bedtools map
allows one to map overlapping features in a B file onto
features in an A file and apply statistics and/or summary operations on those
features.Jun 9, 2020
bedtools map : map overlapping features and calculate sum, count, min, max, mean, median
Jun 8, 2020
print range of columns
input:
column1,column2,column3,column4,column5,column6,column7,column8
output:
column2,column3,column4,column5,column6,column7
Answer
cut -d, -f2-7 <input-file>
or
$ awk -v b=2 -v e=7 'BEGIN{FS=OFS=","} {for (i=b;i<=e;i++) printf "%s%s", $i, (i<e ? OFS : ORS)}' file
b=beginning field number, e=end field number.
Adding a Column of values in a tab delimited file
Input file:
SPATA17 1 217947738
LYPLAL1 1 219383905
FAM47E 4 77192838
SHROOM3 4 77660162
SHROOM3 4 77660731
SHROOM3 4 77662248
Output file:
SPATA17 1 217947738 file1
LYPLAL1 1 219383905 file1
FAM47E 4 77192838 file1
SHROOM3 4 77660162 file1
SHROOM3 4 77660731 file1
SHROOM3 4 77662248 file1
Answer
for file in *; do awk 'BEGIN{OFS="\t"}{print $0, FILENAME}' $file; done
FILENAME is a variable in awk, it expand to current file name that awk is processing.
How to replace dot in linux
https://stackoverflow.com/questions/27205566/how-to-replace-dot-in-linux
/^\.$/ to assure that nothing precedes or follows the dot
# substitute . to NA
awk 'BEGIN {OFS=FS="\t"} {for (i=1;i<=NF;i++) {gsub(/^\.$/,"NA",$i)}}1' file
/^\.$/ to assure that nothing precedes or follows the dot
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