Update documentation for NCBIWWW.py (#4792)

NCBI no longer supports cloud service providers

Bio/Blast/NCBIWWW.py

@@ -94,22 +94,16 @@ def qblast(
     username="blast",
     password=None,
 ):
-    """BLAST search using NCBI's QBLAST server or a cloud service provider.
+    """BLAST search using NCBI's QBLAST server.
 
     Supports all parameters of the old qblast API for Put and Get.
 
     Please note that NCBI uses the new Common URL API for BLAST searches
-    on the internet (http://ncbi.github.io/blast-cloud/dev/api.html). Thus,
-    some of the parameters used by this function are not (or are no longer)
+    on the internet (https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html).
+    Thus, some of the parameters used by this function are not (or are no longer)
     officially supported by NCBI. Although they are still functioning, this
     may change in the future.
 
-    The Common URL API (http://ncbi.github.io/blast-cloud/dev/api.html) allows
-    doing BLAST searches on cloud servers. To use this feature, please set
-    ``url_base='http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi'``
-    and ``format_object='Alignment'``. For more details, please see
-    https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
-
     Some useful parameters:
 
      - program        blastn, blastp, blastx, tblastn, or tblastx (lower case)
@@ -122,7 +116,7 @@ def qblast(
      - matrix_name    Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
      - filter         "none" turns off filtering.  Default no filtering
      - format_type    "HTML", "Text", "ASN.1", or "XML".  Def. "XML".
-     - entrez_query   Entrez query to limit Blast search
+     - entrez_query   Entrez query to limit Blast search - only applies when searching nucleotide BLASTDBs
      - hitlist_size   Number of hits to return. Default 50
      - megablast      TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
      - short_query    TRUE/FALSE whether to adjust the search parameters for a
@@ -133,7 +127,7 @@ def qblast(
 
     This function does no checking of the validity of the parameters
     and passes the values to the server as is.  More help is available at:
-    https://ncbi.github.io/blast-cloud/dev/api.html
+    https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html
 
     """
     programs = ["blastn", "blastp", "blastx", "tblastn", "tblastx"]

Doc/Tutorial/chapter_blast.rst

@@ -90,10 +90,7 @@ which are basically analogous to the different parameters you can set on
 the BLAST web page. We’ll just highlight a few of them here:
 
 -  The argument ``url_base`` sets the base URL for running BLAST over
-   the internet. By default it connects to the NCBI, but one can use
-   this to connect to an instance of NCBI BLAST running in the cloud.
-   Please refer to the documentation for the ``qblast`` function for
-   further details.
+   the internet. By default it connects to the NCBI.
 
 -  The ``qblast`` function can return the BLAST results in various
    formats, which you can choose with the optional ``format_type``