All of the major Bio* projects contain libraries to parse BLAST XML output:

• Bioperl - use the SearchIO module with option -format=>'blastxml'
• BioPython - their tutorial recommends to use XML output for parsing
• BioRuby - Bio::Blast.reports will read an XML file

Once you figure out how to extract the required fields, writing to CSV is quite easy in any of these languages.

Also, don't forget that running blastall with the -m 8 or -m 9 options will generate tab-delimited output (but if I recall correctly, not including the aligned sequences, which you need).

You can use XSLT to transform your xml to a tabular format:

<xsl:stylesheet version="1.0" xmlns:xsl="&lt;a href=" http:="" www.w3.org="" 1999="" XSL="" Transform"="" rel="nofollow">http://www.w3.org/1999/XSL/Transform"
 xmlns="http://www.w3.org/1999/xhtml"
 >


<xsl:output method="text"/>

<xsl:template match="/">
<xsl:apply-templates select="BlastOutput"/>
</xsl:template>



<xsl:template match="BlastOutput">
<xsl:variable name="queryDef" select="BlastOutput_query-def"/>
<xsl:variable name="queryLen" select="BlastOutput_query-len"/>
<xsl:for-each select="BlastOutput_iterations/Iteration/Iteration_hits/Hit">
<xsl:variable name="hitDef" select="Hit-def"/>
<xsl:variable name="hitLen" select="Hit-len"/>
<xsl:for-each select="Hit_hsps/Hsp">
<xsl:value-of select="$queryDef"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="$queryLen"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="$hitDef"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="$hitLen"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_bit-score"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_evalue"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_query-from"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_query-to"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_hit-from"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_hit-to"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_query-frame"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_hit-frame"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_identity"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_positive"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_gaps"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_align-len"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_qseq"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_hseq"/>
<xsl:text>    </xsl:text>
<xsl:value-of select="Hsp_midline"/>
<xsl:text>
</xsl:text>
</xsl:for-each>
</xsl:for-each>
</xsl:template>



</xsl:stylesheet>

Example:

xsltproc --novalid blast2csv.xsl jeter.blast.xml

Result:

No definition line    99            159.983    9.34813e-45    1    99    1    105    1    1    99    99    6    105    ATGCCCGCCCTGCGCCCCGCTCTGCT---GTGGGCGCTGCTGGCGCTCTGGCTGTGCTG---CGCGGCCCCCGCGCATGCATTGCAGTGTCGAGATGGCTATGAA    ATGCCCGCCCTGCGCCCCGCTCTGCTAAAGTGGGCGCTGCTGGCGCTCTGGCTGTGCTGAAACGCGGCCCCCGCGCATGCATTGCAGTGTCGAGATGGCTATGAA    ||||||||||||||||||||||||||   ||||||||||||||||||||||||||||||   |||||||||||||||||||||||||||||||||||||||||||
No definition line    99            66.2076    1.5844e-16    1    36    106    141    1    1    36    36    0    36    ATGCCCGCCCTGCGCCCCGCTCTGCTGTGGGCGCTG    ATGCCCGCCCTGCGCCCCGCTCTGCTGTGGGCGCTG    ||||||||||||||||||||||||||||||||||||

For this purpose you can open the xml Blastoutput file in speardsheet as an external data source. You can also find NOBLAST(New Options for BLAST) useful for this purpose.NOBLAST is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database.please read the complete publication here and download it from Here

Bioperl gives some specific advice to deal with this problem.

I have developped a small R package able to do that. It is available on Github here.
Using the function NCBI_BLAST_XML2DT() you can load your NCBI BLAST XML result file as an R data.table.
If you have multiple related XML files you can do the same thing using the function aggregate_NCBI_BLAST_XMLs2DT().
Follow the documentation in the README for install, and create an issue in the repository if you have a problem.
Good luck !