kmers
$ lexicmap utils kmers -h
View k-mers captured by the masks
Attention:
1. Mask index (column mask) is 1-based.
2. Prefix means the length of shared prefix between a k-mer and the mask.
3. K-mer positions (column pos) are 1-based.
For reference genomes with multiple sequences, the sequences were
concatenated to a single sequence with intervals of N's.
4. Reversed means if the k-mer is reversed for suffix matching.
Usage:
lexicmap utils kmers [flags] -d <index path> [-m <mask index>] [-o out.tsv.gz]
Flags:
-h, --help help for kmers
-d, --index string ► Index directory created by "lexicmap index".
-m, --mask int ► View k-mers captured by Xth mask. (0 for all) (default 1)
-f, --only-forward ► Only output forward k-mers.
-o, --out-file string ► Out file, supports and recommends a ".gz" suffix ("-" for stdout).
(default "-")
Global Flags:
-X, --infile-list string ► File of input file list (one file per line). If given, they are
appended to files from CLI arguments.
--log string ► Log file.
--quiet ► Do not print any verbose information. But you can write them to a file
with --log.
-j, --threads int ► Number of CPU cores to use. By default, it uses all available cores.
(default 16)
-
The default output is captured k-mers of the first mask.
$ lexicmap utils kmers --quiet -d demo.lmi/ | head -n 20 | csvtk pretty -t mask kmer prefix number ref pos strand reversed ---- ------------------------------- ------ ------ --------------- ------- ------ -------- 1 AAAAAAAAAAAAAAAGACAACAAAAGACATA 8 1 GCF_002950215.1 3870418 - yes 1 AAAAAAAAACAAACATTTGCGGCGGGGCCAT 8 1 GCF_000742135.1 2043044 + no 1 AAAAAAAAACCAGAAATCACACGCCAACTCC 8 1 GCF_002949675.1 1345415 + yes 1 AAAAAAAAACGATTATCCTCAATTAATTTCT 8 1 GCF_000392875.1 814251 + no 1 AAAAAAAAACGCTTCTACATCGAGCAGCGAG 8 1 GCF_001457655.1 941619 + yes 1 AAAAAAAAACGCTTTGTAACTCGATTGATAG 8 1 GCF_009759685.1 997945 + yes 1 AAAAAAAAACTGCTGTCCCTGGTCCGTCAGG 8 1 GCF_002950215.1 4262890 - yes 1 AAAAAAAAAGATTTGATTTTTTTCATTAATA 8 1 GCF_000392875.1 766998 - yes 1 AAAAAAAAAGCATTTTTTCGATCTCTTTACG 8 1 GCF_000392875.1 1623731 + yes 1 AAAAAAAAAGTTTCCGGGACACTACCTAACC 8 1 GCF_000017205.1 5804200 - yes 1 AAAAAAAAATTATTTTGCTAATCAATAGGTC 8 1 GCF_000006945.2 4886411 - yes 1 AAAAAAAACAAAGAATTATTACACAACATTC 8 1 GCF_003697165.2 4055655 + yes 1 AAAAAAAACACGGACTTATTGAAATCGTATT 8 1 GCF_000392875.1 746746 + yes 1 AAAAAAAACCAACTTTGAAAAAAGTAATGTA 8 1 GCF_000148585.2 917529 - yes 1 AAAAAAAACCATATTATGTCCGATCCTCACA 8 1 GCF_000392875.1 1060650 + yes 1 AAAAAAAACCCGCCGAAGCGGGTTTTTTTAT 8 1 GCF_000742135.1 1612499 + no 1 AAAAAAAACCTAATGGTAAATAACGTTTTGG 8 1 GCF_006742205.1 2346818 + yes 1 AAAAAAAACGAAAAACGGTAACACGGGAATT 8 1 GCF_001544255.1 1605298 + yes 1 AAAAAAAACGACTCCAGAGAGATCATCGTAT 8 1 GCF_000392875.1 1279686 + yesOnly forward k-mers.
$ lexicmap utils kmers --quiet -d demo.lmi/ -f | head -n 20 | csvtk pretty -t mask kmer prefix number ref pos strand reversed ---- ------------------------------- ------ ------ --------------- ------- ------ -------- 1 AAAAAAAAACAAACATTTGCGGCGGGGCCAT 8 1 GCF_000742135.1 2043044 + no 1 AAAAAAAAACGATTATCCTCAATTAATTTCT 8 1 GCF_000392875.1 814251 + no 1 AAAAAAAACCCGCCGAAGCGGGTTTTTTTAT 8 1 GCF_000742135.1 1612499 + no 1 AAAAAAAACGGTTCAGCTGACCAGCCAGCTG 8 1 GCF_002950215.1 401140 + no 1 AAAAAAAAGAACAAATTCGAGGAAAAAGAAG 9 1 GCF_001027105.1 1268573 + no 1 AAAAAAAAGATATTGAAGTTAAAGTAATTTG 9 1 GCF_000742135.1 3038258 + no 1 AAAAAAAAGCCCACGAACCGGGGGCAATATC 9 1 GCF_002950215.1 3578394 + no 1 AAAAAAAAGCCCCGCCGAAGCGGGGCTTTTT 9 1 GCF_000017205.1 5110420 + no 1 AAAAAAAAGGATTATAACAAAATTTTGTCAT 9 1 GCF_001544255.1 426716 + no 1 AAAAAAAAGGCTTTACGGATGATCCGATGGA 9 1 GCF_009759685.1 3033057 + no 1 AAAAAAAAGTAATTGCAGCTATTATTGGGAC 10 1 GCF_001027105.1 437272 + no 1 AAAAAAAAGTATTAAGCAACTGACTAAAAGT 10 1 GCF_006742205.1 1841209 + no 1 AAAAAAAAGTCACAATTATTGGTGCCGGTTT 13 1 GCF_000392875.1 1508457 - no 1 AAAAAAAAGTCATCAAGGATTATTTGAGTTA 12 1 GCF_001457655.1 1847867 + no 1 AAAAAAAAGTCATCGCTTTATCTGTCAGTAT 12 1 GCF_001544255.1 156689 - no 1 AAAAAAAAGTCATCTTCGGATGGCTTTTTTA 12 1 GCF_000148585.2 1363150 - no 1 AAAAAAAAGTCCATCCTGCAGCATAAAATAA 11 1 GCF_000742135.1 4671015 + no 1 AAAAAAAAGTCCCTGCTGTTTGCCCAGTCCT 11 1 GCF_000006945.2 3796 - no 1 AAAAAAAAGTCCGCTGATAAGGCTTGAAAAG 11 3 GCF_002949675.1 2356807 + no -
Specify the mask.
