Merge pull request #8 from 4dn-dcic/dev

Dev
4dn-dcic · Apr 2, 2017 · 81a0d71 · 81a0d71
2 parents f3637c3 + a8a8dc3
commit 81a0d71
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Rpairix
 Title: Rpairix
-Version: 0.0.3
+Version: 0.0.4
 Authors@R: person("Soo", "Lee", email = "[email protected]", role = c("aut", "cre"))
 Description: R binder for pairix, tool for querying a pair of genomic ranges in a pairs file (pairix-indexed bgzipped text file)
 Depends:

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(px_exists)
 export(px_keylist)
 export(px_query)
 export(px_seq1list)
@@ -9,3 +10,4 @@ useDynLib(Rpairix,get_keylist)
 useDynLib(Rpairix,get_keylist_size)
 useDynLib(Rpairix,get_lines)
 useDynLib(Rpairix,get_size)
+useDynLib(Rpairix,key_exists)
diff --git a/R/px_exists.R b/R/px_exists.R
@@ -0,0 +1,30 @@
+#' Check function on pairix-indexed pairs file.
+#'
+#' This function allows you to check if a key (chr for 1D, chr pair for 2D) exists in a pairs file.
+#'
+#' @param filename a pairs file, or a bgzipped text file (sometextfile.gz) with an index file sometextfile.gz.px2 in the same folder.
+#' @param key a pair of chromosomes in the query string format (e.g. "chr1|chr2"), or a chromosome for a 1D-indexed pairs file (e.g. "chr1"). 
+#'
+#' @keywords pairix check
+#' @export px_exists
+#' @examples
+#' filename = system.file(".","test_4dn.pairs.gz", package="Rpairix")
+#' key = "chrX|chrX"
+#' res = px_exists(filename, key)
+#' print(res)
+#'
+#' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz",package="Rpairix")
+#' key = "10|20"
+#' res = px_exists(filename, key)
+#' print(res)
+#'
+#' filename = system.file(".","merged_nodups.space.chrblock_sorted.subsample1.txt.gz",
+#' package="Rpairix")
+#' key = "10|20"
+#' res = px_exists(filename, key)
+#' print(res)
+#' @useDynLib Rpairix key_exists
+px_exists<-function(filename, key){
+  out = .C("key_exists", filename, key, as.integer(0))
+  return(out[[3]][1])
+}
diff --git a/R/px_keylist.R b/R/px_keylist.R
@@ -7,12 +7,19 @@
 #' @keywords pairix query 2D
 #' @export px_keylist
 #' @examples
+#' filename = system.file(".","test_4dn.pairs.gz", package="Rpairix")
+#' res = px_keylist(filename)
+#' print(res)
+#'
 #' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz",package="Rpairix")
 #' res = px_keylist(filename)
+#' print(res)
+#'
 #' filename = system.file(".","merged_nodups.space.chrblock_sorted.subsample1.txt.gz",
 #' package="Rpairix")
-#'
 #' res = px_keylist(filename)
+#' print(res)
+#'
 #' @useDynLib Rpairix get_keylist_size get_keylist
 px_keylist<-function(filename){
    # first-round, get the max length and the number of items in the key list.

diff --git a/R/px_query.R b/R/px_query.R
@@ -10,20 +10,28 @@
 #' @keywords pairix query 2D
 #' @export px_query
 #' @examples
-#' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz",package="Rpairix")
+#' filename = system.file(".","test_4dn.pairs.gz", package="Rpairix")
+#' querystr = "chrX|chrX"
+#' res = px_query(filename, querystr)
+#' print(res)
+#'
+#' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz", package="Rpairix")
 #' querystr = "10:1-1000000|20"
-#' res = px_query(filename,querystr)
+#' res = px_query(filename, querystr)
+#' print(res)
 #'
 #' filename = system.file(".","merged_nodups.space.chrblock_sorted.subsample1.txt.gz",
 #' package="Rpairix")
 #' querystr = "10:1-1000000|20"
-#' res = px_query(filename,querystr)
+#' res = px_query(filename, querystr)
+#' print(res)
+#'
 #' @useDynLib Rpairix get_size get_lines
 px_query<-function(filename, querystr, max_mem=100000000, stringsAsFactors=FALSE){
 
