Merge pull request #3 from sidora-tools/r_package

turn pandora2eager into an R package.

.Rbuildignore

@@ -0,0 +1,9 @@
+^pandora2eager\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+.credentials
+pandora2eager.sif
+pandora2eager.sh
+p2e_singularity.def
+helptext.sh
+build_singularity_with_docker.sh

.gitignore

@@ -1,2 +1,7 @@
 .credentials
 pandora2eager.sif
+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store

DESCRIPTION

@@ -0,0 +1,15 @@
+Package: pandora2eager
+Title: Prepare an input TSV file for nf-core/eager with informations from Pandora
+Version: 0.2.2
+Authors@R: 
+    person("Thiseas Christos", "Lamnidis", email = "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-4485-8570"))
+Description: Provided with a list of Pandora Sequencing IDs, pandora2eager.R will pull Site, Individual, Library 
+  and Sequencing information from Pandora and create a TSV file with the information needed to run nf-core/eager
+    on data from these Sequencing IDs.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
+Imports: 
+    stringr

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2021
+COPYRIGHT HOLDER: THISEAS C. LAMNIDIS

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2021 pandora2eager authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+export(infer_color_chem)
+export(infer_library_specs)

R/infer_columns.R

@@ -0,0 +1,98 @@
+#' Infer colour chemistry from sequencer name
+#'
+#' @param x character. The sequencer name as it appears in Pandora.
+#'
+#' @return integer
+#' @export
+infer_color_chem <- function(x) {
+  color_chem <- NULL
+  if (x %in% c("K00233 (HiSeq4000)","D00829 (HiSeq2500)","M02279 (MiSeq1)", "M06210 (MiSeq2)")) {
+    color_chem=4
+  } else if (x %in% c("NS500382 (Rosa)","NS500559 (Tosca)" )) {
+    color_chem=2
+  } else if (x %in% c("MinIon 1", "MinIon 2", "MinIon HKI")) {
+    color_chem=NA
+    message("MinIon sequencing does not have color chemistry. Set to NA.")
+  } else {
+    message("Color chemistry inference was not successful. Uninferred color chemistries set to 'Unknown'. Contact: [email protected].")
+    color_chem="Unknown"
+  }
+  return(as.integer(color_chem))
+}
+
+#' Infer strandedness and udg_treatment from protocol number
+#'
+#' @param x character. The libary protocol as it appears in Pandora.
+#'
+#' @return character vector
+#' @export
+infer_library_specs <- function(x) {
+  udg_treatment <- NULL
+  strandedness <- NULL
+  words <- stringr::str_split(x, " " , simplify = T)
+  ## ssLib non-UDG
+  if ((words[,1] == "ssLibrary" || words[,1] == "SsLibrary") && utils::tail(words[1,],1) == "2018") {
+    strandedness = "single"
+    udg_treatment = "none"
+
+    ## ssLib Unknown UDG
+  } else if (words[,1] == "ssLibrary" && utils::tail(words[1,],1) == "EVA") {
+    message("Inference of UDG treatment failed for protocol '",x,"'. Setting to 'Unknown'.
+You will need to fill in this information manually, since this protocol could refer to either UDG treatment.
+")
+    strandedness = "single"
+    udg_treatment = "Unknown"
+
+    ## ssLib automated non-UDG Leipzig
+  } else if (words[,1] == "Automated_ss_library_preparation_noUDG_EVA_CoreUnit") {
+    strandedness = "single"
+    udg_treatment = "none"
+
+    ## ssLib automated half-UDG Leipzig
+  } else if (words[,1] == "Automated_ss_library_preparation_partialUDG_EVA_CoreUnit") {
+    strandedness = "single"
+    udg_treatment = "half"
+
+    ## External
+  } else if (words[,1] %in% c("Extern", "External")) {
+    strandedness = "Unknown"
+    udg_treatment = "Unknown"
+    message("Cannot infer strandedness and UDG treatment for external libraries. Setting both to \"Unknown\".")
+
+    ## Modern DNA
+  } else if (words[,1] == "Illumina") {
+    strandedness = "double"
+    udg_treatment = "none"
+
+    ## dsLib
+  } else if (words[,1] == "dsLibrary") {
+    strandedness = "double"
+
+    ## Non UDG
+    if (words[,3] == "UDG" ) {
+      udg_treatment = "none"
+
+      ## Half UDG
+    } else if (words[,3] == "half") {
+      udg_treatment = "half"
+
+      ## Full UDG
+    } else if (words[,3] == "full") {
+      udg_treatment = "full"
+    }
+
+    ## Blanks
+  } else if (words[,1] == "Capture") {
+    udg_treatment = "none"
+    strandedness = "double"
+
+    ## Inference failed?
+  } else {
+    message("Inference of strandedness and UDG treatment failed for library protocol '",x,"'. Setting both fields to 'Unknown'. Please fill in this informations manually.
+Contact [email protected] if you think the library protocol stated could be automatically inferred.
+")
+    udg_treatment = "Unknown"
+    strandedness = "Unknown"
+  }
+  return(c(strandedness, udg_treatment))
+}

