solidity-custom

[ctseto]

From a previous github issue in re Simka:

"If you still need to recover kmer sequences, for instance recovering subsets of kmers according to their presence/absence in some datasets, you may have a look at the software DSK : http://github.com/GATB/dsk and its option -solidity-custom."

I presume it is dsk -file contigs1.fa,contigs2.fa -solidity-kind custom -solidity-custom , though I'm not quite sure what the -solidity-custom option is specifying for. Is it a file with a list of kmers ("specifies list of files where kmer must be present"). I generally get "Kmer solidity custom has different number of values (11) than banks (2)"; where banks appears to correspond to the number of files appended to flag -file.

[rchikhi]

Hi Charles,

The way I understand the -solidity-custom option from the source code, is:

1. it's not really well documented :)
2. the argument should be a string of 0 or 1 integers, where a 0 indicates that the kmer cannot be above the -abundance-min threshold for that dataset, and 1 indicates that on the contrary, it needs to be above.
3. the string should be in the same order as the files in the -file option.

I'm basing my observations on : https://github.com/GATB/gatb-core/blob/862ffc949bd3ff556442dc83b5af3666f58195d4/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp#L295

E.g. if you have three input files, and -file file1.fa,file2.fa,file3.fa -abundance-min 3,5,3 -solidity-kind custom -solidity-custom 101, then a k-mer is output if it is seen 3 times or more in files 1 and 3, and seen less than 5 times in file2.

That's a bit odd, but that's how I understand the source code..

Probably @rizkg could confirm.

Rayan

[rizkg]

Hi,

Yes Rayan, you are correct about the usage. Sorry that it is not better documented.
The idea is that it allows to output kmers that are specific to something.