary uid="48583463">
|
||
<OBJ_TYPE>VARIANT</OBJ_TYPE>
|
||
<ST>nstd102</ST>
|
||
<SV>nsv3972446</SV>
|
||
<Study_type></Study_type>
|
||
<Variant_count>0</Variant_count>
|
||
<dbVarPublicationList>
|
||
</dbVarPublicationList>
|
||
<dbVarStudyOrgList>
|
||
</dbVarStudyOrgList>
|
||
<Method_type_weight>Non-BAC</Method_type_weight>
|
||
<Tax_ID>9606</Tax_ID>
|
||
<Organism>human</Organism>
|
||
<dbVarSubmittedAssemblyList>
|
||
</dbVarSubmittedAssemblyList>
|
||
<dbVarRemappedAssemblyList>
|
||
</dbVarRemappedAssemblyList>
|
||
<dbVarPlacementList>
|
||
<dbVarPlacement>
|
||
<Chr>3</Chr>
|
||
<Chr_accession_version>NC_000003.12</Chr_accession_version>
|
||
<Contig_accession_version></Contig_accession_version>
|
||
<Chr_start>37017508</Chr_start>
|
||
<Chr_end>37017509</Chr_end>
|
||
<Chr_inner_start>0</Chr_inner_start>
|
||
<Chr_inner_end>0</Chr_inner_end>
|
||
<Chr_outer_start>0</Chr_outer_start>
|
||
<Chr_outer_end>0</Chr_outer_end>
|
||
<Assembly>GRCh38 (hg38)</Assembly>
|
||
<Assembly_accession>GCF_000001405.26</Assembly_accession>
|
||
<Assembly_tax_ID>9606</Assembly_tax_ID>
|
||
<Placement_type>Submitted genomic</Placement_type>
|
||
</dbVarPlacement>
|
||
<dbVarPlacement>
|
||
<Chr>3</Chr>
|
||
<Chr_accession_version>NC_000003.11</Chr_accession_version>
|
||
<Contig_accession_version></Contig_accession_version>
|
||
<Chr_start>37058999</Chr_start>
|
||
<Chr_end>37059000</Chr_end>
|
||
<Chr_inner_start>0</Chr_inner_start>
|
||
<Chr_inner_end>0</Chr_inner_end>
|
||
<Chr_outer_start>0</Chr_outer_start>
|
||
<Chr_outer_end>0</Chr_outer_end>
|
||
<Assembly>GRCh37.p13</Assembly>
|
||
<Assembly_accession>GCF_000001405.25</Assembly_accession>
|
||
<Assembly_tax_ID>9606</Assembly_tax_ID>
|
||
<Placement_type>Remapped</Placement_type>
|
||
</dbVarPlacement>
|
||
<dbVarPlacement>
|
||
<Chr>3</Chr>
|
||
<Chr_accession_version>NC_000003.10</Chr_accession_version>
|
||
<Contig_accession_version></Contig_accession_version>
|
||
<Chr_start>37034003</Chr_start>
|
||
<Chr_end>37034004</Chr_end>
|
||
<Chr_inner_start>0</Chr_inner_start>
|
||
<Chr_inner_end>0</Chr_inner_end>
|
||
<Chr_outer_start>0</Chr_outer_start>
|
||
<Chr_outer_end>0</Chr_outer_end>
|
||
<Assembly>NCBI36 (hg18)</Assembly>
|
||
<Assembly_accession>GCF_000001405.12</Assembly_accession>
|
||
<Assembly_tax_ID>9606</Assembly_tax_ID>
|
||
<Placement_type>Remapped</Placement_type>
|
||
</dbVarPlacement>
|
||
</dbVarPlacementList>
|
||
<dbVarGeneList>
|
||
<dbVarGene>
|
||
<id>4292</id>
|
||
<name>MLH1</name>
|
||
</dbVarGene>
|
||
<dbVarGene>
|
||
<id>100131713</id>
|
||
<name>RPL29P11</name>
|
||
</dbVarGene>
|
||
</dbVarGeneList>
|
||
<dbVarMethodList>
|
||
<string>Multiple</string>
|
||
</dbVarMethodList>
|
||
<dbVarClinicalSignificanceList>
|
||
<string>Pathogenic</string>
|
||
</dbVarClinicalSignificanceList>
|
||
<dbVarVariantTypeList>
|
||
<string>indel</string>
|
||
</dbVarVariantTypeList>
|
||
<Validation_status_weight>0</Validation_status_weight>
|
||
<Variant_call_count>1</Variant_call_count>
|
||
<Validation_status></Validation_status>
|
||
</DocumentSummary>
|
||
...
