merge-search-results

$ lexicmap utils merge-search-results -h
Merge a query's search results from multiple indexes

Attention:
  1. These search results should come from the same ONE query.
     If not, please specify one query with the flag -q/--query
  2. We assume that genome IDs are distinct across all indexes.
  3. One or more input files are accepted, via positional parameters
     and/or a file list via the flag -X/--infile-list.
  4. Both the default 20- and 24-column formats are supported,
     and formats better be consistent across all input files.
     If not, the output format would be the one with a valid record.

Usage:
  lexicmap utils merge-search-results [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 merge-search-results
  -o, --out-file string      ► Out file, supports the ".gz" suffix ("-" for stdout). (default "-")
  -q, --query string         ► Query ID to merge

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)

lexicmap index -O demo_part1.lmi -X <(ls refs/*.fa.gz | awk 'NR<=5')
lexicmap index -O demo_part2.lmi -X <(ls refs/*.fa.gz | awk 'NR>=6 && NR<=10')
lexicmap index -O demo_part3.lmi -X <(ls refs/*.fa.gz | awk 'NR>10')

query=bench/b.gene_E_coli_16S.fasta

# in practice, one can search in multiple cluster nodes
for index in demo_*.lmi; do
    lexicmap search $query -d $index -o t.lexicmap@$index.tsv.gz --debug
done

lexicmap utils merge-search-results -o t.lexicmap.tsv.gz t.lexicmap@*.tsv.gz

22:41:03.963 [INFO] 15 genome hits merged from 3 files for query: NC_000913.3:4166659-4168200

# search with multiple queries
for index in demo_*.lmi; do
    lexicmap search bench/*.fasta -d $index -o t.lexicmap2@$index.tsv.gz --debug
done

# this would failed
lexicmap utils merge-search-results -o t.lexicmap2.tsv.gz t.lexicmap2@*.tsv.gz

22:46:07.807 [ERRO] inconsistent queries: 'blaLAQ__NG_076677.1' in file 't.lexicmap2@demo_part2.lmi.tsv.gz' and 'blaSHV__NG_242606.1' in file 't.lexicmap2@demo_part1.lmi.tsv.gz. Please specify one query with flag -q/--query

# specify one query

lexicmap utils merge-search-results -o t.lexicmap2.tsv.gz t.lexicmap2@*.tsv.gz \
    -q NC_000913.3:4166659-4168200
    
22:49:01.076 [INFO] 15 genome hits merged from 3 files for query: NC_000913.3:4166659-4168200

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