   # first-round, get the max length and the number of lines of the result.
   out =.C("get_size", filename, querystr, as.integer(0), as.integer(0), as.integer(0))
-  if(out[[5]][1] == -1 ) return(NULL)  ## error
+  if(out[[5]][1] == -1 ) { message("Can't open input file"); return(NULL) }  ## error
   str_len = out[[4]][1]
   n=out[[3]][1]
   total_size = str_len * n

diff --git a/R/px_seq1list.R b/R/px_seq1list.R
@@ -7,8 +7,13 @@
 #' @keywords pairix query 2D
 #' @export px_seq1list
 #' @examples
+#' filename = system.file(".","test_4dn.pairs.gz", package="Rpairix")
+#' res = px_seq1list(filename)
+#' print(res)
+#'
 #' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz",package="Rpairix")
 #' res = px_seq1list(filename)
+#' print(res)
 px_seq1list<-function(filename){
   seqpairs = px_keylist(filename)
   seq1_list = unique(sapply(seqpairs,function(xx)strsplit(xx,'|',fixed=T)[[1]][1]))

diff --git a/R/px_seq2list.R b/R/px_seq2list.R
@@ -7,8 +7,13 @@
 #' @keywords pairix query 2D
 #' @export px_seq2list
 #' @examples
+#' filename = system.file(".","test_4dn.pairs.gz", package="Rpairix")
+#' res = px_seq2list(filename)
+#' print(res)
+#'
 #' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz",package="Rpairix")
 #' res = px_seq2list(filename)
+#' print(res)
 px_seq2list<-function(filename){
   seqpairs = px_keylist(filename)
   seq2_list = unique(sapply(seqpairs,function(xx)strsplit(xx,'|',fixed=T)[[1]][2]))

diff --git a/R/px_seqlist.R b/R/px_seqlist.R
@@ -7,8 +7,13 @@
 #' @keywords pairix query 2D
 #' @export px_seqlist
 #' @examples
+#' filename = system.file(".","test_4dn.pairs.gz", package="Rpairix")
+#' res = px_seqlist(filename)
+#' print(res)
+#'
 #' filename = system.file(".","merged_nodup.tab.chrblock_sorted.txt.gz",package="Rpairix")
 #' res = px_seqlist(filename)
+#' print(res)
 px_seqlist<-function(filename){
   seqpairs = px_keylist(filename)
   seq1_list = unique(sapply(seqpairs,function(xx)strsplit(xx,'|',fixed=T)[[1]][1]))

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ R --no-site-file --no-environ --no-save --no-restore CMD INSTALL --install-tests
 To install a specific version,
 ```
 library(devtools)
-install_url("https://github.com/4dn-dcic/Rpairix/archive/0.0.3.zip")
+install_url("https://github.com/4dn-dcic/Rpairix/archive/0.0.4.zip")
 ```
 
 
@@ -72,43 +72,42 @@ px_seq2list(filename)
 * The filename is sometextfile.gz and an index file sometextfile.gz.px2 must exist.
 * The return value is a vector of second chromosomes.
 
+### Check if a chromosome pair (or chromosome, for 1D) exists
+```
+px_exists(filename, key)
+```
+* The filename is sometextfile.gz and an index file sometextfile.gz.px2 must exist.
+* Key is a chromosome pair (or a chromosome for 1D)
+* The return value is 1 (exists), 0 (not exist), or -1 (error)
 
