[protocols] [khmer] calc-best-assembly.py

Wed Jan 8 13:15:08 PST 2014

Yes, velvet assembly files are named in that way except "fa" instead of "fq"
not to get confused as the files are fasta format. I am around the campus
and can stop by your office if you mind emails back and forth. Thanks for
your help!

Regards,
Yiseul

On Wed, Jan 8, 2014 at 3:54 PM, Michael R. Crusoe <mcrusoe at msu.edu> wrote:

>
> On Sat, Jan 4, 2014 at 10:26 AM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>
>> Hi Michael,
>>
>> I am sorry for my late reply. Thanks for your help again!
>>
>> Yes, assemstats3.py worked.
>>
>> I am running all of this in a directory named assembly created on HPCC.
>>
>> When I ran the command you asked, the output says "cat: grouplist.txt: No
>> such file or directory".
>>
>
>
> Are your velvet assembly files named in the format
> "kak.groupNNNN.pe.fq.gz" where NNNN is a four digit number between 0 and
> 1,000 inclusive?
>
>
>
>>
>> Regards,
>> Yiseul
>>
>>
>> On Fri, Jan 3, 2014 at 6:05 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>>
>>> Does the invocation of assemstats3.py work?
>>>
>>> This is being run in /mnt/assembly, yes?
>>>
>>> What is the output of this command?
>>>
>>> for group in $(cat grouplist.txt); do echo
>>>  '$group.*velvet.*.d/contigs.fa'; ls  $group.*velvet.*.d/contigs.fa; done
>>>
>>>
>>> On Fri, Jan 3, 2014 at 5:11 PM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>>>
>>>> Thanks for your help in advance!
>>>>
>>>> Basically, I am following the Kalamazoo metagenomic assembly protocol
>>>> with my viral metagenomic dataset. In the assembly step, the protocol runs
>>>> dataset with three different assemblers but I wanted to test only with the
>>>> velvet. I am not an expert on writing a script and trying to modify the one
>>>> below only for velvet output by deleting the part underlined. When I ran
>>>> it, the error message says "too few arguments". Could you help me with
>>>> modifying the script only from one assembler? Please let me know if I am
>>>> not making myself clear.
>>>>
>>>>
>>>> for i in {0..1000};
>>>> do
>>>>      groupid=$(printf kak.group%04d $i);
>>>>      if [ -e ${groupid}.pe.fq.gz ]; then
>>>>         echo $groupid
>>>>      fi
>>>> done > grouplist.txt
>>>>
>>>> for group in $(cat grouplist.txt)
>>>> do
>>>>    python /usr/local/share/khmer/sandbox/calc-best-assembly.py -q $group.{*velvet.*.d/contigs.fa*,*idba.d/scaffold.fa,*spades.d/contigs.fasta*} -o $group.best.fa
>>>> done > best-assemblies.txt
>>>>
>>>> python /usr/local/share/khmer/sandbox/multi-rename.py testasm *.best.fa > final-assembly.fa
>>>>
>>>>
>>>> Regards,
>>>> Yiseul
>>>>
>>>>
>>>> On Fri, Jan 3, 2014 at 4:57 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>>>>
>>>>> Please :-)
>>>>>
>>>>>
>>>>> On Fri, Jan 3, 2014 at 4:40 PM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> Can I ask one more question for you?
>>>>>>
>>>>>> Regards,
>>>>>> Yiseul
>>>>>>
>>>>>>
>>>>>> On Fri, Jan 3, 2014 at 4:16 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>>>>>>
>>>>>>> You are welcome!
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jan 3, 2014 at 4:14 PM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>>>>>>>
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>> Yiseul
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Jan 3, 2014 at 4:11 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>>>>>>>>
>>>>>>>>> It is in the protocols-v0.8.3 branch of khmer:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> https://github.com/ged-lab/khmer/blob/protocols-v0.8.3/sandbox/calc-best-assembly.py
>>>>>>>>>
>>>>>>>>> Install instructions are at:
>>>>>>>>> https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/1-quality.html#install-software
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Fri, Jan 3, 2014 at 4:07 PM, Yiseul Kim <kimyise2 at msu.edu>wrote:
>>>>>>>>>
>>>>>>>>>> Hello,
>>>>>>>>>>
>>>>>>>>>> Could someone help me with finding the location of
>>>>>>>>>> *calc-best-assembly.py*? The newly released metagenomic assembly
>>>>>>>>>> protocol (
>>>>>>>>>> https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/4-assemble.html)
>>>>>>>>>> says it is located under /khmer/sandbox but I am not able to find it. Any
>>>>>>>>>> help would be appreciated.
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>> Yiseul
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> khmer mailing list
>>>>>>>>>> khmer at lists.idyll.org
>>>>>>>>>> http://lists.idyll.org/listinfo/khmer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Michael R. Crusoe: Software Engineer and Bioinformatician
>>>>>>>>> mcrusoe at msu.edu
>>>>>>>>>  @ the Genomics, Evolution, and Development lab; Michigan State
>>>>>>>>> University
>>>>>>>>> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670
>>>>>>>>> @biocrusoe <http://twitter.com/biocrusoe>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Michael R. Crusoe: Software Engineer and Bioinformatician
>>>>>>> mcrusoe at msu.edu
>>>>>>>  @ the Genomics, Evolution, and Development lab; Michigan State
>>>>>>> University
>>>>>>> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670
>>>>>>> @biocrusoe <http://twitter.com/biocrusoe>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Michael R. Crusoe: Software Engineer and Bioinformatician
>>>>> mcrusoe at msu.edu
>>>>>  @ the Genomics, Evolution, and Development lab; Michigan State
>>>>> University
>>>>> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670
>>>>> @biocrusoe <http://twitter.com/biocrusoe>
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Michael R. Crusoe: Software Engineer and Bioinformatician
>>> mcrusoe at msu.edu
>>>  @ the Genomics, Evolution, and Development lab; Michigan State
>>> University
>>> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670
>>> @biocrusoe <http://twitter.com/biocrusoe>
>>>
>>
>>
>
>
> --
> Michael R. Crusoe: Software Engineer and Bioinformatician  mcrusoe at msu.edu
>  @ the Genomics, Evolution, and Development lab; Michigan State University
> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670    @biocrusoe<http://twitter.com/biocrusoe>
>
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