In [1]:
%pylab inline
import requests
Populating the interactive namespace from numpy and matplotlib
In [25]:
base_url = 'http://www.ebi.ac.uk/ena/data/search'
SRP = 'ERP006990'
results = requests.get(base_url, params=dict([("query", SRP), ("result", "read_study"), ("display", "xml")]))
In [27]:
results.text
Out[27]:
'<?xml version="1.0" encoding="UTF-8"?>\n<ROOT request="query=ERP006990&result=read_study&display=xml">\n<STUDY accession="ERP006990" alias="E-MTAB-2941" broker_name="ArrayExpress" center_name="Department of Molecular Neuroscience, UCL Institute of Neurology">\n <IDENTIFIERS>\n <PRIMARY_ID>ERP006990</PRIMARY_ID>\n <SECONDARY_ID>PRJEB7282</SECONDARY_ID>\n <SUBMITTER_ID namespace="Department of Molecular Neuroscience, UCL Institute of Neurology">E-MTAB-2941</SUBMITTER_ID>\n </IDENTIFIERS>\n <DESCRIPTOR>\n <STUDY_TITLE>Analysis of ribosomal occupancy with ribosome profiling.</STUDY_TITLE>\n <STUDY_TYPE existing_study_type="Other"/>\n <STUDY_ABSTRACT>Ribosome profiling was prepared in parallel with RNA-seq, using the same protocol for cDNA library preparation.</STUDY_ABSTRACT>\n <CENTER_PROJECT_NAME>Analysis of ribosomal occupancy with ribosome profiling.</CENTER_PROJECT_NAME>\n <STUDY_DESCRIPTION>Ribosome profiling was prepared in parallel with RNA-seq, using the same protocol for cDNA library preparation.</STUDY_DESCRIPTION>\n </DESCRIPTOR>\n <STUDY_LINKS>\n <STUDY_LINK>\n <URL_LINK>\n <LABEL>E-MTAB-2941 in ArrayExpress</LABEL>\n <URL>http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2941</URL>\n </URL_LINK>\n </STUDY_LINK>\n <STUDY_LINK>\n <XREF_LINK>\n <DB>ENA-SAMPLE</DB>\n <ID>ERS543983-ERS543985</ID>\n </XREF_LINK>\n </STUDY_LINK>\n <STUDY_LINK>\n <XREF_LINK>\n <DB>ENA-EXPERIMENT</DB>\n <ID>ERX561998-ERX562000</ID>\n </XREF_LINK>\n </STUDY_LINK>\n <STUDY_LINK>\n <XREF_LINK>\n <DB>ENA-RUN</DB>\n <ID>ERR605044-ERR605046</ID>\n </XREF_LINK>\n </STUDY_LINK>\n <STUDY_LINK>\n <XREF_LINK>\n <DB>ENA-SUBMISSION</DB>\n <ID>ERA358123</ID>\n </XREF_LINK>\n </STUDY_LINK>\n <STUDY_LINK>\n <XREF_LINK>\n <DB>ENA-FASTQ-FILES</DB>\n <ID><![CDATA[http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=ERP006990&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>\n </XREF_LINK>\n </STUDY_LINK>\n <STUDY_LINK>\n <XREF_LINK>\n <DB>ENA-SUBMITTED-FILES</DB>\n <ID><![CDATA[http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=ERP006990&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>\n </XREF_LINK>\n </STUDY_LINK>\n </STUDY_LINKS>\n <STUDY_ATTRIBUTES>\n <STUDY_ATTRIBUTE>\n <TAG>ENA-SPOT-COUNT</TAG>\n <VALUE>482857141</VALUE>\n </STUDY_ATTRIBUTE>\n <STUDY_ATTRIBUTE>\n <TAG>ENA-BASE-COUNT</TAG>\n <VALUE>24142857050</VALUE>\n </STUDY_ATTRIBUTE>\n <STUDY_ATTRIBUTE>\n <TAG>ENA-FIRST-PUBLIC</TAG>\n <VALUE>2015-03-01</VALUE>\n </STUDY_ATTRIBUTE>\n <STUDY_ATTRIBUTE>\n <TAG>ENA-LAST-UPDATE</TAG>\n <VALUE>2014-09-16</VALUE>\n </STUDY_ATTRIBUTE>\n <STUDY_ATTRIBUTE>\n <TAG>ArrayExpress</TAG>\n <VALUE>E-MTAB-2941</VALUE>\n </STUDY_ATTRIBUTE>\n </STUDY_ATTRIBUTES>\n</STUDY>\n</ROOT>'
In [22]:
url = "https://www.ebi.ac.uk/ena/data/warehouse/search?query=%22geo_circ%28-0.587%2C-90.5713%2C170%29%22&result=sequence_release&display=text&download=gzip"
results = requests.get(url)
results.json()
---------------------------------------------------------------------------
JSONDecodeError Traceback (most recent call last)
<ipython-input-22-158813dddb1f> in <module>
1 url = "https://www.ebi.ac.uk/ena/data/warehouse/search?query=%22geo_circ%28-0.587%2C-90.5713%2C170%29%22&result=sequence_release&display=text&download=gzip"
2 results = requests.get(url)
----> 3 results.json()
~/anaconda3/lib/python3.7/site-packages/requests/models.py in json(self, **kwargs)
895 # used.
