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virus-evolution / gofasta

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gofasta snps -> open : no such file or directory #9

Closed tseemann closed 3 years ago

tseemann commented 3 years ago

No matter what I do gofasta snps prints, open : no such file or directoryv v0,0.3

benjamincjackson commented 3 years ago

Could you provide an example of a command that you did run?

❯ gofasta snps -h
Find snps relative to a reference.

Example usage:
    gofasta snps -r reference.fasta -q alignment.fasta -o snps.csv

The output is a csv-format file with one line per query sequence, and two columns:
'query' and 'SNPs', the second of which is a "|"-delimited list of snps in that query.

If input and output files are not specified, the behaviour is to read the query alignment
from stdin and write the snps file to stdout, e.g. you could do this:
    cat alignment.fasta | gofasta snps -r reference.fasta > snps.csv

Usage:
  gofasta snps [flags]

Flags:
  -h, --help               help for snps
  -o, --outfile string     Output to write (default "stdout")
  -q, --query string       Alignment of sequences to find snps in, in fasta format (default "stdin")
  -r, --reference string   Reference sequence, in fasta format
  ❯ gofasta snps -r WH04.fa -q small.fasta
query,SNPs
Australia/NT12/2020,C3037T|T8782C|C14408T|C15324T|C20468T|A23403G|C28144T
Australia/NT13/2020,C3037T|T8782C|C14408T|C15324T|C20468T|A23403G|C28144T
Australia/NT14/2020,A2480G|C2558T|A2832G|T8782C|C14805T|C18526T|G26144T|C28144T
Australia/NT16/2020,C3037T|T8782C|C14408T|A23403G|A24862G|C28144T
Australia/NT17/2020,C3037T|T8782C|C14408T|A23403G|A24862G|C28144T
Jinke233 commented 1 year ago

Could you help me? I meet the same problem with you!