I have some files with content that change from file to file.
Each file have 2 sections of lines separated by a blank line.
I never know how many lines or characters there are in either section.
The file can look something like this.
This is a file
with some text
and some more text
This code only gives the first line from each section.
awk 'BEGIN {RS="\n\n"; FS="\n";} {print $1 }' file
I need each section split up to work with.
Prints first part:
sed '/^$/q' test.txt
Prints second part:
sed '1,/^$/d' test.txt
Since this is tagged bash, might as well have a native-bash solution.
sections=( )
current_section=
while REPLY=; IFS= read -r || [[ $REPLY ]]; do
if [[ $REPLY ]]; then
# preserve newlines within the sections
if [[ $current_section ]]; then
current_section+=$'\n'"$REPLY"
else
current_section+=$REPLY
fi
else
sections+=( "$current_section" )
current_section=
fi
done <file
This will put your file's individual sections into a bash array called sections.
You can print the contents of that array like so:
printf -- '---\n%s\n---\n' "${sections[#]}"
...or iterate over it to do as you please:
for section in "${sections[#]}"; do
: do something with "$section" here
done
Set RS to a null/blank value to get awk to operate on sequences of blank lines.
From the POSIX specification for awk:
RS
The first character of the string value of RS shall be the input record separator; a by default. If RS contains more than one character, the results are unspecified. If RS is null, then records are separated by sequences consisting of a plus one or more blank lines, leading or trailing blank lines shall not result in empty records at the beginning or end of the input, and a shall always be a field separator, no matter what the value of FS is.
IFS=";"
sections=($(awk -v RS= '{print $0 ";"}' filename))
IFS=; sets the internal field separator from space (default) to a semicolon
$(awk -v RS= '{print $0 ";"}' filename) prints out sections separated by double new lines and outputs a ; after each section. Another way to achieve the same result is awk -v ORS=';' -v RS= '{print}'
sections=(awk_output_here) splits the awk output based on the IFS and assigns each section as an array element. Hence, $sections contains each section split on ;. An individual section may be accessed with ${sections[0]} where 0 is an index.
The above awk trick works because it is a use case or convention in awk.
Another technique is to have blank lines separate records. By a special dispensation, an empty string as the value of RS indicates that records are separated by one or more blank lines. When RS is set to the empty string, each record always ends at the first blank line encountered.
Supposing that there are precisely two parts, this very simple Perl trick will print the the standard output until it encounters an empty line, and then the remainder to error;
perl -ne 'if (1../^$/) { print STDOUT } else { print STDERR }'
e.g.
cat tmp0 | perl -ne 'if (1../^$/) { print STDOUT } else { print STDERR }' > tmp1 2> tmp2
tmp1:
This is a file
with some text
tmp2:
and some more text
Related
I am trying to change long names in rows starting with >, so that I only keep the part till Stage_V_sporulation_protein...:
>tr_A0A024P1W8_A0A024P1W8_9BACI_Stage_V_sporulation_protein_AE_OS=Halobacillus_karajensis_OX=195088_GN=BN983_00096_PE=4_SV=1
MTFLWAFLVGGGICVIGQILLDVFKLTPAHVMSSFVVAGAVLDAFDLYDNLIRFAGGGATVPITSFGHSLLHGAMEQADEHGVIGVAIGIFELTSAGIASAILFGFIVAVIFKPKG
>tr_A0A060LWV2_A0A060LWV2_9BACI_SpoIVAD_sporulation_protein_AEB_OS=Alkalihalobacillus_lehensis_G1_OX=1246626_GN=BleG1_2089_PE=4_SV=1
MIFLWAFLVGGVICVIGQLLMDVVKLTPAHTMSTLVVSGAVLAGFGLYEPLVDFAGAGATVPITSFGNSLVQGAMEEANQVGLIGIITGIFEITSAGISAAIIFGFIAALIFKPKG
I am doing a loop:
cat file.txt | while read line; do
if [[ $line = \>* ]] ; then
cut -d_ -f1-4 $line;
fi;
done
but in addresses files but not rows in the file (I get cut: >>tr_A0A024P1W8_A0A024P1W8_9BACI_Stage_V_sporulation_protein_AE_OS=Halobacillus_karajensis_OX=195088_GN=BN983_00096_PE=4_SV=1: No such file or directory).
