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

[Yiseul Kim]

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>
>
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