<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello Paolo,<div><br></div><div>When originally designing the programs, my thought was similar to this, combine all of the suffix arrays together. Unfortunately this is not very efficient, it takes a long time to combine those suffix arrays and it produces a very very large file as you can imagine. Also, one of my design goals was to be able to split the work across multiple machines, with a single file you are limited to using just one machine. So what I did instead is to union the results of mcp_sarray, this is the union_mcp command.</div><div><br></div><div>Later though, I did find a need to combine suffix arrays however only programmatically, I never wrote a command line program. This is using the BCSuffixArrayUnionEnumerator.</div><div><br></div><div>Anyways, what I did in my work was to write a shell script to loop through all the chromosome files, such as this:</div><div><br></div><div><br></div><div><div># i is mouse chromosomes</div><div># j is human chromosomes</div><div>for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y; do</div><div> for j in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>mcp_sarray N human_chr${j} mouse_chr${i} h${j}_m${i} 40</div><div> done</div><div>done</div><div><br></div><div><br></div><div>I actually did something a little more complicated than this because I distributed the work across a cluster of machines. However, this will produce result files with hA_mB where A and B are chromosome numbers, then you can use another script to combine all of them together to produce a single result.</div><div><br></div><div><br></div><div><div># i is mouse chromosomes</div><div># j is human chromosomes</div><div>union_mcp h1_m1 h2_m1 hm_1</div><div>L=1</div><div>K=2</div><div>for j in 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do</div><div> union_mcp hm_${L} h${j}_m1 hm_${K}</div><div> K=$((K + 1))</div><div> L=$((L + 1))</div><div>done</div><div><br></div><div>for i in 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y; do</div><div> for j in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>union_mcp hm_${L} h${j}_m${i} hm_${K}</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>K=$((K + 1))</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>L=$((L + 1))</div><div> done</div><div>done</div><div><br></div><div><br></div><div>This produces files hm_K where K is an increasing number. The file with the largest K at the end is your final result file.</div><div><br></div><div><br></div></div></div><div>cheers</div><div>Scott</div><div><br></div><div><br></div><div>On Jul 16, 2008, at 2:40 PM, paolo siniselli wrote:</div><div><div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font: inherit;">Hi Scott,<br>How can I combine all the suffix array files for an organism into a single suffix array so that mcp_sarray is just run once?<br>I'd like to compare two sarray files for each two organisms comparison such as human vs mouse...<br>thanks<br><br><br><br>--- <b>Lun 14/7/08, Scott Christley <i><<a href="mailto:schristley@mac.com">schristley@mac.com</a>></i></b> ha scritto:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">Da: Scott Christley <<a href="mailto:schristley@mac.com">schristley@mac.com</a>><br>Oggetto: Re: [Biococoa-dev] Biococoa2 Install issue<br>A: <a href="mailto:paolo_siniselli@yahoo.it">paolo_siniselli@yahoo.it</a><br>Cc: "biococoa" <<a href="mailto:biococoa-dev@bioinformatics.org">biococoa-dev@bioinformatics.org</a>><br>Data: Luned́ 14 luglio 2008, 23:27<br><br><div id="yiv2007688281">Hello Paolo,<div><br></div><div>There is an environment configuration script that comes with GNUstep, you need to "source" this script to setup the GNUstep environment before compiling or running applications. Maybe something like this:</div><div><br></div><div>. /usr/share/GNUstep/Makefiles/GNUstep.sh<br></div><div><br></div><div>As a side note, some of the reports I've heard from people is that the GNUstep which comes with Debian is old and has bugs, I cannot say how well it will work with BioCocoa.</div><div><br></div><div>cheers</div><div>Scott</div><div><br></div><div><br></div><div><div>On Jul 14, 2008, at 2:06 PM, paolo siniselli wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">I'm trying to install BioCocoa2 on my Linux Debian (Lenny)<br>I've already installed GNUstep<br>So I went into truck/GNUstep folder and I typed "make install" but I received an error back:<br>GNUmakefile:27: *** You need to run the GNUstep configuration script before compiling!. Stop.<br><br>Those are the files in GNUstep directory:<br>aminoacids.plist GNUmakefile.postamble GNUmakefile.subproj<br>GNUmakefile GNUmakefile.preamble nucleotides.plist<br><br>And those are the file in truck direcotry:<br>BCAppKit BioCocoa.xcodeproj Examples Publications.txt<br>BCFoundation Copying.txt GNUstep Readme.txt<br>BC.icns DeveloperDocs license.txt Resources<br>BioCocoa_Prefix.h Documentation main.c Tests<br><br>Thanks<br>Paolo<br></td></tr></tbody></table><br> <hr size="1"> Posta, news, sport, oroscopo: tutto in una sola pagina<br> <a rel="nofollow" target="_blank" href="http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52437/*http://www.yahoo.it/latuapagina">Crea l'home page che piace a te!</a>._______________________________________________<br>Biococoa-dev mailing list<br><a rel="nofollow" target="_blank" href="mailto:Biococoa-dev@bioinformatics.org">Biococoa-dev@bioinformatics.org</a><br><a rel="nofollow" target="_blank" href="http://www.bioinformatics.org/mailman/listinfo/biococoa-dev">http://www.bioinformatics.org/mailman/listinfo/biococoa-dev</a><br></blockquote></div><br></div></blockquote></td></tr></tbody></table><br> <hr size="1"> Posta, news, sport, oroscopo: tutto in una sola pagina<br> <a href="http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52437/*http://www.yahoo.it/latuapagina" target="_blank">Crea l'home page che piace a te!</a>.</blockquote></div><br></div></body></html>