fu-virfilter

Filter sequences from VirFinder predictions CSV file.

  Usage: fu-virfilter [options] <virfinder> <fasta>

  Files:
    <virfinder>                VirFinder output file (csv format)
    <fasta-file>               FASTA file to filter

  Options:
    -p, --max-pvalue FLOAT     Maximum p-value to keep [default: 0.05]
    -s, --min-score FLOAT      Minimum score [default: 0.90]
    --min-len INT              Minimum length [default: 100]
    --max-len INT              Maximum length [default: 1000000]

  Other options:
    --sep CHAR                 Separator [default: ,]
    -v, --verbose              Verbose output
    -h, --help                 Show this help

Example input and output

Virfinder output:

"","name","length","score","pvalue"
"1","k141_48132 flag=1 multi=2.0000 len=317",317,0.805265057231112,0.003813306852036
"2","k141_58828 flag=1 multi=1.0000 len=302",302,0.386511266211445,0.27648460774578
"3","k141_80217 flag=1 multi=2.0000 len=310",310,0.245554967660862,0.424905660377358

While the FASTA file is:

>k141_74870 flag=1 multi=2.0000 len=369
AAAGGCGTGTGTGCCTTGAGCCTTAGACCATGTGAATTGTAAATCAGTGTATAGCCGGCGATACCGGTTTTCTTGTTCA
TCGCACGGCAGAAGCCTCCATCTATCACAAACAGCTTGCCATTGGCCCTGACAGGGTTCTCTCCCTCTATTGCGTGAAC
GGTGTATGTCCATTTATGATATGCGCATCATCATCATACAGCCCGAACTCGTGCAGTATCTGACAGCAGAAGCTCTTAT
CGTAATACCTGCTGTAATATGGGTTAGAAGGCTCTTCCCACATGCTCTTGTCTGTAACATATTCCATCTCAAAGGTCTT
AAGCCTTCTGCCGCACAGCGGTGATTTTTCTCCTCCCCACAAAAACCACATA
>k141_106952 flag=1 multi=2.0000 len=384
GCGGGCGTTACCCCGGAAGCGGCATGGAGGGCCTGGGAGAAACCGTCCCACAGGCTGCGGCTGCAGCGGCAGTCCGCGA
GGGAGACCGGATACCAGCGGACCAGGGGGTCGGCCGCGACGCGCCGCCCGGTCCCGCCGGTGAGGATGCGCAGCCCCCC
GGATTCTGCGGGCAGGCGGACCTCCAGATCTTCCGTGACCGGGGTCTGACAGGCCAGGACCGAGACCCATTCCTCCCCG
CGGCGGAGCGCCACACGGCACTTTCCGCAGGTCCCATTCCCGCCGCAGGGGCTGTCCAGCCAGAGACCGGCCGCACGGC
AGGCCTCCATCAGCGTGCTTCCCAGGGGGACGGAGCAGCGCACGTCCGCCGGGAGAAAGCGTACCTGT