Mixing
How to match two file from two different folder if the part of the file name matches
0
I have files with matching strings in their names located in different locations and I need to match them.
Here is what the files looks like,
na_files
/Users/AS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou
/Users/AS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou
/Users/AS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou
And the following list of files in other directory
lb_files
/Users/DS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib
/Users/DS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib
/Users/DS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib
And I need to match the na_files and lb_files from both lists, to proceed with.
So I tried, using
na_files = grep("cou", list.files(DIR, recursive=T, full.names=T), value=T)
lb_files = grep("lib", list.files(DIR, recursive=T, full.names=T), value=T)
all_patients = NA
for(curr_file_idx in 1:length(pa_files)){
curr_file = pat_files[curr_file_idx]
libsize_file = libsize_files[curr_file_idx]
curr_pa = data.frame(fread(curr_file))
pa_id = strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id = substr(patient_id, 1, 5)
libsize = data.frame(fread(libsize_file))
pa_id2 = strsplit(libsize_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id2 = substr(pa_id2, 1, 5)
if(patient_id != pa_id2){
print(pa_id)
print(pa_id2)
print("WRONG LB")
return(1)
}
But this substring pattern only search one file and throws error for the rest.
Error in strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]] :
subscript out of bounds
I need any regular expression or a pattern which would work for all files. I need the exactly the this part after the period .M4DF, .MSFG, .MOHUA should be matching from the three files.
r substr
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
add a comment |
0
I have files with matching strings in their names located in different locations and I need to match them.
Here is what the files looks like,
na_files
/Users/AS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou
/Users/AS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou
/Users/AS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou
And the following list of files in other directory
lb_files
/Users/DS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib
/Users/DS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib
/Users/DS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib
And I need to match the na_files and lb_files from both lists, to proceed with.
So I tried, using
na_files = grep("cou", list.files(DIR, recursive=T, full.names=T), value=T)
lb_files = grep("lib", list.files(DIR, recursive=T, full.names=T), value=T)
all_patients = NA
for(curr_file_idx in 1:length(pa_files)){
curr_file = pat_files[curr_file_idx]
libsize_file = libsize_files[curr_file_idx]
curr_pa = data.frame(fread(curr_file))
pa_id = strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id = substr(patient_id, 1, 5)
libsize = data.frame(fread(libsize_file))
pa_id2 = strsplit(libsize_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id2 = substr(pa_id2, 1, 5)
if(patient_id != pa_id2){
print(pa_id)
print(pa_id2)
print("WRONG LB")
return(1)
}
But this substring pattern only search one file and throws error for the rest.
Error in strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]] :
subscript out of bounds
I need any regular expression or a pattern which would work for all files. I need the exactly the this part after the period .M4DF, .MSFG, .MOHUA should be matching from the three files.
r substr
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
add a comment |
0
0
0
I have files with matching strings in their names located in different locations and I need to match them.
Here is what the files looks like,
na_files
/Users/AS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou
/Users/AS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou
/Users/AS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou
And the following list of files in other directory
lb_files
/Users/DS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib
/Users/DS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib
/Users/DS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib
And I need to match the na_files and lb_files from both lists, to proceed with.
So I tried, using
na_files = grep("cou", list.files(DIR, recursive=T, full.names=T), value=T)
lb_files = grep("lib", list.files(DIR, recursive=T, full.names=T), value=T)
all_patients = NA
for(curr_file_idx in 1:length(pa_files)){
curr_file = pat_files[curr_file_idx]
libsize_file = libsize_files[curr_file_idx]
curr_pa = data.frame(fread(curr_file))
pa_id = strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id = substr(patient_id, 1, 5)
libsize = data.frame(fread(libsize_file))
pa_id2 = strsplit(libsize_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id2 = substr(pa_id2, 1, 5)
if(patient_id != pa_id2){
print(pa_id)
print(pa_id2)
print("WRONG LB")
return(1)
}
But this substring pattern only search one file and throws error for the rest.
Error in strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]] :
subscript out of bounds
I need any regular expression or a pattern which would work for all files. I need the exactly the this part after the period .M4DF, .MSFG, .MOHUA should be matching from the three files.
r substr
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
I have files with matching strings in their names located in different locations and I need to match them.
Here is what the files looks like,
na_files
/Users/AS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou
/Users/AS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou
/Users/AS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou
And the following list of files in other directory
lb_files
/Users/DS/SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib
/Users/DS/SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib
/Users/DS/SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib
And I need to match the na_files and lb_files from both lists, to proceed with.