896 pass
--> 897 return complexjson.loads(self.text, **kwargs)
898
899 @property
~/anaconda3/lib/python3.7/json/__init__.py in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
346 parse_int is None and parse_float is None and
347 parse_constant is None and object_pairs_hook is None and not kw):
--> 348 return _default_decoder.decode(s)
349 if cls is None:
350 cls = JSONDecoder
~/anaconda3/lib/python3.7/json/decoder.py in decode(self, s, _w)
335
336 """
--> 337 obj, end = self.raw_decode(s, idx=_w(s, 0).end())
338 end = _w(s, end).end()
339 if end != len(s):
~/anaconda3/lib/python3.7/json/decoder.py in raw_decode(self, s, idx)
353 obj, end = self.scan_once(s, idx)
354 except StopIteration as err:
--> 355 raise JSONDecodeError("Expecting value", s, err.value) from None
356 return obj, end
JSONDecodeError: Expecting value: line 1 column 1 (char 0)
In [19]:
results.url
Out[19]:
'https://www.ebi.ac.uk/ena/data/search?query=ERP006990&result=read_experiment'
In [20]:
results.text
Out[20]:
'<!doctype html>\r\n<html class="no-js" lang="en">\r\n<head>\r\n <meta charset="utf-8">\r\n\r\n <!-- Use the .htaccess and remove these lines to avoid edge case issues.\r\n More info: h5bp.com/b/378 -->\r\n <!-- <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"> --> <!-- Not yet implemented -->\r\n\r\n <meta name="description" content="EMBL-EBI"><!-- Describe what this page is about -->\r\n <meta name="keywords" content="bioinformatics, europe, institute"><!-- A few keywords that relate to the content of THIS PAGE (not the whol project) -->\r\n <meta name="author" content="EMBL-EBI"><!-- Your [project-name] here -->\r\n\r\n <!-- Mobile viewport optimized: j.mp/bplateviewport -->\r\n <meta name="viewport" content="width=device-width,initial-scale=1">\r\n\r\n <!-- Place favicon.ico and apple-touch-icon.png in the root directory: mathiasbynens.be/notes/touch-icons -->\r\n\r\n <!-- CSS: implied media=all -->\r\n <!-- CSS concatenated and minified via ant build script-->\r\n\r\n <!-- you can replace this with [projectname]-colours.css. See http://frontier.ebi.ac.uk/web/style/colour for details of how to do this -->\r\n <!-- also inform ES so we can host your colour palette file -->\r\n <link rel="stylesheet" href="//www.ebi.ac.uk/web_guidelines/css/compliance/develop/embl-petrol-colours.css" type="text/css" media="screen">\r\n\r\n <!-- for production the above can be replaced with -->\r\n <link rel="stylesheet" href="//www.ebi.ac.uk/web_guidelines/css/compliance/mini/ebi-fluid-embl.css">\r\n\r\n <style type="text/css">\r\n\t #elixir-ribbon h5 {\r\n\t\t display: inline;\r\n\t\t padding: 0 !important;\r\n\t }\r\n\t #elixir-ribbon {\r\n\t\t padding-bottom: 0.3rem;\r\n\t }\r\n #cookie-banner {\r\n display: none;\r\n }\r\n /* You have the option of setting a maximum width for your page, and making sure everything is centered */\r\n /* body { max-width: 1600px; margin: 0 auto; } */\r\n </style>\r\n\r\n\r\n\r\n <!-- All JavaScript at the bottom, except for Modernizr / Respond.\r\n Modernizr enables HTML5 elements & feature detects; Respond is a polyfill for min/max-width CSS3 Media Queries\r\n For optimal performance, use a custom Modernizr build: www.modernizr.com/download/ -->\r\n\r\n <!