msa() seems unable to process input sequences in a fasta file, I keep getting (t is an input fasta file with two short AA sequences):

```r

v <- AAStringSet(c(mt="FIPLLVVILFAVDTGLFISTQQQVT",wt="FIPLLVVILFAVHTGLFISTQQQVT"))
t <- tempfile(fileext=".fasta")
on.exit(unlink(t),add=TRUE)
writeXStringSet(v,t)
m <- msa(t, type="protein")

```

Output:

```

use default substitution matrix


ERROR: Cannot open input file. No alignment!

Error in msaClustalW(t, type = "protein") : ClustalW finished with errors

```

If I track down what happens to the inputSeq argument in msa(), it seems it gets turned into upper case regardless if its a file or if its an input AAStringSet:

https://code.bioconductor.org/browse/msa/blob/RELEASE_3_17/R/helperFunctions.R#L56 , see line 56

If I change that to instead just: return(inputSeq) , it works.:

```
> devtools::load_all("~/git/bioconductor/msa/")
ℹ Loading msa
> v <- AAStringSet(c(mt="FIPLLVVILFAVDTGLFISTQQQVT",wt="FIPLLVVILFAVHTGLFISTQQQVT"))
t <- tempfile(fileext=".fasta")
on.exit(unlink(t),add=TRUE)
writeXStringSet(v,t)
m <- msa(t, type="protein")
use default substitution matrix
> m
CLUSTAL 2.1

Call:
   msa(t, type = "protein")

MsaAAMultipleAlignment with 2 rows and 25 columns
    aln
[1] FIPLLVVILFAVDTGLFISTQQQVT
[2] FIPLLVVILFAVHTGLFISTQQQVT
Con FIPLLVVILFAV?TGLFISTQQQVT
>
```


```
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Oslo
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
[1] msa_1.33.1          Biostrings_2.68.1   GenomeInfoDb_1.36.1
[4] XVector_0.40.0      IRanges_2.34.1      S4Vectors_0.38.1
[7] BiocGenerics_0.46.0

loaded via a namespace (and not attached):
 [1] renv_1.0.2              bitops_1.0-7            stringi_1.7.12
 [4] digest_0.6.33           magrittr_2.0.3          pkgload_1.3.2.1
 [7] fastmap_1.1.1           rprojroot_2.0.3         processx_3.8.2
[10] pkgbuild_1.4.2          sessioninfo_1.2.2       brio_1.1.3
[13] urlchecker_1.0.1        ps_1.7.5                promises_1.2.1
[16] BiocManager_1.30.22     purrr_1.0.2             codetools_0.2-19
[19] cli_3.6.1               shiny_1.7.5             rlang_1.1.1
[22] crayon_1.5.2            ellipsis_0.3.2          remotes_2.4.2.1
[25] withr_2.5.0             cachem_1.0.8            devtools_2.4.5
[28] tools_4.3.1             memoise_2.0.1           GenomeInfoDbData_1.2.10
[31] httpuv_1.6.11           vctrs_0.6.3             R6_2.5.1
[34] mime_0.12               lifecycle_1.0.3         zlibbioc_1.46.0
[37] stringr_1.5.0           fs_1.6.3                htmlwidgets_1.6.2
[40] usethis_2.2.2           miniUI_0.1.1.1          desc_1.4.2
[43] callr_3.7.3             later_1.3.1             glue_1.6.2
[46] profvis_0.3.8           Rcpp_1.0.11             rstudioapi_0.15.0
[49] xtable_1.8-4            htmltools_0.5.6         testthat_3.1.10
[52] compiler_4.3.1          prettyunits_1.1.1       RCurl_1.98-1.12
```