<html><head></head><body><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;">Dear all,</div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><br></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><span>The blast_text module in Bio.SearchIO.BlastIO contains a parser for plain-text output from Blast.</span></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><span></span>NCBI and Biopython itself recommend against parsing plain-text Blast output.<br></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;">As far as I can tell, this module currently has no documentation and no tests.</div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;">The module relies on the deprecated module <span>Bio.Blast.<span>NCBIStandalone, which relies on the deprecated module Bio.ParserSupport.</span></span></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><span><span><br></span></span></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><span><span>Can we deprecate <span><span>Bio.SearchIO.BlastIO</span></span>.blast_text ?</span></span></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><br></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;">Best,</div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;">-Michiel<br></div><div class="ydpc0bec2bbyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"> <br></div></body></html>