-- Full build -->\r\n\t<script type="text/javascript" src="https://java.com/js/dtjava.js"></script>\r\n\t<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>\r\n\t<script type="text/javascript">\r\n function deployIt(jnlpurl) {\r\n dtjava.launch(\r\n {\r\n \turl: jnlpurl,\r\n \tparams: {\r\n \t}\r\n },\r\n {\r\n \tjvm: "1.8.0+",\r\n \tjavafx: "2.2+"\r\n }\r\n );\r\n return false;\r\n }\r\n\r\n </script>\r\n \t<!-- custom build (lacks most of the "advanced" HTML5 support -->\r\n \t<script src="//www.ebi.ac.uk/web_guidelines/js/libs/modernizr.custom.49274.js"></script>\r\n\r\n\t<script type="text/javascript">\r\n\t\tvar context = window.location.href.substring(0, window.location.href.indexOf("data") + 5) + "ena_indexer.nocache.js"\r\n\t\tdocument.write(\'<script type="text/javascript" src="\'+context+\'"></script\')\r\n\r\n\t\tfunction textSearch() {\r\n\t\t\tdocument.getElementById("default-search").style.display = "inline";\r\n\t\t\tdocument.getElementById("upload-file").style.display = "none";\r\n\t\t\treturn false;\r\n\t\t}\r\n\r\n\t\tfunction uploadFile() {\r\n\t\t\tdocument.getElementById("default-search").style.display = "none";\r\n\t\t\tdocument.getElementById("upload-file").style.display = "inline";\r\n\t\t\treturn false;\r\n\t\t}\r\n\r\n\t\tfunction addQueryToTextBox() {\r\n\t\t\tvar query = \'query\';\r\n\t\t\tif (window.location.href.indexOf("warehouse/search") < 0 && window.location.href.indexOf("query") > -1)\r\n\t\t\t\tdocument.getElementById("local-searchbox").value = decodeURIComponent((new RegExp(\'[?|&]\' + query + \'=\' + \'([^&;]+?)(&|#|;|$)\').exec(location.search)||[,""])[1].replace(/\\+/g, \'%20\'));\r\n\t\t}\r\n\t</script>\r\n</head>\r\n\r\n<body class="level2 gwt-app">\r\n\t<div id="wrapper" class="container_24">\r\n\t 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alpha" id="local-title" align="center">\r\n\t\t\t\t\t<h1>\r\n\t\t\t\t\t\t<a href="//www.ebi.ac.uk/ena" title="Back to ENA">\r\n\t\t\t\t\t\t\t<img src="//www.ebi.ac.uk/web_guidelines/images/logos/ena/ENA-logo.png" alt="European Nucleotide Archive" width="288" height="82" style="border: 0px;"/>\r\n\t\t\t\t\t\t</a>\r\n\t\t\t\t\t</h1>\r\n\t\t\t\t</div>\r\n\r\n\t\t\t\t<div class="grid_12 omega">\r\n\t\t\t\t\t<form id="local-search" name="local-search" action="/ena/data/search" method="get">\r\n\t\t\t\t\t\t<fieldset>\r\n\t\t\t\t\t\t\t<div class="left">\r\n\t\t\t\t\t\t\t\t<label>\r\n\t\t\t\t\t\t\t\t\t<input type="text" name="query" id="local-searchbox">\r\n\t\t\t\t\t\t\t <script>\r\n\t\t\t\t\t\t\t \taddQueryToTextBox();\r\n\t\t\t\t\t\t\t </script>\r\n\t\t\t\t\t\t\t\t</label>\r\n\t\t\t\t\t\t\t\t<span class="examples">Examples: <a href="/ena/data/search?query=BN000065" title="ENA accession (e.g. BN000065)">BN000065</a>, <a href="/ena/data/search?query=histone" title="Free text search (e.g. 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Remember: you\'ll need a class of "last" for whichever one will show up last... For example: -->\r\n\t\t\t\t\t\t<!--\r\n\t\t\t\t\t\t<li class="functional last"><a href="#" class="icon icon-generic" data-icon="\\">Feedback</a></li>\r\n\t\t\t\t\t\t -->\r\n\t\t\t\t\t</ul>\r\n\t\t\t\t</nav>\r\n\t\t </div>\r\n\t </header>\r\n\r\n\t\t<div id="content" role="main" class="grid_24 clearfix">\r\n\t\t\t<!