 ## Example run
 ```
 > library(Rpairix)
-> filename = "inst/merged_nodup.tab.chrblock_sorted.txt.gz"
-> querystr = "10:1-1000000|20"
+> filename = "inst/test_4dn.pairs.gz"
+> querystr = "chr10:1-3000000|chr20"
 > res = px_query(filename,querystr)
 > print(res)
-  V1 V2     V3   V4 V5 V6       V7     V8
-1  0 10 624779 1361  0 20 40941397  97868
-2 16 10 948577 2120 16 20 59816485 148396
->
-> keys = px_keylist("inst/merged_nodup.tab.chrblock_sorted.txt.gz")
+                   V1    V2      V3    V4      V5 V6 V7
+1 SRR1658581.51740952 chr10  157600 chr20  167993  -  -
+2 SRR1658581.33457260 chr10 2559777 chr20 7888262  -  +
+> keys = px_keylist(filename)
 > length(keys)
-[1] 1239
+[1] 800
 > keys[1:10]
-[1] "1|1"  "1|10" "1|11" "1|12" "1|13" "1|14" "1|15" "1|16" "1|17" "1|18"
->
->chrs = px_seqlist("inst/merged_nodup.tab.chrblock_sorted.txt.gz")
->chrs
- [1] "1"          "10"         "11"         "12"         "13"        
- [6] "14"         "15"         "16"         "17"         "18"        
-[11] "19"         "2"          "20"         "21"         "22"        
-[16] "3"          "4"          "5"          "6"          "7"         
-[21] "8"          "9"          "GL000191.1" "GL000192.1" "GL000193.1"
-[26] "GL000194.1" "GL000195.1" "GL000196.1" "GL000197.1" "GL000198.1"
-[31] "GL000199.1" "GL000200.1" "GL000201.1" "GL000202.1" "GL000203.1"
-[36] "GL000204.1" "GL000205.1" "GL000206.1" "GL000208.1" "GL000209.1"
-[41] "GL000210.1" "GL000211.1" "GL000212.1" "GL000213.1" "GL000214.1"
-[46] "GL000215.1" "GL000216.1" "GL000217.1" "GL000218.1" "GL000219.1"
-[51] "GL000220.1" "GL000221.1" "GL000222.1" "GL000223.1" "GL000224.1"
-[56] "GL000225.1" "GL000226.1" "GL000227.1" "GL000228.1" "GL000229.1"
-[61] "GL000230.1" "GL000231.1" "GL000232.1" "GL000233.1" "GL000234.1"
-[66] "GL000235.1" "GL000236.1" "GL000237.1" "GL000238.1" "GL000239.1"
-[71] "GL000240.1" "GL000241.1" "GL000242.1" "GL000243.1" "GL000244.1"
-[76] "GL000245.1" "GL000246.1" "GL000247.1" "GL000248.1" "GL000249.1"
-[81] "MT"         "NC_007605"  "X"          "Y"     
+ [1] "chr1|chr1"            "chr1|chr10"           "chr1|chr11"          
+ [4] "chr1|chr12"           "chr1|chr13"           "chr1|chr14"          
+ [7] "chr1|chr15"           "chr1|chr16"           "chr1|chr17"          
+[10] "chr1|chr17_ctg5_hap1"
+> chrs = px_seqlist(filename)
+> length(chrs)
+[1] 82
+> chrs[1:10]
+ [1] "chr1"                  "chr1_gl000191_random"  "chr1_gl000192_random" 
+ [4] "chr10"                 "chr11"                 "chr11_gl000202_random"
+ [7] "chr12"                 "chr13"                 "chr14"                
+[10] "chr15"                
+> px_exists(filename, "chr10|chr20")
+[1] 1
 ```
 
 
@@ -122,3 +121,19 @@ document()
 Individual R functions are written and documented in `R/`. The `src/rpairixlib.c` is the main C source file. Raw data files are under `inst/`.
 
 
+## Version history
+### 0.0.4
+* Function px_exists is now added.
+* Source is synced with pairix/pypairix 0.1.1.
+* 4dn pairs example is added
+
+### 0.0.3
+* corrected a typo in README
+
+### 0.0.2
+* cleaned up repo
+* added more instructions in README
+
+### 0.0.1
+* initial release
+
diff --git a/Rpairix.Rproj b/Rpairix.Rproj
@@ -1,4 +1,4 @@
-Version: 1.0
+Version: 0.0.4
 
 RestoreWorkspace: No
 SaveWorkspace: No

diff --git a/inst/test_4dn.pairs.gz b/inst/test_4dn.pairs.gz
diff --git a/inst/test_4dn.pairs.gz.px2 b/inst/test_4dn.pairs.gz.px2
diff --git a/man/px_exists.Rd b/man/px_exists.Rd
diff --git a/man/px_keylist.Rd b/man/px_keylist.Rd
diff --git a/man/px_query.Rd b/man/px_query.Rd
diff --git a/man/px_seq1list.Rd b/man/px_seq1list.Rd
diff --git a/man/px_seq2list.Rd b/man/px_seq2list.Rd
diff --git a/man/px_seqlist.Rd b/man/px_seqlist.Rd
diff --git a/src/Rpairix.so b/src/Rpairix.so