tests/testthat/_snaps/HMMER.md

In currocam/utilsHMMER: HMMERutils

mock phmmer works

Code
  .
Output
  # A tibble: 116 x 47
     algor~1 uuid  stats~2 stats~3 stats~4 stats.Z stats~5 stats~6 stats~7 stats~8
     <chr>   <chr>   <dbl>   <int> <chr>     <dbl>   <int>   <int>   <int>   <int>
   1 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   2 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   3 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   4 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   5 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   6 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   7 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   8 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
   9 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
  10 phmmer  017C~       1     116 0.07     546676       0    3511     116  546676
  # ... with 106 more rows, 37 more variables: stats.user <dbl>,
  #   stats.domZ_setby <int>, stats.n_past_bias <int>, stats.sys <dbl>,
  #   stats.n_past_fwd <int>, stats.total <dbl>, stats.nmodels <int>,
  #   stats.nincluded <int>, stats.n_past_vit <int>, stats.nreported <int>,
  #   stats.domZ <dbl>, hits.archScore <chr>, hits.ph <chr>, hits.arch <chr>,
  #   hits.kg <chr>, hits.ndom <int>, hits.extlink <chr>, hits.taxid <chr>,
  #   hits.acc <chr>, hits.taxlink <chr>, hits.desc <chr>, hits.pvalue <dbl>, ...

mock hmmscan works

Code
  .
Output
  # A tibble: 1 x 36
    algori~1 uuid  stats~2 stats~3 stats~4 stats.Z stats~5 stats~6 stats~7 stats~8
    <chr>    <chr>   <dbl>   <int> <chr>     <dbl>   <int>   <int>   <int>   <int>
  1 hmmscan  2D5A~       1       1 0.06      19632       0     282       1       1
  # ... with 26 more variables: stats.user <dbl>, stats.domZ_setby <int>,
  #   stats.n_past_bias <int>, stats.sys <dbl>, stats.n_past_fwd <int>,
  #   stats.total <dbl>, stats.nmodels <int>, stats.nincluded <int>,
  #   stats.n_past_vit <int>, stats.nreported <int>, stats.domZ <dbl>,
  #   hits.flags <int>, hits.nregions <int>, hits.ndom <int>, hits.name <chr>,
  #   hits.score <dbl>, hits.bias <chr>, hits.taxid <chr>, hits.acc <chr>,
  #   hits.domains <list>, hits.nincluded <int>, hits.evalue <dbl>, ...

mock hmmsearch works

Code
  .
Output
  # A tibble: 110 x 47
     algor~1 uuid  stats~2 stats~3 stats~4 stats.Z stats~5 stats~6 stats~7 stats~8
     <chr>   <chr>   <dbl>   <int> <chr>     <dbl>   <int>   <int>   <int>   <int>
   1 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   2 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   3 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   4 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   5 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   6 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   7 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   8 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
   9 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
  10 hmmsea~ CB34~       1     110 0.06     565928       0   19129     110  565928
  # ... with 100 more rows, 37 more variables: stats.user <dbl>,
  #   stats.domZ_setby <int>, stats.n_past_bias <int>, stats.sys <dbl>,
  #   stats.n_past_fwd <int>, stats.total <dbl>, stats.nmodels <int>,
  #   stats.nincluded <int>, stats.n_past_vit <int>, stats.nreported <int>,
  #   stats.domZ <dbl>, hits.archScore <chr>, hits.ph <chr>, hits.arch <chr>,
  #   hits.kg <chr>, hits.ndom <int>, hits.extlink <chr>, hits.acc2 <chr>,
  #   hits.taxid <chr>, hits.acc <chr>, hits.taxlink <chr>, hits.desc <chr>, ...

mock phmmer with wrong input fails

Code
  .
Warning <http_400>
  Bad Request (HTTP 400).
Output
  NULL

mock hmmscan with wrong input fails

Code
  .
Warning <http_400>
  Bad Request (HTTP 400).
Output
  NULL

mock hmmsearch with wrong input fails

Code
  .
Warning <http_400>
  Bad Request (HTTP 400).
Output
  NULL

currocam/utilsHMMER documentation built on Feb. 19, 2023, 9:54 p.m.