<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I’m going to CC Michael Campbell on this. I wasn’t really involved with any of the pseudogene accessory scripts and protocols that went with the MAKER-P publication nor have I really been involved with pseudogene annotation in general. So Michael might have more insight here.<div class=""><br class=""></div><div class="">—Carson<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 7, 2017, at 2:44 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">Hello:<br class=""><br class="">I am trying to identify pseudo genes following <a href="http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene" class="">http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene</a><br class=""><br class="">After I get the blast result, I am trying to scan pseudogenes by the command "python pseudo_wrap.py parameter". But I got the following errors. Do you have any ideas and suggestions about the errors? Thanks.<br class=""><br class=""></div><div class="">##below shows reported errors<br class=""></div><div class="">Traceback (most recent call last):<br class=""> File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py", line 4330, in <module><br class=""> parse.get_qualified4(blast,fasta,E,I,L,P,Q)<br class=""> File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py", line 3050, in get_qualified4<br class=""> N = sizes[L[0]]<br class=""><span style="color:rgb(255,0,0)" class="">KeyError: 'maker-Contig2656-snap-gene-1.9-mRNA-1'</span><br class="">Traceback (most recent call last):<br class=""> File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/script_step3b.py", line 98, in <module><br class=""> oup.write("%s\t%s\t%s\t%s\n" % (all_contigs[i][0][0],<br class=""><span style="color:rgb(255,0,0)" class="">IndexError: list index out of range</span><br class="">Done!<br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""></div>
_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></body></html>