$ lexicmap utils kmers --quiet -d demo.lmi/ --mask 12345 | head -n 20 | csvtk pretty -t mask kmer prefix number ref pos strand reversed ----- ------------------------------- ------ ------ --------------- ------- ------ -------- 12345 CATTAGTAAAAACCAACTTAGTTACGACACG 8 1 GCF_001027105.1 1823411 + no 12345 CATTAGTAAAACATTTTGAACCTGTGATTGA 8 1 GCF_006742205.1 1192019 + no 12345 CATTAGTAAAAGTCGTTTGGTAAAGCGATTA 8 1 GCF_001027105.1 1334989 + yes 12345 CATTAGTAAACGTACAAAACTATTGGTTAGA 8 1 GCF_001027105.1 2037559 + yes 12345 CATTAGTAAATCCAGGAATCCTAACCGACGA 8 1 GCF_001027105.1 963152 + yes 12345 CATTAGTAACGCGTACGAAACCGTAGTAAGT 8 1 GCF_001027105.1 1958187 + yes 12345 CATTAGTAAGTTGTCGGTCTAACGCGGATTA 8 1 GCF_002950215.1 2882180 + yes 12345 CATTAGTACATTCAAGTATTATTCATTAAAC 8 1 GCF_009759685.1 665376 + yes 12345 CATTAGTACCGATAGGACATCATGAACACAA 8 1 GCF_002950215.1 4677222 + yes 12345 CATTAGTACCTTCATCGCTATCCCATTAGGC 8 1 GCF_000006945.2 92542 + yes 12345 CATTAGTACGTGTCCCGCAAAGAGAAAGAAC 8 1 GCF_000006945.2 3412102 + yes 12345 CATTAGTAGAAAAATACAAAGGCATTTATGA 11 1 GCF_900638025.1 665985 - no 12345 CATTAGTAGAAAATTGATAATCTAAGAGTTC 11 1 GCF_002950215.1 2940281 + no 12345 CATTAGTAGAAATGGGCAAAGAATAGGAAAA 11 1 GCF_000148585.2 81286 + no 12345 CATTAGTAGAAGAAATTGCAGCAAGTATTAA 14 1 GCF_001027105.1 621160 + no 12345 CATTAGTAGAAGAACTGAAGTTAGTGCCTAT 14 1 GCF_001096185.1 2113047 + no 12345 CATTAGTAGAAGAAGACCAAGCACGACGCAT 15 1 GCF_000392875.1 891723 + no 12345 CATTAGTAGAAGAGTTGTTCGTCAGTTACGG 13 1 GCF_001544255.1 831068 - no 12345 CATTAGTAGAAGATTTAGTGGCAAGCTCAAT 13 1 GCF_001457655.1 1280653 + no“reversed” means means if the k-mer is reversed for suffix matching. E.g.,
CATTAGTAAAAGTCGTTTGGTAAAGCGATTAis reversed, so you need to reverse it before searching in the genome.$ seqkit locate -p $(echo CATTAGTAAAAGTCGTTTGGTAAAGCGATTA | rev) refs/GCF_001027105.1.fa.gz -M | csvtk pretty -t seqID patternName pattern strand start end ------------- ------------------------------- ------------------------------- ------ ------- ------- NZ_CP011526.1 ATTAGCGAAATGGTTTGCTGAAAATGATTAC ATTAGCGAAATGGTTTGCTGAAAATGATTAC + 1334989 1335019 -
For all masks. The result might be very big, therefore, writing to gzip format is recommended.
$ lexicmap utils kmers -d demo.lmi/ --mask 0 -o kmers.tsv.gz $ zcat kmers.tsv.gz | csvtk freq -t -f mask -nr | head -n 10 mask frequency 24088 322 15814 295 13923 293 27102 291 13922 282 15967 281 10001 280 15986 272 16440 269a faster way
seq 1 $(lexicmap utils masks -d demo.lmi/ --quiet | wc -l) \ | rush --eta 'echo -e {}"\t"$(lexicmap utils kmers -d demo.lmi/ -m {} -f --quiet | csvtk nrow)' \ | csvtk add-header -t -n mask,seeds \ | csvtk sort -t -k seeds:nr \ | head -n 10 -
Lengths of shared prefixes between probes and captured k-mers.
zcat kmers.tsv.gz \ | csvtk grep -t -f reversed -p no \ | csvtk plot hist -t -f prefix -o prefix.hist.png \ --xlab "length of common prefixes between captured k-mers and masks"
The output (TSV format) is formatted with csvtk pretty.