Made changes in assign_job_queue.R, cleanup.R, lineage.R, msa.R, tree.R #106
Conversation
jananiravi
added
outreachy
R/msa.R
Outdated
| @@ -196,7 +196,7 @@ createMSA_PDF <- function(fasta_path, out_path = NULL, | |||
| #' will be saved. | |||
| #' | |||
| #' @importFrom Biostrings readAAStringSet | |||
| #' | |||
| #' @importFrom stats kalign | |||
There was a problem hiding this comment.
The stats package does not export kalign(), but looking at the nearby code, we may need to incorporate some code from here: https://github.com/mhahsler/rMSA/blob/master/R/kalign.R
There was a problem hiding this comment.
This is likely outside the scope of this PR/issue, but a great find!!
R/tree.R
Outdated
| @@ -57,10 +57,10 @@ | |||
| #' here("src/FastTree") | |||
| #' } | |||
| convertFA2Tree <- function(fa_path = here("data/alns/pspa_snf7.fa"), | |||
| tre_path = here("data/alns/pspa_snf7.tre"), | |||
| .data$tre_path = here("data/alns/pspa_snf7.tre"), | |||
There was a problem hiding this comment.
This .data is not needed.
| @@ -57,11 +57,8 @@ | |||
| #' here("src/FastTree") | |||
| #' } | |||
| convertFA2Tree <- function(fa_path = here("data/alns/pspa_snf7.fa"), | |||
There was a problem hiding this comment.
If these default/example files don't exist, we could remove them. Otherwise, placeholders that work might be a good idea!
R/lineage.R
Outdated
| @@ -395,10 +395,10 @@ IPG2Lineage <- function(accessions, ipg_file, | |||
| { | |||
| # browser() | |||
| acc <- accessions[i] | |||
| acc_inds <- which(mergedTax$Protein == acc) | |||
| acc_inds <- which(.data$mergedTax$Protein == acc) | |||
There was a problem hiding this comment.
This is not needed and makes me think that the IPG2Lineage() function defined in acc2lin.R may be more recent/relevant. mergedTax looks like it may have been pulled from the Global Environment at some point in the past -- it will not work as it exists in this function.
Again, this is outside the scope of this issue, but something we will need to disambiguate (acc2lin.R vs lineage.R)/correct moving forward!
Description
What kind of change(s) are included?
Checklist
Please ensure that all boxes are checked before indicating that this pull request is ready for review.
@the-mayer I have added a
globals.RforProteininLineage.RAs suggested. The names of most of the functions have been changed. I can update those in the issue if you'd want that.[x] generate_fa2tre: function not found but I add
.data$to ‘tre_path’ in the updated function[x] get_proc_medians : : no visible global function definition for ‘median’
[x] generate_msa: no visible global function definition for ‘kalign’
[ ] getJobsWithStates: not found
[x] get_proc_medians : : no visible global function definition for ‘median’
[x] IPG2Lineage updated from ipg2lin
[x] ipg2lin: no visible binding for global variable ‘Protein’
[x] ipg2lin: no visible binding for global variable ‘mergedTax’
[x] ipg2lin: no visible binding for global variable ‘gca_ipg_dt’
[x] ipg2lin: no visible binding for global variable ‘assembly_path’
[x] ipg2lin: no visible binding for global variable ‘Lineage’
[x] ipr2viz: no visible binding for global variable ‘iprscan_cols’
[x] ipr2viz: no visible binding for global variable ‘Name’
[x] ipr2viz: no visible binding for global variable ‘Lineage_short’
[x] ipr2viz: no visible binding for global variable ‘QueryName’
[x] ipr2viz: no visible binding for global variable ‘PcPositive’
[x] ipr2viz: no visible binding for global variable ‘AccNum’.
I finished these variables ipr2viz in my previous PR which were approved but even though the PR wasn't merged they have been updated.
[x] write_proc_medians_table: no visible binding for global variable ‘median_seconds’