{ "info": { "author": "Ardan Patwardhan", "author_email": "ardan@ebi.ac.uk", "bugtrack_url": null, "classifiers": [], "description": "==========================\npubmed-author-affiliations\n==========================\nCommand line tool the takes one or a list of Pubmed IDs or DOIs,\nsearches Pubmed for corresponding author affiliations and \noutputs the information to file\n\n\nCommand line options\n--------------------\n-h, --help Show help text\n-i PUBMEDID, --pubmedid PUBMEDID Search for author affiliations for single Pubmed ID\n-d doi, --doi doi Search for author affiliations for a single DOI\n-f file, --infile file File with a list of Pubmed IDs and DOIs (they can be mixed). One entry per line.\n-x format, --format format Output format. Choices=['json' (default),'text']. 'text' option produces tab separated\n table, denormalised in the sense that the pubmed ID/DOI is repeated on multiple rows\n if there are multiple authors with related affiliations.\n\nExample runs\n------------\nPubmed input and JSON output:\n\n.. code-block::\n\n python pubmedAuthorAffiliation.py -i 27863242\n\nOutput:\n\n.. code-block::\n\n {'articleTitle': 'Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.', 'journalTitle': 'Cell', 'authorList': [{'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Shao', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'S'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Murray', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Brown', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'A'}, {'firstName': 'n/a', 'institute': 'University of California', 'lastName': 'Taunton', 'affiliation': 'Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.', 'country': 'USA', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Ramakrishnan', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'V'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Hegde', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: rhegde@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'RS'}], 'pubmedId': '27863242', 'error': False}\n {'articleTitle': 'Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.', 'journalTitle': 'Cell', 'authorList': [{'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Shao', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'S'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Murray', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Brown', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'A'}, {'firstName': 'n/a', 'institute': 'University of California', 'lastName': 'Taunton', 'affiliation': 'Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.', 'country': 'USA', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Ramakrishnan', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'V'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Hegde', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: rhegde@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'RS'}], 'pubmedId': '27863242', 'error': False}\n\nDOI input and text output:\n\n.. code-block::\n\n python pubmedAuthorAffiliation.py -d 10.1016/j.molcel.2016.11.013 -x text\n\nOutput:\n\n.. code-block::\n\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tL\tTafur\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tY\tSadian\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tNA\tHoffmann\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tAJ\tJakobi\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tR\tWetzel\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tWJH\tHagen\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tC\tSachse\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n 27867008\tMolecular cell\tMolecular Structures of Transcribing RNA Polymerase I.\tn/a\tCW\tM\u00fcller\tEuropean Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Electronic address: cmueller@embl.de.\tGermany\tEuropean Molecular Biology Laboratory (EMBL)\n\nInput file with mixed DOI and Pubmed. Text output written to a file:\n\n.. code-block::\n\n python pubmedAuthorAffiliation.py -f emdb-2010.txt -x text > /tmp/out.txt\n\nIn this case unrecognized lines are ignored, e.g.:\n\n.. code-block::\n\n WARNING:root:processList: id not recognized: id\n\n\nCode testing\n------------\nThis will go through lists of selected Pubmed and DOI known to work:\n\n.. code-block::\n\n python test_pubmedAuthorAffiliation.py\n\n\n", "description_content_type": "text/x-rst", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/emdb-empiar/pubmed-author-affiliations", "keywords": "", "license": "Apache 2", "maintainer": "", "maintainer_email": "", "name": "pubmed-author-affiliation", "package_url": "https://pypi.org/project/pubmed-author-affiliation/", "platform": "", "project_url": "https://pypi.org/project/pubmed-author-affiliation/", "project_urls": { "Homepage": "https://github.com/emdb-empiar/pubmed-author-affiliations" }, "release_url": "https://pypi.org/project/pubmed-author-affiliation/0.3/", "requires_dist": null, "requires_python": "", "summary": "Search for author affiliations from Pubmed for a list of Pubmed IDs and DOIs", "version": "0.3" }, "last_serial": 4097664, "releases": { "0.3": [ { "comment_text": "", "digests": { "md5": "656ec6fcadadae4bc17a92939d0e0062", "sha256": "d3c46d00fe0d07286396fdda6ee3bb8c22c6ead639302c6ffcf0f7755069ab94" }, "downloads": -1, "filename": "pubmed_author_affiliation-0.3-py2-none-any.whl", "has_sig": false, "md5_digest": "656ec6fcadadae4bc17a92939d0e0062", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 19434, "upload_time": "2018-07-24T16:47:08", "url": "https://files.pythonhosted.org/packages/62/8a/b8a0d9d815edab7b186821c1139f5f85cfbc5a32d7b5c2da60e1c2f4ea18/pubmed_author_affiliation-0.3-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "0b591373fc04187de9163901f4f339c9", "sha256": "6b58f6574ab5ec0320854c5c69b08431c9b9a33f5cf67610bff9d3145494565f" }, "downloads": -1, "filename": "pubmed-author-affiliation-0.3.tar.gz", "has_sig": false, "md5_digest": "0b591373fc04187de9163901f4f339c9", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 15534, "upload_time": "2018-07-24T16:47:09", "url": "https://files.pythonhosted.org/packages/ec/b2/5f2d5288f3f93441e65ee8c39364254f8f5d323c2732a88f4ee8dbaa270b/pubmed-author-affiliation-0.3.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "656ec6fcadadae4bc17a92939d0e0062", "sha256": "d3c46d00fe0d07286396fdda6ee3bb8c22c6ead639302c6ffcf0f7755069ab94" }, "downloads": -1, "filename": "pubmed_author_affiliation-0.3-py2-none-any.whl", "has_sig": false, "md5_digest": "656ec6fcadadae4bc17a92939d0e0062", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 19434, "upload_time": "2018-07-24T16:47:08", "url": "https://files.pythonhosted.org/packages/62/8a/b8a0d9d815edab7b186821c1139f5f85cfbc5a32d7b5c2da60e1c2f4ea18/pubmed_author_affiliation-0.3-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "0b591373fc04187de9163901f4f339c9", "sha256": "6b58f6574ab5ec0320854c5c69b08431c9b9a33f5cf67610bff9d3145494565f" }, "downloads": -1, "filename": "pubmed-author-affiliation-0.3.tar.gz", "has_sig": false, "md5_digest": "0b591373fc04187de9163901f4f339c9", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 15534, "upload_time": "2018-07-24T16:47:09", "url": "https://files.pythonhosted.org/packages/ec/b2/5f2d5288f3f93441e65ee8c39364254f8f5d323c2732a88f4ee8dbaa270b/pubmed-author-affiliation-0.3.tar.gz" } ] }