ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
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0
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lhuang7 ▴ 50
@lhuang7-7824
Last seen 3.9 years ago
United States

Hi,

I try to create an annotation file using the function ParseMetaFromGtfFile() from SCAN.UPC package but get a warning message with no output file generated.

After searching the archive I found this 3-year old post related to the same issue (ParseMetaFromGtfFile is.na() error).

The following is the code snippet I used:

library(SCAN.UPC)

ParseMetaFromGtfFile(gtfFilePath = "gencode.v25.annotation.gtf", 
                     fastaFilePattern = "GRCh38.primary_assembly.genome.fa", 
                     outFilePath = "GRCh38_Annotation.txt",  
                     featureTypes = "protein_coding", 
                     attributeType = "gene_id")

# Saving GTF data to temporary files
# Done parsing 10000 lines from gencode.v25.annotation.gtf
# Done parsing 20000 lines from gencode.v25.annotation.gtf
# ...
# Done parsing 2570000 lines from gencode.v25.annotation.gtf
# Warning message:
# In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
sessionInfo()
# R version 3.4.1 (2017-06-30)
# 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 
# [8] methods   base     
# 
# other attached packages:
#  [1] SCAN.UPC_2.18.0     sva_3.25.4          BiocParallel_1.11.6
#  [4] genefilter_1.59.0   mgcv_1.8-19         nlme_3.1-131       
#  [7] foreach_1.4.3       affyio_1.47.0       affy_1.55.0        
# [10] GEOquery_2.43.0     oligo_1.41.1        Biostrings_2.45.3  
# [13] XVector_0.17.0      IRanges_2.11.12     S4Vectors_0.15.5   
# [16] oligoClasses_1.39.1 Biobase_2.37.2      BiocGenerics_0.23.0
# 
# loaded via a namespace (and not attached):
#  [1] SummarizedExperiment_1.7.5 splines_3.4.1             
#  [3] lattice_0.20-35            colorspace_1.3-3          
#  [5] yaml_2.1.14                blob_1.1.0                
#  [7] XML_3.98-1.9               survival_2.41-3           
#  [9] rlang_0.1.2                DBI_0.7                   
# [11] bit64_0.9-7                matrixStats_0.52.2        
# [13] GenomeInfoDbData_0.99.1    stringr_1.2.0             
# [15] zlibbioc_1.23.0            codetools_0.2-15          
# [17] memoise_1.1.0              ff_2.2-13                 
# [19] GenomeInfoDb_1.13.4        BiocInstaller_1.26.1      
# [21] AnnotationDbi_1.39.2       preprocessCore_1.39.0     
# [23] Rcpp_0.12.12               xtable_1.8-2              
# [25] limma_3.33.7               DelayedArray_0.3.19       
# [27] annotate_1.55.0            affxparser_1.49.0         
# [29] bit_1.1-12                 digest_0.6.12             
# [31] stringi_1.1.5              GenomicRanges_1.29.12     
# [33] grid_3.4.1                 tools_3.4.1               
# [35] bitops_1.0-6               magrittr_1.5              
# [37] RCurl_1.95-4.8             RSQLite_2.0               
# [39] tibble_1.3.4               MASS_7.3-47               
# [41] autoinst_0.0.0.9000        Matrix_1.2-11             
# [43] lubridate_1.6.0            httr_1.3.1                
# [45] iterators_1.0.8            R6_2.2.2                  
# [47] compiler_3.4.1

Did I do anything wrong? Can anyone kindly guide me to fix this problem?

Thanks,

Lei

annotation SCAN.UPC • 1.2k views
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I'll look into this and get back to you.

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Thanks Stephen!

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@stephen-piccolo-6761
Last seen 3.5 years ago
United States

Thanks for letting me know about this. Some of the information that is often stored in the second column was stored in a different location within the file. I believe I have fixed the problem. I'll post it as soon as I can to the devel server. But for now, send me an email, and I'll send you the fix.

As an aside, I implemented this parser before other GTF parsers were ubiquitous. For more advanced GTF parsing, it would be best to use one of those (e.g., https://bioconductor.org/packages/devel/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf)

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Thanks for the quick fix!

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