[Biopython] Biopython error

[Téletchéa Stéphane]

Le 23/08/2016 à 13:42, Téletchéa Stéphane a écrit :
>
> Not sure if this is related, but I have been warned that pubmed will 
> change all of its
> requests to https by the end of september:
> https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/

By the way, this means biopython will need some update, some links are 
for documentation, but others are direct links ...

Since a new release is in under preparation, here is my small findings 
using a simple grep (biopython (1.65)):


grep -Ri '\.ncbi.nlm' *|grep -v pyc
Bio/Geo/__init__.py:http://www.ncbi.nlm.nih.gov/geo/
Bio/Geo/Record.py:See http://www.ncbi.nlm.nih.gov/geo/
Bio/Phylo/_cdao_owl.py:        <rdfs:comment>drawing from seqloc 
categories from NCBI at 
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on</rdfs:comment>
Bio/SearchIO/BlastIO/__init__.py:  - Web interface: 
http://blast.ncbi.nlm.nih.gov/
Bio/SearchIO/BlastIO/__init__.py:  - User guide: 
http://www.ncbi.nlm.nih.gov/books/NBK1762/
Bio/SearchIO/BlastIO/__init__.py:http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd
Bio/SearchIO/BlastIO/blast_xml.py:# for more info: 
http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd
Bio/SearchIO/BlastIO/blast_xml.py: 
'"http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n')
Bio/Blast/NCBIWWW.py:http://blast.ncbi.nlm.nih.gov/
Bio/Blast/NCBIWWW.py: http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
Bio/Blast/NCBIWWW.py:    # Parameters taken from 
http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
Bio/Blast/NCBIWWW.py:    # Additional parameters are taken from 
http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
Bio/Blast/NCBIWWW.py:    request = 
_Request("http://blast.ncbi.nlm.nih.gov/Blast.cgi",
Bio/Blast/NCBIWWW.py:    # Parameters taken from 
http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
Bio/Blast/NCBIWWW.py:        request = 
_Request("http://blast.ncbi.nlm.nih.gov/Blast.cgi",
Bio/Blast/NCBIXML.py:ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd
Bio/SwissProt/__init__.py: (http://www.ncbi.nlm.nih.gov/Taxonomy/)
Bio/SeqIO/FastaIO.py:    # 
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans
Bio/SeqIO/SffIO.py:http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats
Bio/SeqIO/InsdcIO.py:http://www.ncbi.nlm.nih.gov/Genbank/
Bio/GenBank/Scanner.py:http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
Bio/codonalign/codonseq.py:    .. _`Nei and Gojobori (1986)`: 
http://www.ncbi.nlm.nih.gov/pubmed/3444411
Bio/codonalign/codonseq.py:    .. _`Li et al. (1985)`: 
http://www.ncbi.nlm.nih.gov/pubmed/3916709
Bio/Entrez/__init__.py:http://www.ncbi.nlm.nih.gov/Entrez/
Bio/Entrez/__init__.py:http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi'
Bio/Entrez/__init__.py: 
http://www.ncbi.nlm.nih.gov/entrez/query/static/espell_help.html
Bio/Entrez/__init__.py:    cgi = 
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi'
Bio/Entrez/DTDs/references.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/pmc-1.dtd:    pmid   - pubmed id (see 
www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed)
Bio/Entrez/DTDs/common.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/common.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/common.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/common.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd: 
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
Bio/Entrez/DTDs/archivecustom-models.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/articlemeta.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/DTDs/articlemeta.ent: www.ncbi.nlm.nih.gov/entrez/
Bio/Entrez/Parser.py:                source = 
"http://www.ncbi.nlm.nih.gov/dtd/"

Best,

Stéphane

-- 
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org