Subject: Re: [BioPython] (no subject) - msg#00018

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[BioPython] (no subject)

Hi, I am new to bipyton trying to use ncbistandalone parser to parse my blast out put which is in txt format. the parser works well for older blast uptputs but breaks down for newer blast outputs. Can someone suggest me a way to overcome this blast parser's problem? Thanks _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython

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Re: [BioPython] plain txt blast output - xml instead

Rohini Damle wrote: > Hi, > I am new to bipyton trying to use ncbistandalone parser to parse my blast > out put which is in txt format. > the parser works well for older blast uptputs but breaks down for newer > blast outputs. The NCBI standalone blast and web blast plain text output keeps changing slightly, and as a result, the parser isn't always up to date. > Can someone suggest me a way to overcome this blast parser's > problem? We recommend you use the XML output instead (this is possible with both online blast and the standalone tools). For the stand alone tools, repeat your searches with the command line option -m 7 to get XML output. If you are using the Bio.NCBIStandalone.blastall() command, use argument align_view to set this. You still use NCBIStandalone.Iterator (if you have multiple queries) but now use NCBIXML.BlastParser instead of NCBIStandalone.BlastParser e.g. http://bugzilla.open-bio.org/attachment.cgi?id=293&action=view Peter _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython

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[BioPython] (no subject)

Hi, I am new to bipyton trying to use ncbistandalone parser to parse my blast out put which is in txt format. the parser works well for older blast uptputs but breaks down for newer blast outputs. Can someone suggest me a way to overcome this blast parser's problem? Thanks _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython

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Re: [BioPython] plain txt blast output - xml instead

Rohini Damle wrote: > Hi, > I am new to bipyton trying to use ncbistandalone parser to parse my blast > out put which is in txt format. > the parser works well for older blast uptputs but breaks down for newer > blast outputs. The NCBI standalone blast and web blast plain text output keeps changing slightly, and as a result, the parser isn't always up to date. > Can someone suggest me a way to overcome this blast parser's > problem? We recommend you use the XML output instead (this is possible with both online blast and the standalone tools). For the stand alone tools, repeat your searches with the command line option -m 7 to get XML output. If you are using the Bio.NCBIStandalone.blastall() command, use argument align_view to set this. You still use NCBIStandalone.Iterator (if you have multiple queries) but now use NCBIXML.BlastParser instead of NCBIStandalone.BlastParser e.g. http://bugzilla.open-bio.org/attachment.cgi?id=293&action=view Peter _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython