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

Wed Jan 8 14:02:50 PST 2014

Yes, it does.

Regards,
Yiseul

On Wed, Jan 8, 2014 at 4:52 PM, Michael R. Crusoe <mcrusoe at msu.edu> wrote:

> Okay. So does it create the grouplist.txt file?
>
>
> On Wed, Jan 8, 2014 at 4:49 PM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>
>> Here you go.
>>
>> kak.group0000.nodn.pe.fa.gz
>> kak.group0000.pe.fa.gz
>> kak.group0001.nodn.pe.fa.gz
>> kak.group0001.pe.fa.gz
>> .
>> .
>> .
>> kak.group0028.nodn.pe.fa.gz
>> kak.group0028.pe.fa.gz
>>
>> Regards,
>> Yiseul
>>
>>
>> On Wed, Jan 8, 2014 at 4:45 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>>
>>> What is the output of `ls kak.group*.pe.fa.gz`?
>>>
>>>
>>>
>>> On Wed, Jan 8, 2014 at 4:42 PM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>>>
>>>> I already reflected the change of naming scheme… Sorry that I did not
>>>> mention this earlier.
>>>>
>>>> Regards,
>>>> Yiseul
>>>>
>>>>
>>>> On Wed, Jan 8, 2014 at 4:36 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>>>>
>>>>> Okay, then you need to modify the fourth line of your script to
>>>>> reflect the change you made to the naming scheme:
>>>>>
>>>>> "     if [ -e ${groupid}.pe.fa.gz ]; then"
>>>>>
>>>>>
>>>>> On Wed, Jan 8, 2014 at 4:15 PM, Yiseul Kim <kimyise2 at msu.edu> wrote:
>>>>>
>>>>>> 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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>> --
>>>>> 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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