[maker-devel] Error from Pseudo gene identification scripts

[Michael Campbell]

Hi Quanwei,

My guess would be a file format issue, but the code has evolved since I worked with it. The last time that ran it the fasta header had to contain only the sequence ID without a space after it. That was the big gotcha that I remember.

I’ve ccd Shin-Han Shiu on this one. The pipeline was developed in his lab.

Thanks,
Mike

> On Dec 8, 2017, at 8:46 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Thank you Carson and Michael.
> 
> Best
> Quanwei
> 
> 2017-12-07 23:42 GMT-05:00 Carson Holt <carsonhh at gmail.com>:
>> 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.
>> 
>> —Carson
>> 
>>> On Dec 7, 2017, at 2:44 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>> 
>>> Hello:
>>> 
>>> I am trying to identify pseudo genes following http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene
>>> 
>>> 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.
>>> 
>>> ##below shows reported errors
>>> Traceback (most recent call last):
>>>   File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py", line 4330, in <module>
>>>     parse.get_qualified4(blast,fasta,E,I,L,P,Q)
>>>   File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py", line 3050, in get_qualified4
>>>     N = sizes[L[0]]
>>> KeyError: 'maker-Contig2656-snap-gene-1.9-mRNA-1'
>>> Traceback (most recent call last):
>>>   File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/script_step3b.py", line 98, in <module>
>>>     oup.write("%s\t%s\t%s\t%s\n" % (all_contigs[i][0][0],
>>> IndexError: list index out of range
>>> Done!
>>> 
>>> Best
>>> Quanwei
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>> 
> 
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