So I tried, using
na_files = grep("cou", list.files(DIR, recursive=T, full.names=T), value=T)
lb_files = grep("lib", list.files(DIR, recursive=T, full.names=T), value=T)
all_patients = NA
for(curr_file_idx in 1:length(pa_files)){
curr_file = pat_files[curr_file_idx]
libsize_file = libsize_files[curr_file_idx]
curr_pa = data.frame(fread(curr_file))
pa_id = strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id = substr(patient_id, 1, 5)
libsize = data.frame(fread(libsize_file))
pa_id2 = strsplit(libsize_file, "[.][P][Z][T][-]")[[1]][[2]]
pa_id2 = substr(pa_id2, 1, 5)
if(patient_id != pa_id2){
print(pa_id)
print(pa_id2)
print("WRONG LB")
return(1)
}
But this substring pattern only search one file and throws error for the rest.
Error in strsplit(curr_file, "[.][P][Z][T][-]")[[1]][[2]] :
subscript out of bounds
I need any regular expression or a pattern which would work for all files. I need the exactly the this part after the period .M4DF, .MSFG, .MOHUA should be matching from the three files.
r substr
r substr
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
edited Nov 21 '18 at 14:14
user1017373
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
asked Nov 21 '18 at 13:42
user1017373user1017373
70411025
70411025
add a comment |
add a comment |
1 Answer
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based on your data, extract the file names for na_files and lb_files
na_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou")
lb_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib")
na_files_name<-stringi::stri_extract(na_files,regex = "[^.]+") #extracts file name up to first .
lb_files_name<-stringi::stri_extract(lb_files,regex = "[^.]+")
na_files_name %in% lb_files_name #checks the file names match
answered Nov 21 '18 at 14:03
e.matte.matt
8517
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
add a comment |
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1 Answer
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based on your data, extract the file names for na_files and lb_files
na_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou")
lb_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib")
na_files_name<-stringi::stri_extract(na_files,regex = "[^.]+") #extracts file name up to first .
lb_files_name<-stringi::stri_extract(lb_files,regex = "[^.]+")
na_files_name %in% lb_files_name #checks the file names match
answered Nov 21 '18 at 14:03
e.matte.matt
8517
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
add a comment |
0
based on your data, extract the file names for na_files and lb_files
na_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou")
lb_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib")
na_files_name<-stringi::stri_extract(na_files,regex = "[^.]+") #extracts file name up to first .
lb_files_name<-stringi::stri_extract(lb_files,regex = "[^.]+")
na_files_name %in% lb_files_name #checks the file names match
answered Nov 21 '18 at 14:03
e.matte.matt
8517
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
add a comment |
0
0
0
based on your data, extract the file names for na_files and lb_files
na_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou")
lb_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib")
na_files_name<-stringi::stri_extract(na_files,regex = "[^.]+") #extracts file name up to first .
lb_files_name<-stringi::stri_extract(lb_files,regex = "[^.]+")
na_files_name %in% lb_files_name #checks the file names match
answered Nov 21 '18 at 14:03
e.matte.matt
8517
based on your data, extract the file names for na_files and lb_files
na_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.cou","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.cou","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.cou")
lb_files<-c("SAB-M-13.M4DF-2.T-bR.r1-v1_0-ADDFF.0087.AD.lib","SAB-M-32.MSFG-2.T-bR.r1-v1_0-ADDFF.3989.AD.lib","SAB-M-3.PZT-MOHUA-3.T-bR.r1-v1_0-ADDFF.6188.AD.lib")
na_files_name<-stringi::stri_extract(na_files,regex = "[^.]+") #extracts file name up to first .
lb_files_name<-stringi::stri_extract(lb_files,regex = "[^.]+")
na_files_name %in% lb_files_name #checks the file names match
answered Nov 21 '18 at 14:03
e.matte.matt
8517
answered Nov 21 '18 at 14:03
e.matte.matt
8517
answered Nov 21 '18 at 14:03
e.matte.matt
8517
answered Nov 21 '18 at 14:03
e.matte.matt
8517
8517
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
add a comment |
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
Sorry I need exactly the part after period to matching with files from two directories. For example M4DF, MSFG and MOHUA
– user1017373
Nov 21 '18 at 14:12
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
this is tricky as your file name patter isn't consistent as MOHUA as PZT- preceding it.
– e.matt
Nov 22 '18 at 9:34
add a comment |
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