My desired output is:
>tr_A0A024P1W8_A0A024P1W8_9BACI
MTFLWAFLVGGGICVIGQILLDVFKLTPAHVMSSFVVAGAVLDAFDLYDNLIRFAGGGATVPITSFGHSLLHGAMEQADEHGVIGVAIGIFELTSAGIASAILFGFIVAVIFKPKG
>tr_A0A060LWV2_A0A060LWV2_9BACI
MIFLWAFLVGGVICVIGQLLMDVVKLTPAHTMSTLVVSGAVLAGFGLYEPLVDFAGAGATVPITSFGNSLVQGAMEEANQVGLIGIITGIFEITSAGISAAIIFGFIAALIFKPKG
How do I change actual rows?
With the current state of the question, it seems easiest to do:
awk '/^>/ {print $1,$2,$3,$4; next}1' FS=_ OFS=_ file.txt
Lines that match the > at the beginning of the line get only the first four fields printed, separated by _ (the value of OFS). Lines that do not match are printing unchanged.
One way using sed:
sed -E '/^>/s/(.*)_Stage_V_sporulation_protein/\1/' file
A sed one-liner would be:
sed '/^>/s/^\(\([^_]*_\)\{3\}[^_]*\).*/\1/' file
Use this Perl one-liner to process the headers in your FASTA file:
perl -lpe 'if ( m{^>} ) { #f = split m{_}, $_; splice #f, 4; $_ = join "_", #f; }' file.txt > out.txt
The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-p : Loop over the input one line at a time, assigning it to $_ by default. Add print $_ after each loop iteration.
-l : Strip the input line separator ("\n" on *NIX by default) before executing the code in-line, and append it when printing.
The one-liner uses split to split the input string on underscore into the array #f.
Then splice is used to remove from the array all elements except for the first 4 elements.
Finally, join joins these elements on an underscore.
All of the above is wrapped inside if ( m{^>} ) { ... } in order to limit the costly string manipulations only to the FASTA headers (the lines that start with >).
SEE ALSO:
perldoc perlrun: how to execute the Perl interpreter: command line switches
Using bash how do I find a string and update the string next to it for example pass value
my.site.com|test2.spin:80
proxy_pass.map
my.site2.com test2.spin:80
my.site.com test.spin:8080;
Expected output is to update proxy_pass.map with
my.site2.com test2.spin:80
my.site.com test2.spin:80;
I tried using awk
awk '{gsub(/^my\.site\.com\s+[A-Za-z0-9]+\.spin:8080;$/,"my.site2.comtest2.spin:80"); print}' proxy_pass.map
but does not seem to work. Is there a better way to approch the problem. ?
One awk idea, assuming spacing needs to be maintained:
awk -v rep='my.site.com|test2.spin:80' '
BEGIN { split(rep,a,"|") # split "rep" variable and store in
site[a[1]]=a[2] # associative array
}
$1 in site { line=$0 # if 1st field is in site[] array then make copy of current line
match(line,$1) # find where 1st field starts (in case 1st field does not start in column #1)
newline=substr(line,1,RSTART+RLENGTH-1) # save current line up through matching 1st field
line=substr(line,RSTART+RLENGTH) # strip off 1st field
match(line,/[^[:space:];]+/) # look for string that does not contain spaces or ";" and perform replacement, making sure to save everything after the match (";" in this case)
newline=newline substr(line,1,RSTART-1) site[$1] substr(line,RSTART+RLENGTH)
$0=newline # replace current line with newline
}
1 # print current line
' proxy_pass.map
This generates:
my.site2.com test2.spin:80
my.site.com test2.spin:80;
If the input looks like:
$ cat proxy_pass.map
my.site2.com test2.spin:80
my.site.com test.spin:8080;
This awk script generates:
my.site2.com test2.spin:80
my.site.com test2.spin:80;
NOTES:
if multiple replacements need to be performed I'd suggest placing them in a file and having awk process said file first
the 2nd match() is hardcoded based on OP's example; depending on actual file contents it may be necessary to expand on the regex used in the 2nd match()
once satisified with the result the original input file can be updated in a couple ways ... a) if using GNU awk then awk -i inplace -v rep.... or b) save result to a temp file and then mv the temp file to proxy_pass.map
If the number of spaces between the columns is not significant, a simple
proxyf=proxy_pass.map
tmpf=$$.txt
awk '$1 == "my.site.com" { $2 = "test2.spin:80;" } {print}' <$proxyf >$tmpf && mv $tmpf $proxyf
should do. If you need the columns to be lined up nicely, you can replace the print by a suitable printf .... statement.
