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<div>Then can we move <span>Bio/Blast/NCBIStandalone.py and <span>Bio/ParserSupport.py into Bio.SearchIO ?</span></span></div><div>Or integrate those two modules into Bio.SearchIO.<span>BlastIO.blast_text ?</span></div><div><span>It's confusing to have two deprecated modules at the top level of Bio/*, and remind ourselves each time that actually they should not be removed.</span></div><div><span><br></span></div><div><span>Best,</span></div><div><span>-Michiel<br></span></div></div><div id="yahoo_quoted_3217509906" class="yahoo_quoted">
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On Thursday, November 22, 2018, 7:12:25 PM GMT+9, Peter Cock <p.j.a.cock@googlemail.com> wrote:
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<div><div dir="ltr">So leave the code and its warnings as they are for the time being,<br clear="none">but perhaps stronger wording in the documentation that using<br clear="none">the "blast-text" parser in SearchIO is not encouraged?<br clear="none"><br clear="none">i.e. Add a note here?:<br clear="none"><a shape="rect" href="https://github.com/biopython/biopython/blob/biopython-172/Bio/SearchIO/__init__.py#L189" target="_blank">https://github.com/biopython/biopython/blob/biopython-172/Bio/SearchIO/__init__.py#L189</a><br clear="none"><br clear="none">And a stronger caveat than "Newer versions may not always work" here?:<br clear="none"><a shape="rect" href="https://biopython.org/wiki/SearchIO" target="_blank">https://biopython.org/wiki/SearchIO</a><br clear="none"><br clear="none">Peter<div class="yqt2980261388" id="yqtfd43000"><br clear="none">On Thu, Nov 22, 2018 at 9:59 AM Wibowo Arindrarto <<a shape="rect" ymailto="mailto:bow@bow.web.id" href="mailto:bow@bow.web.id">bow@bow.web.id</a>> wrote:<br clear="none">><br clear="none">> Dear Michiel, Peter, and everyone,<br clear="none">><br clear="none">> I actually prefer to have the text parsing functionality in<br clear="none">> maintenance mode: no addition of new features, but also not removing<br clear="none">> it entirely. We probably can make a few things clearer / more visible<br clear="none">> in our documentation: that this was developed using the text output of<br clear="none">> old BLAST releases and that we will not be adding support or updating<br clear="none">> it to work with text output from new releases.<br clear="none">><br clear="none">> So far, I have seen only very minor (if any) maintenance work related<br clear="none">> to the text output parser. And I believe it still has its uses in<br clear="none">> those corner cases where one really needs to parse the text output<br clear="none">> from an irreproducible BLAST search. So it seems to me that we would<br clear="none">> be losing more (functionality-wise) by deprecating it, rather than<br clear="none">> keeping it in maintenance mode.<br clear="none">><br clear="none">> With kind regards,<br clear="none">> Bow<br clear="none">> On Wed, Nov 21, 2018 at 5:25 PM Peter Cock <<a shape="rect" ymailto="mailto:p.j.a.cock@googlemail.com" href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br clear="none">> ><br clear="none">> > Hi Michiel,<br clear="none">> ><br clear="none">> > This is up to Bow really - does he want to continue to support<br clear="none">> > parsing plain text human readable BLAST output in SearchIO?<br clear="none">> ><br clear="none">> > I've not tried the new BLAST+ 2.8.0alpha release, but am not<br clear="none">> > aware of any current problems with the parser - although as<br clear="none">> > you note, the NCBI and parts of our own documentation do<br clear="none">> > not recommend parsing it - and it could easily break with the<br clear="none">> > next BLAST+ release.<br clear="none">> ><br clear="none">> > I agree from a code cleanliness perspective, it would be nice<br clear="none">> > to remove this and Bio/ParserSupport.py as well. Sadly while<br clear="none">> > we've had deprecation warnings in place for direct use of<br clear="none">> > Bio.ParserSupport or Bio.Blast.NCBIStandalone, indirect<br clear="none">> > use via SearchIO has been deliberately handled without<br clear="none">> > a warning.<br clear="none">> ><br clear="none">> > Minor correction: Bio.Blast.NCBIStandalone has got tests in<br clear="none">> > test_NCBITextParser.py, and indirectly via the SearchIO tests.<br clear="none">> > In fact it has a respectable 90% test coverage:<br clear="none">> ><br clear="none">> > <a shape="rect" href="https://codecov.io/gh/biopython/biopython/src/master/Bio/Blast/NCBIStandalone.py" target="_blank">https://codecov.io/gh/biopython/biopython/src/master/Bio/Blast/NCBIStandalone.py</a><br clear="none">> ><br clear="none">> > Likewise for Bio.ParserSupport:<br clear="none">> ><br clear="none">> > <a shape="rect" href="https://codecov.io/gh/biopython/biopython/src/master/Bio/ParserSupport.py" target="_blank">https://codecov.io/gh/biopython/biopython/src/master/Bio/ParserSupport.py</a><br clear="none">> ><br clear="none">> > Peter<br clear="none">> > On Wed, Nov 21, 2018 at 2:54 AM Michiel de Hoon <<a shape="rect" ymailto="mailto:mjldehoon@yahoo.com" href="mailto:mjldehoon@yahoo.com">mjldehoon@yahoo.com</a>> wrote:<br clear="none">> > ><br clear="none">> > > Dear all,<br clear="none">> > ><br clear="none">> > > The blast_text module in Bio.SearchIO.BlastIO contains a parser for plain-text output from Blast.<br clear="none">> > > NCBI and Biopython itself recommend against parsing plain-text Blast output.<br clear="none">> > > As far as I can tell, this module currently has no documentation and no tests.<br clear="none">> > > The module relies on the deprecated module Bio.Blast.NCBIStandalone, which relies on the deprecated module Bio.ParserSupport.<br clear="none">> > ><br clear="none">> > > Can we deprecate Bio.SearchIO.BlastIO.blast_text ?<br clear="none">> > ><br clear="none">> > > Best,<br clear="none">> > > -Michiel<br clear="none">> > ><br clear="none">> > > _______________________________________________<br clear="none">> > > Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none">> > > <a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br clear="none">> > _______________________________________________<br clear="none">> > Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none">> > <a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br clear="none"></div></div></div>
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