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README.md

synExtra: Extensions for synapser

Sage Bionetworks develops and maintains synapser, an R client for interfacing with Synapse. This package builds on top of synapser to streamline its usage in a functional programming (FP) paradigm. The package can be installed directly from GitHub by running the following from R:

if( !require(devtools) ) install.packages( "devtools" )
devtools::install_github( "ArtemSokolov/synExtra" )

The functionality can be loosely grouped into three categories: 1) downloading and uploading of files, 2) traversal of the Synapse directory structure, and 3) miscellaneous inspection of Synapse entities

1) Downloading and uploading of files

File downloading from Synapse is done primarily via synapser::synGet(). Since the follow-up action is often to load the downloaded file, a canonical synGet() call retrieves the local filename of the downloaded file:

fn <- synapser::synGet( "syn15663039", downloadLocation = "/data/myproject" )$path
X <- readr::read_csv( fn )

If multiple files are to be downloaded, the above code would be wrapped inside a for loop or a purrr::map()-family call:

## 1. Downloading multiple files using a for loop
fns <- c()
for( id in c("syn1710445", "syn1695376", "syn1710429") )
    fns[id] <- synapser::synGet( id, downloadLocation = "/data/myproject" )$path

## 2. Downloading multiple files using purrr::map() family of functions
fns <- purrr::map_chr( c("syn1710445", "syn1695376", "syn1710429"),
                       ~synapser::synGet( .x, downloadLocation = "/data/myproject" )$path )

An alternative solution provided by synExtra creates a downloader function that is linked to a specific local path. The downloader returns location of the downloaded file(s), thereby streamlining the process:

syn <- synExtra::synDownloader( "/data/myproject" )

# Pass Synapse IDs directly to the downloader
fns <- syn( "syn1710445", "syn1695376", "syn1710429" )

# Or store them in a vector and pass that vector instead
ids <- c( "syn1710445", "syn1695376", "syn1710429" )
fns <- syn( ids )

# In either case, fns is now a character vector of local paths
# [1] "/data/myproject/PANCAN12.IlluminaGA_miRNASeq.miRNA.tumor_whitelist"    
# [2] "/data/myproject/PANCAN12.IlluminaHiSeq_miRNASeq.miRNA.normal_whitelist"
# [3] "/data/myproject/PANCAN12.MDA_RPPA_Core.RPPA.tumor_whitelist"           

An important feature of the downloader is that it recognizes whether its arguments are valid synapse IDs. Any argument not recognized to be one is assumed to be a local filename already.

syn( "localFile.csv" )      ## returns "localFile.csv"

This allows for development of tools that abstract away the distinction of local files and files residing on Synapse. For example, consider a simple csvpeek.R script which displays the first 10 lines of a .csv file:

synapser::synLogin()
syn <- synExtra::synDownloader( "./.syn" )
fn <- syn( commandArgs( trailingOnly=TRUE )[1] )
readr::read_csv( fn, col_types=readr::cols(), n_max = 10 )

Such a script accepts local filenames as well as synapse IDs; in the latter case, the file is automatically downloaded to the local .syn directory. The distinction is completely transparent to the user who would use csvpeek.R as follows:

Rscript csvpeek.R localFile.csv
Rscript csvpeek.R syn15663039

File uploading

Similarly, file uploading to Synapse is done primarily via synapser::synStore(). However, uploading a large number of files in a complicated directory structure can become tedious. synExtra provides a wrapper synStoreMany() that functions effectively like the Linux mv command. The function takes two arguments: a local path and the synapse ID of the Project/Folder where the files are to be uploaded to.

synExtra::synStoreMany( "/home/sokolov/devel/synExtra", "syn12180284" )

## The function understands local paths
synExtra::synStoreMany( ".", "syn12180284" )

## As well as relative paths
synExtra::synStoreMany( "../myOtherFolder", "syn12180284" )

2) Traversal of the Synapse directory structure

Similarly to a local filesystem, Synapse entities are organized in a hierarchical fashion. synExtra provides several functions for traversing this hierarchy. First, there is synAncestry(), which takes one or more of synapse IDs and retrieves their full parentId ancestry up to their respective projects:

synAncestry( "syn15663039", "syn1695362" )
# $syn15663039
# [1] "syn15663039" "syn15673834" "syn15673837" "syn12180284"
#
# $syn1695362
# [1] "syn1695362" "syn1695324" "syn2812925" "syn300013" 

In the example above, syn12180284 and syn300013 are the Synapse projects that host the corresponding entities. Note that synAncestry() accepts individual IDs, as well as lists and vectors of IDs. All of the following calls are equivalent:

synAncestry( "syn15663039", "syn1695362" )
synAncestry( c("syn15663039", "syn1695362") )
synAncestry( list("syn15663039", "syn1695362") )
synAncestry( list("syn15663039"), list("syn1695362") )

The second function for traversing the Synapse hierarchy looks in the opposite direction. It's a wrapper around synGetChildren() that returns a named vector of synapse IDs, rather than a Python object. As with synAncestry(), this second function understands individual IDs, as well as lists and vectors of IDs:

synChildren( "syn6185321", "syn5049679" )
# $syn6185321
#          hairpin fasta miRNA mature structure
#           "syn6185324"           "syn6185325"
#
# $syn5049679
# hsa_MTI_6.1.csv
#    "syn5049680"

The last traversal function allows you to identify the synapse ID of an arbitrary descendant, using the names of entities on the traversal path. For example, suppose we want to retrieve the synapse ID of C4 Raw Data/mRNA/Counts/htseq-count/H9.144.7.7.txt from the Progenitor Cell Biology Consortium project. We can do so by calling synPluck() with the synapse ID of the project (syn1773109) as the first argument:

synPluck("syn1773109", "C4 Raw Data", "mRNA", "Counts", "htseq-count", "H9.144.7.7.txt")
# [1] "syn2822560"

## Or equivalently
synPluck("syn1773109", c("C4 Raw Data", "mRNA", "Counts", "htseq-count", "H9.144.7.7.txt"))
synPluck("syn1773109", list("C4 Raw Data", "mRNA", "Counts", "htseq-count", "H9.144.7.7.txt"))

3) Miscellaneous

synExtra provides several additional utility functions. These allow you to

  • determine if something is a valid Synapse ID,
  • retrieve the entity name by Synapse ID,
  • and rename an entity identified by its Synapse ID.
isSynID( "syn1234", "syn", "syn123ab" )
# [1]  TRUE FALSE FALSE
isSynID( list( mtcars, 123, "syn123" ) )
# [1] FALSE FALSE  TRUE

synName( "syn1896429", "syn1901530" )
#                            syn1896429                              syn1901530 
#        "ESTIMATE_scores_PANCAN11.tsv" "ESTIMATE_scores_PANCAN11_RNASeqV2.tsv"
synName( c("syn2247543", "syn2653626"), list("syn1773111", "syn2246520") )
# syn2247543    syn2653626    syn1773111    syn2246520 
#     "mRNA" "methylation"         "BAM"         "BED" 

# synRename() returns the provided Synapse ID for easy integration with %>% pipe
synRename( "syn123", "newfilename.csv" )
# [1] "syn123"

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Extension of `synapser`, a Synapse R client developed by Sage Bionetworks

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