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

[Michael R. Crusoe]

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>
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