pandora2eager.R → exec/pandora2eager.R

@@ -8,95 +8,7 @@ library(dplyr, warn.conflicts = F)
 library(readr)
 library(tidyr)
 library(stringr)
-
-## Infer colour chemistry from sequencer name
-infer_color_chem <- function(x) {
-  color_chem <- NULL
-    if (x %in% c("K00233 (HiSeq4000)","D00829 (HiSeq2500)","M02279 (MiSeq1)", "M06210 (MiSeq2)")) {
-    color_chem=4
-  } else if (x %in% c("NS500382 (Rosa)","NS500559 (Tosca)" )) {
-    color_chem=2
-  } else if (x %in% c("MinIon 1", "MinIon 2", "MinIon HKI")) {
-    color_chem=NA
-    message("MinIon sequencing does not have color chemistry. Set to NA.")
-  } else {
-    message("Color chemistry inference was not successful. Uninferred color chemistries set to 'Unknown'. Contact: [email protected].")
-    color_chem="Unknown"
-  }
-  return(as.integer(color_chem))
-}
-
-## Infer strandedness and udg_treatment from protocol number
-infer_library_specs <- function(x) {
-  udg_treatment <- NULL
-  strandedness <- NULL
-  words <- str_split(x, " " , simplify = T)
-  ## ssLib non-UDG
-  if ((words[,1] == "ssLibrary" || words[,1] == "SsLibrary") && tail(words[1,],1) == "2018") {
-    strandedness = "single"
-    udg_treatment = "none"
-
-  ## ssLib Unknown UDG
-  } else if (words[,1] == "ssLibrary" && tail(words[1,],1) == "EVA") {
-    message("Inference of UDG treatment failed for protocol '",x,"'. Setting to 'Unknown'.
-You will need to fill in this information manually, since this protocol could refer to either UDG treatment.
-")
-    strandedness = "single"
-    udg_treatment = "Unknown"
-
-    ## ssLib automated non-UDG Leipzig
-  } else if (words[,1] == "Automated_ss_library_preparation_noUDG_EVA_CoreUnit") {
-    strandedness = "single"
-    udg_treatment = "none"
-
-  ## ssLib automated half-UDG Leipzig
-  } else if (words[,1] == "Automated_ss_library_preparation_partialUDG_EVA_CoreUnit") {
-    strandedness = "single"
-    udg_treatment = "half"
-
-  ## External
-  } else if (words[,1] %in% c("Extern", "External")) {
-    strandedness = "Unknown"
-    udg_treatment = "Unknown"
-    message("Cannot infer strandedness and UDG treatment for external libraries. Setting both to \"Unknown\".")
-
-  ## Modern DNA
-  } else if (words[,1] == "Illumina") {
-    strandedness = "double"
-    udg_treatment = "none"
-
-  ## dsLib
-  } else if (words[,1] == "dsLibrary") {
-    strandedness = "double"
-
-    ## Non UDG
-    if (words[,3] == "UDG" ) {
-      udg_treatment = "none"
-
-    ## Half UDG
-    } else if (words[,3] == "half") {
-      udg_treatment = "half"
-
-    ## Full UDG
-    } else if (words[,3] == "full") {
-      udg_treatment = "full"
-    }
-
-  ## Blanks
-  } else if (words[,1] == "Capture") {
-      udg_treatment = "none"
-      strandedness = "double"
-
-  ## Inference failed?
-  } else {
-      message("Inference of strandedness and UDG treatment failed for library protocol '",x,"'. Setting both fields to 'Unknown'. Please fill in this informations manually. 
-Contact [email protected] if you think the library protocol stated could be automatically inferred.
-")
-    udg_treatment = "Unknown"
-    strandedness = "Unknown"
-  }
-  return(c(strandedness, udg_treatment))
-}
+library(pandora2eager)
 
