opengene/uniquekmer

Generate unique KMERs for every contig in a FASTA file

uniquekmer's Issues

[Question] Clarification of uniqueness

Thank you so much for providing this wonderful tool!

If I search a region of ie. the human genome (chr1:1:50000) against the entire human reference genome, will UniqueKMER return the list of k-mers that map once and only once in the reference genome (between chr1:1:50000?)

or

does UniqueKMER keep only k-mers that map zero times against the reference genome?

I raise this issue to highlight the setting where the input FASTA and the reference genome are derived from the same species. I think this type of tool would be useful; Bloom-filters that count k-mers lack sensitivity to count unique k-mers, as far as I know.

Threading

Hello,

Really useful tool. Is this multi-threaded or single threaded?

Thanks,

Andrew

Wanting to get unique kmers that are larger

Hi all,

I was wondering if there is a way to bypass the k-mer size limit of 32?

Best,
Žiga

Cannot make install

error: src/genomes.cpp:8:10: fatal error: 'omp.h' file not found

[Feature request] give a header to each fasta

I found myself using your tool to obtain more hindsight into kmer presence and absence in genomes, specifically for kmers unique to certain genomes. Because the output of UniqueKmer is in the following form:

>sequence1
kmer1
kmer2
kmer3

tools will count them as one continuous sequence kmer1kmer2kmer3 which is unintended and will even create kmers that do not exist in the original genome.

Could you add an option to give a header to each kmer ? it would then look like this :

>sequence1:kmer:1
kmer1
>sequence1:kmer:2
kmer2
>sequence1:kmer:3
kmer3

I wrote a command line with awk for that but it would be convenient to have it as an option:

awk -i inplace '{if (/>/) {line=$0; sum=0} else {sum+=1; KMER=$0; print line ":kmer:" sum "\n" KMER} }' unique_kmers.fasta

[Feature requested] Can _k_ be increased?

The current limit of k is between 3-32 inclusive. Is it possible to extend this ie. 40? 50?

terminate called after throwing an instance of 'std::out_of_range

I am trying to create a kmerscollection of different viruses using fasta files but I get the error below for some fasta files.

Output 40/500: HW826641.1 JP 2014023536-A/12: Non-Diffusible Plant Virus Vector. unique: 5
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr: __pos (which is 22) > this->size() (which is 21)
/usr/bin/bash: line 1: 25212 Aborted

I am using standart fasta file downloaded from NCBI. I attached one of the problematic file in this issue (I have put it in txt but it his a .fa file normally).

I tried splitting the file in 1000 line but this seemed to not be the problem

Thank you for your time,
TheBiotech

Virus_12305.txt