With your shown samples and attempts please try following awk code. Creating shell variable named var where it stores value my.site.com|test2.spin:80 in it. which further is being passed to awk program. In awk program creating variable named var1 which has shell variable var's value in it.
In BEGIN section of awk using split function to split value of var(shell variable's value container) into array named arr with separator as |. Where num is total number of values delimited by split function. Then using for loop to be running till value of num where it creates array named arr2 with index of current i value and making i+1 as its value(basically 1 is for key of array and next item is value of array).
In main block of awk program checking condition if $1 is in arr2 then print arr2's value else print $2 value as per requirement.
##Shell variable named var is being created here...
var="my.site.com|test2.spin:80"
awk -v var1="$var" '
BEGIN{
num=split(var1,arr,"|")
for(i=1;i<=num;i+=2){
arr2[arr[i]]=arr[i+1]
}
}
{
print $1,(($1 in arr2)?arr2[$1]:$2)
}
' Input_file
OR in case you want to maintain spaces between 1st and 2nd field(s) then try following code little tweak of Above code. Written and tested with your shown samples Only.
awk -v var1="$var" '
BEGIN{
num=split(var1,arr,"|")
for(i=1;i<=num;i+=2){
arr2[arr[i]]=arr[i+1]
}
}
{
match($0,/[[:space:]]+/)
print $1 substr($0,RSTART,RLENGTH) (($1 in arr2)?arr2[$1]:$2)
}
' Input_file
NOTE: This program can take multiple values separated by | in shell variable to be passed and checked on in awk program. But it considers that it will be in format of key|value|key|value... only.
#!/bin/sh -x
f1=$(echo "my.site.com|test2.spin:80" | cut -d'|' -f1)
f2=$(echo "my.site.com|test2.spin:80" | cut -d'|' -f2)
echo "${f1}%${f2};" >> proxy_pass.map
tr '%' '\t' < proxy_pass.map >> p1
cat > ed1 <<EOF
$
-1
d
wq
EOF
ed -s p1 < ed1
mv -v p1 proxy_pass.map
rm -v ed1
This might work for you (GNU sed):
<<<'my.site.com|test2.spin:80' sed -E 's#\.#\\.#g;s#^(\S+)\|(\S+)#/^\1\\b/s/\\S+/\2/2#' |
sed -Ef - file
Build a sed script from the input arguments and apply it to the input file.
The input arguments are first prepared so that their metacharacters ( in this case the .'s are escaped.
Then the first argument is used to prepare a match command and the second is used as the value to be replaced in a substitution command.
The result is piped into a second sed invocation that takes the sed script and applies it the input file.
I have a text file containing several lines of the following format:
name,list_of_subjects,list_of_sports,school
Eg1: john,science\,social,football,florence_school
Eg2: james,painting,tennis\,ping_pong\,chess,highmount_school
I need to parse the text file and print the output of fields ignoring the escaped commas. Here those will be fields 2 or 3 like this:
science, social
tennis, ping_pong, chess
I do not know how to ignore escaped characters. How can I do it with awk or sed in terminal?