 ## Main function that queries pandora, formats info and spits out a table with the necessary information for eager.
 collect_and_format_info<- function(query_list_seq, con) {
@@ -108,12 +20,12 @@ collect_and_format_info<- function(query_list_seq, con) {
       )), con = con
     )
   )
-  
+
   ## Get tabs of Organisms, Protocols and Sequencer names
   df_list <- get_df_list(
     c("TAB_Organism", "TAB_Protocol", "TAB_Sequencing_Sequencer"),con
   )
-  
+
   results <- inner_join(complete_pandora_table, query_list_seq, by=c("sequencing.Full_Sequencing_Id"="Sequencing")) %>%
     select(library.Full_Library_Id, capture.Full_Capture_Id, sequencing.Sequencer, sequencing.Sequencing_Id, individual.Full_Individual_Id, library.Protocol, individual.Organism, raw_data.FastQ_Files) %>%
     ## Infer protocol and Organism names from Pandora indexes
@@ -122,10 +34,10 @@ collect_and_format_info<- function(query_list_seq, con) {
            Sequencer=df_list[["TAB_Sequencing_Sequencer"]][["sequencer.Name"]][`sequencing.Sequencer`]) %>%
     ## Infer SE/PE sequencing from number of FastQs per lane.
     mutate(
-      num_fq=map_int(`raw_data.FastQ_Files`, function(fq) {ncol(str_split(fq, " ", simplify = T))}), 
+      num_fq=map_int(`raw_data.FastQ_Files`, function(fq) {ncol(str_split(fq, " ", simplify = T))}),
       num_r1=map(`raw_data.FastQ_Files`, function(fq) {sum(grepl("_R1_",str_split(fq, " ", simplify = T)))}),
       SeqType=ifelse(num_fq == num_r1, "SE", "PE")) %>%
-    select(-starts_with("num_")) %>% 
+    select(-starts_with("num_")) %>%
     ## Make R1 and R2 columns out of the FastQ file(s)
     mutate(`raw_data.FastQ_Files`=map(`raw_data.FastQ_Files`, function(fq) {str_replace_all(fq, " ([[:graph:]]*_R2_.{3}.fastq.gz)", paste0(";","\\1"))})) %>%
     separate_rows(`raw_data.FastQ_Files`, sep=" ") %>%
@@ -134,13 +46,13 @@ collect_and_format_info<- function(query_list_seq, con) {
     mutate(
       ## Eager cannot handle same lane number for same Library_Id. Therefore lane number for additional sequencing needs to be
       ## artificially inflated (by 8 which is the max lane number in our sequencers). This approach has the advantage that the output
-      ## for a given sequencing ID will be consistent and not dependent on the specific input file passed to this script. 
-      Lane=as.integer(str_replace(`R1`,"[[:graph:]]*_L([[:digit:]]{3})_R[[:graph:]]*", "\\1"))+8*(sequencing.Sequencing_Id-1), 
+      ## for a given sequencing ID will be consistent and not dependent on the specific input file passed to this script.
+      Lane=as.integer(str_replace(`R1`,"[[:graph:]]*_L([[:digit:]]{3})_R[[:graph:]]*", "\\1"))+8*(sequencing.Sequencing_Id-1),
       ## Library Strandedness and UDG Treatment from protocol name
-      Strandedness=map_chr(`Protocol`, function (.) {infer_library_specs(.)[1]}), 
-      UDG_Treatment=map_chr(`Protocol`, function(.){infer_library_specs(.)[2]}), 
+      Strandedness=map_chr(`Protocol`, function (.) {pandora2eager::infer_library_specs(.)[1]}),
+      UDG_Treatment=map_chr(`Protocol`, function(.){pandora2eager::infer_library_specs(.)[2]}),
       ## Colour Chemistry from sequencer name
-      Colour_Chemistry=map_int(`Sequencer`, infer_color_chem),
+      Colour_Chemistry=map_int(`Sequencer`, pandora2eager::infer_color_chem),
       ## BAM column always set to NA
       BAM=NA
     ) %>%
@@ -168,15 +80,15 @@ if (!is.na(args[3]) && args[3] == "--debug") {
   write_tsv(results, "Debug_table.txt")
 } else if (!is.na(args[3]) && ( args[3] == "--rename" || args[3] == "-r")) {
   cat(
-    format_tsv(results %>% 
+    format_tsv(results %>%
                  mutate(Library_ID=str_replace_all(Library_ID, "[.]", "_")) %>% ## Replace dots in the Library_ID to underscores.
-                 select(Sample_Name, Library_ID,  Lane, Colour_Chemistry, 
+                 select(Sample_Name, Library_ID,  Lane, Colour_Chemistry,
                         SeqType, Organism, Strandedness, UDG_Treatment, R1, R2, BAM))
   )
 } else {
   cat(
-    format_tsv(results %>% 
-              select(Sample_Name, Library_ID,  Lane, Colour_Chemistry, 
+    format_tsv(results %>%
+              select(Sample_Name, Library_ID,  Lane, Colour_Chemistry,
                      SeqType, Organism, Strandedness, UDG_Treatment, R1, R2, BAM))
   )
 }

p2e_singularity.def

@@ -3,14 +3,14 @@ From: rocker/tidyverse:4.1.1
 
 %files
   .credentials
-  pandora2eager.R
   helptext.sh
 
 %post
   chmod 644 /.credentials
   apt-get update && apt-get install -y libmariadb-dev
   R --slave -e 'install.packages(c("remotes", "DBI", "RMariaDB"))'
   R --slave -e 'remotes::install_github("sidora-tools/sidora.core", dependencies = TRUE)'
+  R --slave -e 'remotes::install_github("sidora-tools/pandora2eager", dependencies = TRUE)'
 
 %runscript
   #!/bin/bash
@@ -20,12 +20,12 @@ From: rocker/tidyverse:4.1.1
     bash /helptext.sh
   elif [[ ${#@} -gt 1 ]]; then 
     shift
-    /pandora2eager.R ${input} /.credentials $*
+    /usr/local/lib/R/site-library/pandora2eager/exec/pandora2eager.R ${input} /.credentials $*
   else
-    /pandora2eager.R ${input} /.credentials
+    /usr/local/lib/R/site-library/pandora2eager/exec/pandora2eager.R ${input} /.credentials
   fi
 
 %labels
   Author  Thiseas C. Lamnidis
   GithubUrl https://github.com/sidora-tools/pandora2eager.git
-  Version 0.2.1-beta
+  Version 0.2.2