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wenbostar / PGA

PGA: a tool for ProteoGenomics Analysis
http://wenbostar.github.io/PGA/
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Error when running PGA #1

Closed kimthaodao closed 6 years ago

kimthaodao commented 6 years ago

Hi,

I am having a problem when using PGA to generate a protein database from my transcriptome.

Here are the codes I used:

library(PGA)

transcript_seq_file <- system.file("extdata/input", "/Users/kim/Desktop/read_counts_overlapping/Transcriptome_Trinity.fasta",package="PGA")
outdb <- createProDB4DenovoRNASeq(infa=transcript_seq_file,outfile_name = "denovo")

Here is the error:

Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : 
  cannot open file ''

This is the output of sessionInfo()

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] PGA_1.8.0            rTANDEM_1.18.0       Rcpp_0.12.14         XML_3.98-1.9         data.table_1.10.4-3 
 [6] Biostrings_2.46.0    XVector_0.18.0       GenomicRanges_1.30.0 GenomeInfoDb_1.14.0  IRanges_2.12.0      
[11] S4Vectors_0.16.0     BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.38.0             RMySQL_0.10.13             tidyr_0.7.2                bit64_0.9-7               
 [5] splines_3.4.3              Formula_1.2-2              assertthat_0.2.0           latticeExtra_0.6-28       
 [9] blob_1.1.0                 BSgenome_1.46.0            Rsamtools_1.30.0           GenomeInfoDbData_0.99.1   
[13] progress_1.1.2             RSQLite_2.0                backports_1.1.1            lattice_0.20-35           
[17] glue_1.2.0                 digest_0.6.12              RColorBrewer_1.1-2         checkmate_1.8.5           
[21] colorspace_1.3-2           htmltools_0.3.6            Matrix_1.2-12              plyr_1.8.4                
[25] DESeq2_1.18.1              pkgconfig_2.0.1            pheatmap_1.0.8             customProDB_1.18.0        
[29] biomaRt_2.34.0             genefilter_1.60.0          zlibbioc_1.24.0            purrr_0.2.4               
[33] xtable_1.8-2               scales_0.5.0               BiocParallel_1.12.0        htmlTable_1.11.0          
[37] tibble_1.3.4               annotate_1.56.1            ggplot2_2.2.1              AhoCorasickTrie_0.1.0     
[41] GenomicFeatures_1.30.0     SummarizedExperiment_1.8.0 nnet_7.3-12                lazyeval_0.2.1            
[45] survival_2.41-3            magrittr_1.5               memoise_1.1.0              foreign_0.8-69            
[49] prettyunits_1.0.2          tools_3.4.3                matrixStats_0.52.2         stringr_1.2.0             
[53] munsell_0.4.3              locfit_1.5-9.1             cluster_2.0.6              DelayedArray_0.4.1        
[57] AnnotationDbi_1.40.0       bindrcpp_0.2               compiler_3.4.3             rlang_0.1.4               
[61] grid_3.4.3                 RCurl_1.95-4.8             rstudioapi_0.7             VariantAnnotation_1.24.2  
[65] htmlwidgets_0.9            bitops_1.0-6               base64enc_0.1-3            gtable_0.2.0              
[69] DBI_0.7                    R6_2.2.2                   GenomicAlignments_1.14.1   Nozzle.R1_1.1-1           
[73] gridExtra_2.3              rtracklayer_1.38.2         knitr_1.17                 dplyr_0.7.4               
[77] bit_1.1-12                 bindr_0.1                  Hmisc_4.0-3                stringi_1.1.6             
[81] geneplotter_1.56.0         rpart_4.1-11               acepack_1.4.1

Could someone help me with this, please? Thank you.

wenbostar commented 6 years ago

Hi Kim,

You cannot use system.file to specify your own data path. Please use the following code:

library(PGA)
transcript_seq_file <- "/Users/kim/Desktop/read_counts_overlapping/Transcriptome_Trinity.fasta"
outdb <- createProDB4DenovoRNASeq(infa=transcript_seq_file,outfile_name = "denovo")

Please let me know if it works.

Bo

kimthaodao commented 6 years ago

Hi Bo,

Yes it worked. Thank you for your help.

Kim