Substitute \, with a character that your records do not contain normally (e.g. \n), and restore it before printing. For example:
$ awk -F',' 'NR>1{ if(gsub(/\\,/,"\n")) gsub(/\n/,",",$2); print $2 }' file
science,social
painting
Since first gsub is performed on the whole record (i.e $0), awk is forced to recompute fields. But the second one is performed on only second field (i.e $2), so it will not affect other fields. See: Changing Fields.
To be able to extract multiple fields with properly escaped commas you need to gsub \ns in all fields with a for loop as in the following example:
$ awk 'BEGIN{ FS=OFS="," } NR>1{ if(gsub(/\\,/,"\n")) for(i=1;i<=NF;++i) gsub(/\n/,"\\,",$i); print $2,$3 }' file
science\,social,football
painting,tennis\,ping_pong\,chess
See also: What's the most robust way to efficiently parse CSV using awk?.
You could replace the \, sequences by another character that won't appear in your text, split the text around the remaining commas then replace the chosen character by commas :
sed $'s/\\\,/\31/g' input | awk -F, '{ printf "Name: %s\nSubjects : %s\nSports: %s\nSchool: %s\n\n", $1, $2, $3, $4 }' | tr $'\31' ','
In this case using the ASCII control char "Unit Separator" \31 which I'm pretty sure your input won't contain.
You can try it here.
Why awk and sed when bash with coreutils is just enough:
# Sorry my cat. Using `cat` as input pipe
cat <<EOF |
name,list_of_subjects,list_of_sports,school
Eg1: john,science\,social,football,florence_school
Eg2: james,painting,tennis\,ping_pong\,chess,highmount_school
EOF
# remove first line!
tail -n+2 |
# substitute `\,` by an unreadable character:
sed 's/\\\,/\xff/g' |
# read the comma separated list
while IFS=, read -r name list_of_subjects list_of_sports school; do
# read the \xff separated list into an array
IFS=$'\xff' read -r -d '' -a list_of_subjects < <(printf "%s" "$list_of_subjects")
# read the \xff separated list into an array
IFS=$'\xff' read -r -d '' -a list_of_sports < <(printf "%s" "$list_of_sports")
echo "list_of_subjects : ${list_of_subjects[#]}"
echo "list_of_sports : ${list_of_sports[#]}"
done
will output:
list_of_subjects : science social
list_of_sports : football
list_of_subjects : painting
list_of_sports : tennis ping_pong chess
Note that this will be most probably slower then solution using awk.
Note that the principle of operation is the same as in other answers - substitute \, string by some other unique character and then use that character to iterate over the second and third field elemetns.
This might work for you (GNU sed):
sed -E 's/\\,/\n/g;y/,\n/\n,/;s/^[^,]*$//Mg;s/\n//g;/^$/d' file
Replace quoted commas by newlines and then revert newlines to commas and commas to newlines. Remove all lines that do not contain a comma. Delete empty lines.
Using Perl. Change the \, to some control char say \x01 and then replace it again with ,
$ cat laxman.txt
john,science\,social,football,florence_school
james,painting,tennis\,ping_pong\,chess,highmount_school
$ perl -ne ' s/\\,/\x01/g and print ' laxman.txt | perl -F, -lane ' for(#F) { if( /\x01/ ) { s/\x01/,/g ; print } } '
science,social
tennis,ping_pong,chess
You can perhaps join columns with a function.
function joincol(col, i) {
$col=$col FS $(col+1)
for (i=col+1; i<NF; i++) {
$i=$(i+1)
}
NF--
}
This might get used thusly:
{
for (col=1; col<=NF; col++) {
if ($col ~ /\\$/) {
joincol(col)
}
}
}
Note that decrementing NF is undefined behaviour in POSIX. It may delete the last field, or it may not, and still be POSIX compliant. This works for me in BSDawk and Gawk. YMMV. May contain nuts.
