6
The simplest approach would be to remove all numbers after the first . on every line:
$ sed 's/\.[0-9]*/\./' file
target_id length eff_length est_counts tpm
ENST00000583162. 1066 967 1.69899 1.18376
ENST00000583355. 891 792 13.8057 11.7445
ENST00000582528. 5342 5243 21.3223 2.74003
...
3
An awk solution is
awk '{if(NF){gsub(/^ |,$/,""); printf c $0; c=","}else{printf "\n"; c=""}};END{printf "\n"}'
expanded with comments:
{
if(NF) { # if the line isn't empty
gsub(/^ |,$/,""); # remove the first space and last comma
printf c $0; # print the line (without a newline)
c="," # set c to add a comma for the next field
...
3
Here Strings seem to produce a newline at the end:
You can try and see the difference:
cat <<<"test"
cat <(printf '%s' "test")
So, you should use < <(printf '%s' "$line") instead of <<<"$(printf '%s' "$line")".
3
You can use read to split the lines based on whitespace (which it looks like your file uses). Something like this:
while read set year; do
DoStuffWith "$set" "$year"
done <test.txt
Other notes:
Note that I used lowercase variable names in the above example. There are a bunch of all-caps names with special meanings, and the safest way to avoid ...
2
To replace each alphabetic character by the letter N:
tr '[:alpha:]' N < file.txt > file2.txt
2
With GNU awk, you can do
gawk -v start=5 -v end=8 '{
mid = substr($0, start, end-start+1)
print substr($0, 1, start-1) gensub(/./, "N", "g", mid) substr($0, end+1)
}' file
Or with perl
perl -spe 'substr($_, $start-1, $end-$start+1) =~ s/./N/g' -- -start=5 -end=8 file
With both solutions, we pass the start and end values to the program with ...
2
If you have GNU awk (gawk) you could set FIELDWIDTHS to split the line into fields based on character positions. This is particularly convenient for your case in gawk version >= 4.2, which supports a "wildcard" trailing fieldwidth. You can then replace characters in the second field using gsub:
echo ABCDABCDABCD | ./gawk -v i=5 -v n=4 '
BEGIN {FIELDWIDTHS ...
2
I would write:
while IFS= read -r line; do
for ((i=0; i<${#line}; i++)); do
char=${line:i:1}
((count++))
((low <= count && count <= high)) && char=$new_char
printf '%s' "$char"
done
echo
done <"$input"
2
try
awk '{$1=$1*10 ; print }'
this will change first parameter, and print whole line.
to keep formating to 3 digit, use
awk '{$1=sprintf("%.3f",$1*10);print;}'
2
Try this,
awk -F '@' '{print $0"|"$NF}' file
TEST|1234|john.doe@gmail.com|gmail.com
TEST|4533|jeffp12@yahoo.com|yahoo.com
TEST|9030|indoep13@gmx.com|gmx.com
TEST|0903|ramdpe23@gmail.com|gmail.com
1
awk 'NR==1{print "z(A) " $0 " OW HW1 HW2"; next}1'
or
awk 'NR==1{printf "z(A) %s OW HW1 HW2\n", $0; next}1'
or
awk 'NR==1{$0="z(A) " $0 " OW HW1 HW2"}1'
1
sed -e '1s/^/z(A) /' -e '1s/$/ OW HW1 HW2/' < input > output
1 is for the first line, s is for substitute, ^ is beginning-of-line, $ is end-of-line.
1
In ksh, you can also use arrays:
while IFS='#' read -A arr; do
echo "${#arr[@]} items, second item: ${arr[1]}"
done < file
read -A works in Zsh too, but the array indexes are one-based. Bash's read -a works similarly to the ksh one.
1
You can use parameter expansion if that's what you mean. But it's not very readable:
while read a; do
# comments are for the first line A#B#C
f1f2=${a%#*} # remove suffix #C -> A#B
f1=${f1f2%#*} # remove suffix #B -> A
f2=${f1f2#*#} # remove prefix A# -> B
f3=${a##*#} # remove longest prefix: A#B# -> C
echo "$f1,$f2,$f3" # do ...
1
If what you mean by "generic" is that the number of columns can change and you always want to write all of them to a file whose name is defined by the 1st 3 fields, then you can try this:
awk -F\| '{
data=$4
for(i=5;i<=NF;i++){
data = data"|"$(i)
}
print data > "sample_"$1"_"$2"_"$3".CSV"}...
1
You can get the best results from awk:
awk '{ print > "index i"$2 }' < input
You can also do it purely in the shell:
while read a b c
do
printf '%s\n' "$a $b $c" >> "index i$b"
done < input
The awk solution has these advantages:
It will overwrite existing files.
The shell script will append to existing files.
(I suppose that ...
1
sed -E 's,^([0-9]+)/([0-9]+),\2/\1,'
Explanation
sed -E: use sed with extended regular expressions so we don't have to escape the (), etc.
s/foo/bar/: this is the general sed syntax to search for foo and replace it with bar. Here, I've used , instead of /, because there are /s in the expression, and this will simplify it (again avoiding confusing escaping. ...
1
$ tr -d '\n' <file | perl -pe 'substr($_, 9, 4, "P"x4)' | fold -w 5
NNNNN
NNNNP
PPPNN
NNNNN
This first removes all newlines from the data in the input file, then uses substr() in Perl to replace the text at offset 9 of length 4 with upper-case P. The fold utility is then used to fold the lines at five characters. There is no newline at the end of the ...
1
Using sed
To replace characters 5 through 8 with N:
$ sed -E 's/(.{4}).{4}/\1NNNN/' test
ABCDNNNNABCD
How it works:
(.{4}) captures the first four characters in group 1.
.{4} matches the next four characters.
\1NNNN replaces the above with group 1 and four N.
Using GNU awk
$ gawk -F "" '{for (i=5; i<=8; i++) $i="N"} 1' OFS="" test
ABCDNNNNABCD
...
1
You could use perl, which is a pretty powerful text manipulator:
perl -pi -e 's/(^ver="\d+)\.(\d+)\.(\d+)"/"$1.$2." . sprintf("%04d", $3+1) . "\""/e' input
This invokes perl with three options:
-p -- auto-print each line of input
-i -- edit the file in-place
-e -- use the next argument as the code to execute
The code says to do a search & replacement ...
1
Assuming that the patch level is always going to be a string of four digits:
$ ver=1.2.0001
$ printf '%s\n' "$ver" | awk -F '.' '{ printf("%s.%s.%04d\n", $1, $2, $3 + 1) }'
1.2.0002
This uses awk and treats the version as three fields delimited by dots. It prints the first two fields as they are, but adds 1 to the third field and formats the result using %...
1
The easiest way to achieve it is sed:
sed 's/[A-Z]/N/g' file.txt
(add -i if you want in-place file changes).
PS. Note, that the expression above is case sensitive. If you want case-insensitive replacement use something like this:
sed 's/[A-Z]/N/Ig' file.txt
1
Assuming you'd like to append the contents of the file template to the file data only if no line from template already exists in data.
The command for testing whether a line in template is found in data is
grep -xF -f template data
(This is a reasonable thing to do only if template contains less than a few thousands of lines)
This uses the following ...
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