--<div id="enaTwitterNewsContents" class="grid_24"></div>-->\r\n\t\t\t<div id="twitterAndFeedback" class="grid_24" style="display: none">\r\n\t\t\t\t<div id="enaTwitterNewsContents">\r\n\t\t\t\t</div>\r\n\t\t\t</div>\r\n\t\t\t<div id="enaSearchOptions" class="grid_24"></div>\r\n\t\t\t<div id="enaSequenceSearch" class="grid_24"></div>\r\n\t\t\t<div id="enaIndexerContents" class="grid_24"></div>\r\n\t\t\t<div id="enaXrefSearch" class="grid_24"></div>\r\n\t\t\t<div id="enaTraceSearch" class="grid_24"></div>\r\n\t\t\t<div id="enaDataSearch" class="grid_24"></div>\r\n\t\t</div>\r\n\r\n\r\n\t<footer>\r\n\r\n\t\t\t<div id="global-footer" class="grid_24">\r\n\t\t\t\t<div id="elixir-banner" data-color="grey" data-name="ENA" data-use-cdr-logo="true" data-description=" "\r\n\t\t\t\t\t data-use-basic-styles="true" data-more-information-link="https://www.elixir-europe.org/platforms/data/core-data-resources"></div>\r\n\t\t\t\t<script defer="defer" src="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/js/elixirBanner.js"></script>\r\n\r\n\t\t\t\t<nav id="global-nav-expanded">\r\n\t\t\t\t\t<div class="grid_4 alpha">\r\n\t\t\t\t\t\t<h3 class="embl-ebi"><a href="//www.ebi.ac.uk/" title="EMBL-EBI">EMBL-EBI</a></h3>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t\t<div class="grid_4">\r\n\t\t\t\t\t\t<h3 class="services"><a href="//www.ebi.ac.uk/services">Services</a></h3>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t\t<div class="grid_4">\r\n\t\t\t\t\t\t<h3 class="research"><a href="//www.ebi.ac.uk/research">Research</a></h3>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t\t<div class="grid_4">\r\n\t\t\t\t\t\t<h3 class="training"><a href="//www.ebi.ac.uk/training">Training</a></h3>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t\t<div class="grid_4">\r\n\t\t\t\t\t\t<h3 class="industry"><a href="//www.ebi.ac.uk/industry">Industry</a></h3>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t\t<div class="grid_4 omega">\r\n\t\t\t\t\t\t<h3 class="about"><a href="//www.ebi.ac.uk/about">About us</a></h3>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t</nav>\r\n\r\n\t\t\t\t<section id="ebi-footer-meta">\r\n\t\t\t\t\t<p class="address">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK +44 (0)1223 49 44 44</p>\r\n\t\t\t\t\t<p class="legal">Copyright © EMBL-EBI 2013 | EBI is an outstation of the <a href="http://www.embl.org">European Molecular Biology Laboratory</a> | <a href="/about/privacy">Privacy</a> | <a href="/about/cookies">Cookies</a> | <a href="/about/terms-of-use">Terms of use</a></p>\r\n\t\t\t\t</section>\r\n\t\t\t</div>\r\n\r\n\t\t</footer>\r\n\t</div>\r\n\r\n\t<script type="text/javascript">\r\n var localFrameworkVersion = \'compliance\'; // 1.1 or 1.2 or compliance or other\r\n // if you select compliance or other we will add some helpful\r\n // CSS styling, but you may need to add some CSS yourself\r\n var newDataProtectionNotificationBanner = document.createElement(\'script\');\r\n newDataProtectionNotificationBanner.src = \'https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/js/ebi-global-includes/script/5_ebiFrameworkNotificationBanner.js?legacyRequest=\'+localFrameworkVersion;\r\n document.head.appendChild(newDataProtectionNotificationBanner);\r\n newDataProtectionNotificationBanner.onload = function() {\r\n ebiFrameworkRunDataProtectionBanner(); // invoke the banner\r\n };\r\n\t</script>\r\n\t<script defer="defer" src="//www.ebi.ac.uk/web_guidelines/js/foot.js"></script>\r\n\t<script type="text/javascript">\r\n\t\t/*\r\n (function () {\r\n\t\t\tvar url = window.location.href;\r\n\t\t\tvar prefix = \'https://www.ebi.ac.uk/ena/browser/\';\r\n\t\t\tvar line = "The new ENA Browser is now live, with improved options for searching & downloading data!