2blast
$ lexicmap utils 2blast -h
Convert the default search output to blast-style format
LexicMap only stores genome IDs and sequence IDs, without description information.
But the option -g/--kv-file-genome enables adding description data after the genome ID
with a tabular key-value mapping file.
Input:
- Output of 'lexicmap search' with the flag -a/--all.
Usage:
lexicmap utils 2blast [flags]
Flags:
-b, --buffer-size string ► Size of buffer, supported unit: K, M, G. You need increase the value
when "bufio.Scanner: token too long" error reported (default "20M")
-h, --help help for 2blast
-i, --ignore-case ► Ignore cases of sgenome and sseqid
-g, --kv-file-genome string ► Two-column tabular file for mapping the target genome ID (sgenome)
to the corresponding value
-s, --kv-file-seq string ► Two-column tabular file for mapping the target sequence ID (sseqid)
to the corresponding value
-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)
From stdin.
$ seqkit seq -M 500 q.long-reads.fasta.gz \
| seqkit head -n 2 \
| lexicmap search -d demo.lmi/ -a \
| lexicmap utils 2blast --kv-file-genome ass2species.map
Query = GCF_000017205.1_r160
Length = 478
[Subject genome #1/1] = GCF_000017205.1 Pseudomonas aeruginosa
Query coverage per genome = 98.536%
>NC_009656.1
Length = 6588339
HSP cluster #1, HSP #1
Score = 883 bits, Expect = 3.60e-256
Query coverage per seq = 98.536%, Aligned length = 479, Identities = 94.990%, Gaps = 15
Query range = 7-477, Subject range = 4866857-4867328, Strand = Plus/Plus
Query 7 GGTGGCCCTCAAACGAGTCC-AACAGGCCAACGCCTAGCAATCCCTCCCCTGTGGGGCAG 65
||||||| |||||||||||| |||||||| |||||| | ||||||||||||| ||||||
Sbjct 4866857 GGTGGCC-TCAAACGAGTCCGAACAGGCCCACGCCTCACGATCCCTCCCCTGTCGGGCAG 4866915
Query 66 GGAAAATCGTCCTTTATGGTCCGTTCCGGGCACGCACCGGAACGGCGGTCATCTTCCACG 125
|||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct 4866916 GGAAAATCGTCCTTTATGGTCCGTTCCGGGCACGCACCGGAACGGCGGTCAT-TTCCACG 4866974
Query 126 GTGCCCGCCCACGGCGGACCCGCGGAAACCGACCCGGGCGCCAAGGCGCCCGGGAACGGA 185
||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct 4866975 GTGCCCGCC-ACGGCGGACCC-CGGAAACCGACCCGGGCGCCAAGGCGCCCGGGAACGGA 4867032
Query 186 GTA-CACTCGGCGTTCGGCCAGCGACAGC---GACGCGTTGCCGCCCACCGCGGTGGTGT 241
||| |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct 4867033 GTATCACTCGGCGT-CGGCCAGCGACAGCAGCGACGCGTTGCCGCCCACCGCGGTGGTGT 4867091
Query 242 TCACCGAGGTGGTGCGCTCGCTGAC-AAACGCAGCAGGTAGTTCGGCCCGCCGGCCTTGG 300
||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct 4867092 TCACCGAGGTGGTGCGCTCGCTGACGAAACGCAGCAGGTAGTTCGGCCCGCCGGCCTTGG 4867151
Query 301 GACCG-TGCCGGACAGCCCGTGGCCGCCGAACAGTTGCACGCCCACCACCGCGCCGAT-T 358
||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||| |
Sbjct 4867152 GACCGGTGCCGGACAGCCCGTGGCCGCCGAACGGTTGCACGCCCACCACCGCGCCGATCT 4867211
Query 359 GGTTTCGGTTGACGTAGAGGTTGCCGACCCGCGCCAGCTCTTGGATGCGGCGGGCGGTTT 418
|||| ||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct 4867212 GGTTGCGGTTGACGTAGAGGTTGCCGACCCGCGCCAGCTCTTCGATGCGGCGGGCGGTTT 4867271
Query 419 CCTCGTTGCGGCTGTGGACCCCCATGGTCAGGCCGAAACCGGTGGCGTTTGATGGCCCT 477
||||||||||||||||||||||||||||||||||||||||||||||||| ||| ||| |
Sbjct 4867272 CCTCGTTGCGGCTGTGGACCCCCATGGTCAGGCCGAAACCGGTGGCGTT-GATCGCC-T 4867328
Query = GCF_006742205.1_r100
Length = 431
[Subject genome #1/1] = GCF_006742205.1 Staphylococcus epidermidis
Query coverage per genome = 93.968%
>NZ_AP019721.1
Length = 2422602
HSP cluster #1, HSP #1
Score = 740 bits, Expect = 2.39e-213
Query coverage per seq = 93.968%, Aligned length = 408, Identities = 98.284%, Gaps = 4
Query range = 27-431, Subject range = 1321677-1322083, Strand = Plus/Minus
Query 27 TTCATTTAAAACGATTGCTAATGAGTCACGTATTTCATCTGGTTCGGTAACTATACCGTC 86
||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1322083 TTCATCTAAAACGATTGCTAATGAGTCACGTATTTCATCTGGTTCGGTAACTATACCGTC 1322024
Query 87 TACTATGGACTCAGTGTAACCCTGTAATAAAGAGATTGGCGTACGTAATTCATGTG-TAC 145
|||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct 1322023 TACTATGGACTCAGTGTAACCCTGTAATAAAGAGATTGGCGTACGTAATTCATGTGATAC 1321964
Query 146 ATTTGCTATAAAATCTTTTTTCATTTGATCAAGATTATGTTCATTTGTCATATCACAGGA 205
|||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct 1321963 ATTTGCTATAAAATCTTTTTTCATTTGATCAAGATTATGTTCATTTGTCATATCAC-GGA 1321905
Query 206 TGACCATGACAATACCACTTCTACCATTTGTTTGAATTCTATCTATATAACTGGAGATAA 265
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1321904 TGACCATGACAATACCACTTCTACCATTTGTTTGAATTCTATCTATATAACTGGAGATAA 1321845
Query 266 ATACATAGTACCTTGTATTAATTTCTAATTCTAA-TACTCATTCTGTTGTGATTCAAATG 324
|||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct 1321844 ATACATAGTACCTTGTATTAATTTCTAATTCTAAATACTCATTCTGTTGTGATTCAAATG 1321785
Query 325 GTGCTTCAATTTGCTGTTCAATAGATTCTTTTGAAAAATCATCAATGTGACGCATAATAT 384
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1321784 TTGCTTCAATTTGCTGTTCAATAGATTCTTTTGAAAAATCATCAATGTGACGCATAATAT 1321725
Query 385 AATCAGCCATCTTGTT-GACAATATGATTTCACGTTGATTATTAATGC 431
||||||||||||||| |||||||||||||||||||||||||||||||
Sbjct 1321724 CATCAGCCATCTTGTTTGACAATATGATTTCACGTTGATTATTAATGC 1321677
From file.
$ lexicmap utils 2blast r.lexicmap.tsv -o r.lexicmap.txt