removing extensions in a column

With awk:

awk -F'.' '{print $1}' file 

-F option change default field separator(space) to dot(.).
$1 is index of field position(with . field separator).

{ILMN_1343291 TGTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCGCTTTGCTGTTCG NM_001402}.{5} ^^ field index is $1 ^^$2 

With rev and awk:

rev file | awk -F'.' '{print $2}'|rev # reverse characters of each lines,\ print field number 2 with (.) separator \ and reverse the result again 

The rev utility copies the specified files to standard output, reversing the order of characters in every line. If no files are specified, standard input is read.

With sed:

sed 's/.[0-9]*$//' file sed 's/.[^.]*$//' file 

$ point to end of line. In first sed command search for char(.) which followed by zero or more occurrences of numbers and replace them with whitespace.

In second sed command remove everything that followed by (.) and also remove dot(.) itself.

With rev and sed:

rev file| sed 's/.*[.]//' |rev 

Delete everything before dot(.) Also include and remove . itself.

With grep:

grep -oP '.*(?=\.[0-9])' file 

 -o, --only-matching Print only the matched (non-empty) parts of a matching line, with each such part on a separate output line. -P, --perl-regexp Interpret PATTERN as a Perl compatible regular expression (PCRE) 

(?=pattern): Positive Lookahead: The positive lookahead construct is a pair of parentheses, with the opening parenthesis followed by a question mark and an equals sign.

.*(?=\.[0-9]): (positive lookahead) matches everything(.*) followed by one dot(.) and any occurrences of numbers, without making the pattern(\.[0-9]) part of the match.

With rev and grep:

rev file |grep -oP '(?<=[0-9]\.).*' |rev rev file |grep -oP '[0-9]\.\K.*' |rev 

(?<=pattern): Positive Lookbehind. A pair of parentheses, with the opening parenthesis followed by a question mark, "less than" symbol, and an equals sign.

(?<=[0-9]\.).* (positive lookbehind) matches everything which followed by any occurrences of numbers and end with dot(.).

In second grep command, you can use the nifty \K in place of the lookbehind assertion.

With cut:

cut -f1 -d. file cut -c 1-77 file # Print first 77 characters of each line. 

 cut - remove sections from each line of files -d, --delimiter=DELIM use DELIM instead of TAB for field delimiter -f, --fields=LIST select only these fields; -c, --characters=LIST select only these characters 

With while loop:

while read line; do echo "${line::-2}";done <file 

This will work if you have only number with length=1 at the end of each lines and they are fix length. above command remove last two character at the end of every lines in input file. alternative commands is ${line%??}.

Assuming the extensions are all-digit:

perl -pi -e 's/\.\d+$//' /path/to/file 

-i does in-place editing (like in sed). \d means digits, and $ denotes the end of the line.

With awk:

awk 'gsub(/\.[0-9]+$/,"")' /path/to/file 

gawk has an in-place editing option in newer versions, but I am not sure how portable that is. gsub supports an optional parameter, specifying the target column:

awk 'gsub(/\.[0-9]+$/,"",$3)' /path/to/file 

The last form has the undesired side-effect of separating each column by a single space in its output, as if you'd done print $1,..,$NF. I do not know why.

Using awk it is straightforward, just set your field separator as .:

awk -F. '{print $1}' file

Another approach, using the shell (in this case bash):

while IFS=.; read -r lines _; do line+=("$lines"); done <file printf "%s\n" "${line[@]}" ILMN_1343291 TGTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCGCTTTGCTGTTCG NM_001402 ILMN_1343295 CTTCAACAGCGACACCCACTCCTCCACCTTTGACGCTGGGGCTGGCATTG NM_002046 ILMN_1651209 TCACGGCGTACGCCCTCATGGGGAAAATCTCCCCGGTGACTTTCAGGTCC NM_182838

With sed, you can do:

sed 's/\.[0-9][0-9]*$//' x.txt 

Assuming the filename is x.txt. If you want to modify the file inline, use the -i switch of sed as below:

sed -i 's/\.[0-9][0-9]*$//' x.txt 

If you want to preserve the contents of original file, use redirection as below:

sed 's/\.[0-9][0-9]*$//' x.txt > newfile.txt 

This removes everything starting with the dot:

sed 's/\..*//'