<br/>";\r\n\t\t\tvar htmlDivElement = document.createElement("div");\r\n\t\t\thtmlDivElement.style.background = \'#85e085\';\r\n\t\t\thtmlDivElement.style.border = "1px solid black"\r\n\t\t\thtmlDivElement.style.borderRadius = "10px";\r\n\t\t\thtmlDivElement.style.margin = "0px 5px 0px 5px";\r\n\t\t\thtmlDivElement.style.padding = "5px 10px 5px 10px";\r\n\t\t\tif (url.indexOf("/data/view/") > 0) {\r\n\t\t\t\t$.ajax({\r\n url: prefix + \'api/summary/\' + url.substr(url.indexOf("view") + 5),\r\n success: function (result) {\r\n if (result && result.total === 0) {\r\n sendErrorEmail(url);\r\n } else {\r\n var newUrl = prefix + \'view/\' + url.substr(url.indexOf("view") + 5);\r\n htmlDivElement.innerHTML = line +\r\n "Please go to <a href=\'" + newUrl + "\' + target=\'_blank\'>" + newUrl + "</a> " +\r\n "to see this record there.";\r\n document.getElementById("content").prepend(htmlDivElement);\r\n }\r\n },\r\n\t\t\t\t\terror: function(result){\r\n sendErrorEmail(url);\r\n\t\t\t\t\t}\r\n\t\t\t\t});\r\n\r\n\t\t\t} else {\r\n\t\t\t\tif (url.indexOf("/data/sequence/search") > 0) {\r\n\t\t\t\t\tvar newUrl = prefix + \'sequence-search\';\r\n\t\t\t\t\thtmlDivElement.innerHTML = line +\r\n\t\t\t\t\t\t\t"Please go to <a href=\'" + newUrl + "\' + target=\'_blank\'>" + newUrl + "</a> " +\r\n\t\t\t\t\t\t\t"to perform this search there.";\r\n\t\t\t\t} else if (url.indexOf("/data/xref/search") > 0) {\r\n\t\t\t\t\tvar newUrl = prefix + \'xref\';\r\n\t\t\t\t\thtmlDivElement.innerHTML = line +\r\n\t\t\t\t\t\t\t"Please go to <a href=\'" + newUrl + "\' + target=\'_blank\'>" + newUrl + "</a> " +\r\n\t\t\t\t\t\t\t"to perform this search there.";\r\n\t\t\t\t} else if (url.indexOf("/data/warehouse/search") > 0) {\r\n\t\t\t\t\tvar newUrl = prefix + \'advanced-search\';\r\n\t\t\t\t\thtmlDivElement.innerHTML = line +\r\n\t\t\t\t\t\t\t"Please go to <a href=\'" + newUrl + "\' + target=\'_blank\'>" + newUrl + "</a> " +\r\n\t\t\t\t\t\t\t"to perform this search there.";\r\n\t\t\t\t} else if (url.indexOf("/data/search") > 0) {\r\n\t\t\t\t\tvar newUrl = prefix + \'text-search?\' + url.substr(url.indexOf("/data/search") + 13);\r\n\t\t\t\t\thtmlDivElement.innerHTML = line +\r\n\t\t\t\t\t\t\t"Please go to <a href=\'" + newUrl + "\' + target=\'_blank\'>" + newUrl + "</a> " +\r\n\t\t\t\t\t\t\t"to perform this search there.";\r\n\t\t\t\t}\r\n\t\t\t\tdocument.getElementById("content").prepend(htmlDivElement);\r\n\t\t\t}\r\n })();\r\n\r\n function sendErrorEmail(url) {\r\n var data = new FormData();\r\n data.append("to", "suranj@ebi.ac.uk");\r\n data.append("email", "datasubs@ebi.ac.uk");\r\n data.append("name", "ENA Browser");\r\n data.append("message", \'<a href="\' + url + \'">\' + url + \'</a>\');\r\n data.append("isHtml", "true");\r\n data.append("subject", "New Browser non-loaded records");\r\n $.ajax({\r\n type: "POST",\r\n enctype: \'multipart/form-data\',\r\n url: "https://www.ebi.ac.uk/ena/portal/api/support",\r\n data: data,\r\n processData: false,\r\n contentType: false,\r\n success: function (data) {\r\n console.log(\'success\', data);\r\n },\r\n error: function (e) {\r\n console.log(\'error\', e);\r\n }\r\n });\r\n }\r\n\r\n\t\t */\r\n\t\t\t\t\t</script>\r\n</body>\r\n</html>\r\n'
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