Use gawk's FPAT:
awk -v FPAT='(\\\\.|[^,\\\\]*)+' '{print $3}' file
#list_of_sports
#football
#tennis\,ping_pong\,chess
then use gnusub to replace the backslashes:
awk -v FPAT='(\\\\.|[^,\\\\]*)+' '{print gensub("\\\\", "", "g", $3)}' file
#list_of_sports
#football
#tennis,ping_pong,chess
with input csv file
sid,storeNo,latitude,longitude
2,1,-28.03720000,153.42921670
9
I wish to output only the lines with one column, in this example it's line 3.
how can this be done in bash shell script?
Using awk
The following awk would be usfull
$ awk -F, 'NF==1' inputFile
9
What it does?
-F, sets the field separator as ,
NF==1 matches lines with NF, number of fields as 1. No action is provided hence default action, printing the entire record is taken. it is similar to NF==1{print $0}
inputFile input csv file to the awk script
Using grep
The same function can also be done using grep
$ grep -v ',' inputFile
9
-v option prints lines that do not match the pattern
, along with -v greps matches lines that do not contain , field separator
Using sed
$ sed -n '/^[^,]*$/p' inputFile
9
what it does?
-n suppresses normal printing of pattern space
'/^[^,]*$/ selects lines that match the pattern, lines without any ,
^ anchors the regex at the start of the string
[^,]* matches anything other than ,
$ anchors string at the end of string
p action p makes sed to print the current pattern space, that is pattern space matching the input
try this bash script
#!/bin/bash
while read -r line
do
IFS=","
set -- $line
case ${#} in
1) echo $line;;
*) continue;;
esac
done < file
I'm trying to write a script that reads the file content below and extract the value in the 6th column of each line, then print each line without the 6th column. The comma is used as the delimiter.
Input:
123,456,789,101,145,5671,hello world,goodbye for now
223,456,789,101,145,5672,hello world,goodbye for now
323,456,789,101,145,5673,hello world,goodbye for now
What I did was
#!/bin/bash
for i in `cat test_input.txt`
do
COLUMN=`echo $i | cut -f6 -d','`
echo $i | cut -f1-5,7- -d',' >> test_$COLUMN.txt
done
The output I got was
test_5671.txt:
123,456,789,101,145,hello
test_5672.txt:
223,456,789,101,145,hello
test_5673.txt:
323,456,789,101,145,hello
The rest of "world, goodbye for now" was not written into the output files, because it seems like the space between "hello" and "world" was used as a delimiter?
How do I get the correct output
123,456,789,101,145,hello world,goodbye for now
It's not a problem with the cut command but with the for loop you're using. For the first loop run the variable i will only contain 123,456,789,101,145,5671,hello.
If you insist to read the input file line-by-line (not very efficient), you'd better use a read-loop like this:
while read i
do
...
done < test_input.txt
echo '123,456,789,101,145,5671,hello world,goodbye for now' | while IFS=, read -r one two three four five six seven eight rest
do
echo "$six"
echo "$one,$two,$three,$four,$five,$seven,$eight${rest:+,$rest}"
done
Prints:
5671
123,456,789,101,145,hello world,goodbye for now
See the man bash Parameter Expansion section for the :+ syntax (essentially it outputs a comma and the $rest if $rest is defined and non-empty).
Also, you shouldn't use for to loop over file contents.
As ktf mentioned, your problem is not with cut but with the way you're passing the lines into cut. The solution he/she has provided should work.
Alternatively, you could achieve the same behaviour with a line of awk:
awk -F, '{for(i=1;i<=NF;i++) {if(i!=6) printf "%s%s",$i,(i==NF)?"\n":"," > "test_"$6".txt"}}' test_input.txt
For clarity, here's a verbose version:
awk -F, ' # "-F,": using comma as field separator
{ # for each line in file
for(i=1;i<=NF;i++) { # for each column
sep = (i == NF) ? "\n" : "," # column separator
outfile = "test_"$6".txt" # output file
if (i != 6) { # skip sixth column
printf "%s%s", $i, sep > outfile
}
}
}' test_input.txt
an easy method id to use tr commende to convert the espace carracter into # and after doing the cat commande retranslate it into the espace.