|
||
</code></pre>
|
||
|
||
|
||
<h4 id="second-part-of-python-script">second part of Python script:</h4>
|
||
|
||
|
||
<pre><code>#convert xml to python dict object for convenient parsing
|
||
dsdocs = xmltodict.parse(xml)
|
||
|
||
#get set of dbVar DocumentSummary (dsdocs) and print report for each (ds)
|
||
|
||
for ds in dsdocs ['eSummaryResult']['DocumentSummarySet']['DocumentSummary']:
|
||
for p in ds['dbVarPlacementList']['dbVarPlacement']:
|
||
print (ds['@uid'], ds['ST'], ds['SV'],p['Chr'], p['Chr_start'], p['Chr_end'], p['Chr_inner_start'], p['Chr_inner_end'])
|
||
</code></pre>
|
||
|
||
|
||
<h3 id="output">output:</h3>
|
||
|
||
|
||
<pre><code>Count = 55722
|
||
RetMax = 20
|
||
RetStart = 0
|
||
QueryKey = 1
|
||
WebEnv = NCID_1_77655541_130.14.22.76_9001_1560183999_561741772_0MetA0_S_MegaStore
|
||
IdList = ['48583463', '48583462', '48583461', '48583460', '48583459', '48583458', '48583457', '48583456', '48583455', '48583454', '48583453', '48583452', '48583451', '48583450', '48583449', '48583448', '48583447', '48583446', '48583445', '48583444']
|
||
TranslationSet = []
|
||
TranslationStack = [DictElement({'Term': '"variant"[Object Type]', 'Field': 'Object Type', 'Count': '5535034', 'Explode': 'N'}, attributes={}), DictElement({'Term': 'nstd102[All Fields]', 'Field': 'All Fields', 'Count': '55723', 'Explode': 'N'}, attributes={}), 'AND', 'GROUP']
|
||
QueryTranslation = "variant"[Object Type] AND nstd102[All Fields]
|
||
48583463 nstd102 nsv3972446 3 37017508 37017509 0 0
|
||
48583463 nstd102 nsv3972446 3 37058999 37059000 0 0
|
||
48583463 nstd102 nsv3972446 3 37034003 37034004 0 0
|
||
48583462 nstd102 nsv3972445 12 6022792 6022793 0 0
|
||
48583462 nstd102 nsv3972445 12 6131958 6131959 0 0
|
||
48583462 nstd102 nsv3972445 12 6002219 6002220 0 0
|
||
48583461 nstd102 nsv3972444 2 219570775 219570776 0 0
|
||
48583461 nstd102 nsv3972444 2 220435497 220435498 0 0
|
||
48583461 nstd102 nsv3972444 2 220143741 220143742 0 0
|
||
48583460 nstd102 nsv3972443 1 109610052 109610058 0 0
|
||
48583460 nstd102 nsv3972443 1 110152674 110152680 0 0
|
||
48583460 nstd102 nsv3972443 1 109954197 109954203 0 0
|
||
48583459 nstd102 nsv3972442 9 35092494 35092495 0 0
|
||
48583459 nstd102 nsv3972442 9 35092491 35092492 0 0
|
||
48583459 nstd102 nsv3972442 9 35082491 35082492 0 0
|
||
</code></pre>
|
||
</div>
|
||
<!--/.col1-->
|
||
<div class="col2">
|
||
|
||
</div>
|
||
<!--/.col2-->
|
||
<div class="col3">
|
||
|
||
</div>
|
||
<!--/.col3-->
|
||
<div class="col4">
|
||
|
||
</div>
|
||
<!--/.col4-->
|
||
<div class="col5">
|
||
|
||
</div>
|
||
<div class="col6">
|
||
|
||
</div>
|
||
<div class="col7">
|
||
|
||
</div>
|
||
<div class="col8">
|
||
|
||
</div>
|
||
<div class="col9">
|
||
|
||
</div>
|
||
</div><!--/.content-->
|
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</div><!--/.container-->
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<div class="breadcrumbs">You are here:
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<noscript><img alt="" src="/stat?jsdisabled=true&ncbi_app=dbvar&ncbi_db=&ncbi_pdid=static&ncbi_phid=CE8CD9457D201C210000000000500046" /></noscript>
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