I have a table like below, it is a bed file of genome coordinate, I would like to keep only rows with numbers.
Input:
1 141009669 141009952
9 141016322 141016973
GL000195.1 81719 82468
GL000195.1 142613 142923
GL000220.1 119445 119746
HG115_PATCH 101957832 101958132
HG1308_PATCH 130205069 130205369
HG1308_PATCH 130205406 130205773
HG748_PATCH 77577953 77578264
X 200983 202660
y 205180 205702
output:
1 141009669 141009952
9 141016322 141016973
X 200983 202660
y 205180 205702
Thanks in advance!
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command line:
egrep "^[0-9XY]" file
EDIT: originally, this used the same regex as for the R-based example (^[0-9XY]$). This won't work because the full line of the text file contains more characters (such as the coordinates...). Thanks to Alex for pointing this out.
R (because this post is tagged with it):
# assuming your data frame with the coordinates looks like this
df <- data.frame(chr = c("1","2","X","Y", "GL000220.1"),
start = c(1,20,30,40,50),
end = c(11, 21, 31, 41, 51)
)
subset(df, grepl("^[0-9XY]$", chr))
I don't think this works? For example:
$ echo -e '1\n11\n22\n2' | grep -E "^[0-9XY]$"
1
2
Perhaps you might want the following:
$ echo -e '1\n11\n22\nP\n\XY\n2\nZ\nX' | grep -E "^[0-9]{1,2}$|^[XY]$"
1
11
22
2
X
yes, you're right, the dollar sign in the original command I posted was silly (only makes sense for the R-based command)
$ sed -n '/^[0-9,X,Y]/Ip' test.txt
or
$ sed -n '/^[^A-WZ]/Ip' test.txt
1 141009669 141009952
9 141016322 141016973
X 200983 202660
y 205180 205702
with tsv-utils:
$ tsv-filter --iregex '1:^[^A-WZ]' test.txt
1 141009669 141009952
9 141016322 141016973
X 200983 202660
y 205180 205702
A straight forward way:
mainChr = c(as.character(1:22),'x','X','y','Y')
data = read.delim('your.bed',stringsAsFactor = F,header = F)
data_with_mainChr = data[data$V1 %in% mainChr,]
if you want to use readr and dplyr which is more efficient when dealing with big files:
mainChr = c(as.character(1:22),'x','X','y','Y')
library(dplyr); library(readr)
data = read_tsv('your_bed_file',col_names = F)
data_with_mainChr = dplyr::filter(data, X1 %in% mainChr)
you can do the opposite
awk '{print $1}' file | sort | uniq
to find the rows you want to exclude and then exclude them with grep
grep -v -e 'pattern1' -e 'pattern2'
You can almost do this in one line with R and GenomicFeatures + rtracklayer
library(GenomicFeatures)
library(rtracklayer)
## read your table as a random text file
keepStandardChromosomes(GRanges(read.table('your_table.bed',col.names=c('chr','start','stop'))),pruning.mode='coarse')
## read your table in as a bed - if it really is a bonafide .bed then you can simplify a bit
keepStandardChromosomes(import.bed('your_table.bed'),pruning.mode='coarse')
## do the same thing as above but simultaneously save it as a new bed file named "your_table_subset.bed"
export.bed(keepStandardChromosomes(import.bed('your_table.bed'),pruning.mode='coarse'),file='your_table_subset.bed')
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x and y are not numbers but I get what you are asking for. You only want to keep main chromosomes?
yes, exactly, I want just main chromosomes.
Tell us why you have tried so far? If you are interested in fixing your own attempt.