I'm using for loop to iterate through .txt files in a directory and grab specified rows from the files. Afterwards the output is passed to pr command in order to print it as a table. Everything works fine, however I'm manually specifying the number of columns that the table should contain. This is cumbersome when the number of files is not constant.
The command I'm using:
for f in *txt; do awk -F"\t" 'FNR ~ /^(2|6|9)$/{print $2}' $f; done | pr -ts --column 4
How should I modify the command to replace '4' with elements number?
Edit:
The fundamental question was if one can provide matching files number to function outside the loop. Seeing the solutions I guess it is not possible to work around the problem. Until this conclusion the structure of the files was not really relevant.
However taking the above into account, I'm providing the files structure below.
Sample file.txt:
Irrelevant1 text
Placebo 1222327
Irrelevant1 text
Irrelevant2 text
Irrelevant3 text
Treatment1 105956
Irrelevant1 text
Irrelevant2 text
Treatment2 49271
Irrelevant1 text
Irrelevant2 text
The for loop generates the following from 4 *txt files:
1222327
105956
49271
969136
169119
9672
1297357
237210
11581
1189529
232095
13891
Expected pr output using a dynamically generated --column 4:
1222327 969136 1297357 1189529
105956 169119 237210 232095
49271 9672 11581 13891
Assumptions:
all input files generate the same number of output lines (otherwise we can add some code to keep track of the max number of lines and generate blank columns as needed)
Setup (columns are tab-delimited):
$ grep -n xxx f[1-4].txt
f1.txt:6:xxx 1222327
f1.txt:9:xxx 105956
f1.txt:24:xxx 49271
f2.txt:6:xxx 969136
f2.txt:9:xxx 169119
f2.txt:24:xxx 9672
f3.txt:6:xxx 1297357
f3.txt:9:xxx 237210
f3.txt:24:xxx 11581
f4.txt:6:xxx 1189529
f4.txt:9:xxx 232095
f4.txt:24:xxx 13891
One idea using awk to dynamically build the 'table' (replaces OP's current for loop):
awk -F'\t' '
FNR==1 { c=0 }
FNR ~ /^(6|9|24)$/ { ++c ; arr[c]=arr[c] (FNR==NR ? "" : " ") $2 }
END { for (i=1;i<=c;i++) print arr[i] }
' f[1-4].txt | column -t -o ' '
NOTE: we'll go ahead and let column take care of pretty-printing the table with a single space separating the columns, otherwise we could add some more code to awk to right-pad columns with spaces
This generates:
1222327 969136 1297357 1189529
105956 169119 237210 232095
49271 9672 11581 13891
You could just run ls and pipe the output to wc -l. Then once you've got that number you can assign it to a variable and place that variable in your command.
num=$(ls *.txt | wc -l)
I forget how to place bash variables in AWK, but I think you can do that. If not, respond back and I'll try to find a different answer.
Related
I have a file containing several few thousands of lines. The file format is similar to this:
1
H
H 13.1641870 7.1039560 -5.9652740
3
O2H2
H 15.5567440 5.6184980 -4.5255100
H 15.8907030 4.2338600 -5.4917990
O 15.5020000 6.4310000 -7.0960000
O 13.7940000 5.5570000 -8.1620000
2
CH
H 13.0960830 7.7155820 -3.5224750
C 11.0480000 7.4400000 -5.5080000
.
.
.
.
What I want is to split the full file in several files where putting in each file all the information between empty lines. The problem is that the blank lines do not follow a pattern. Some parts of the text have 1 line and others have 10.
Could someone tell me how to separate the file using the blank lines as separator?
Using awk and the data in a file called mainfile
awk 'BEGIN { RS="[\n]+" } { print $0 >> "file"NR".txt" }' mainfile
Set the record separator to one or more line feeds and then print each record to a file dictated by the record number i.e. file1.txt etc
Would you please try the following:
awk -v RS="" '{print > "file" ++i ".txt"; close("file" i ".txt")}' input.txt
If the awk variable RS is set to the null string, then records are separated by blank lines.
It is recommended to close each file to avoid the "too many open files" error.
I have a file named file.txt
$cat file.txt
1./abc/cde/go/ftg133333.jpg
2./abc/cde/go/ftg24555.jpg
3./abc/cde/go/ftg133333.gif
4./abt/cte/come/ftg24555.jpg
5./abc/cde/go/ftg133333.jpg
6./abc/cde/go/ftg24555.pdf
MY GOAL: To get only one line from lines who's first, second and third PATH are the same and have the same file EXTENSION.
Note each PATH is separated by forward slash "/". Eg in the first line of the list, the first PATH is abc, second PATH is cde and third PATH is go.
File EXTENSION is .jpg, .gif,.pdf... always at the end of the line.
HERE IS WHAT I TRIED
sort -u -t '/' -k1 -k2 -k3
My thoughts
Using / as a delimiter gives me 4 fields in each line. Sorting them with "-u" will remove all but 1 line with unique First, Second and 3rd field/PATH. But obviously, I didn't take into account the EXTENSION(jpg,pdf,gif) in this case.
MY QUESTION
I need a way to grep only 1 of the lines if the first, second and third field are same and have the same EXTENSION using "/" as delimiter to divide it into fields. I want to output it to a another file, say file2.txt.
In the file2.txt, how do I add a word say "KALI" before the extension in each line, so it will look something like /abc/cde/go/ftg13333KALI.jpg using line 1 as an example in file.txt above.
Desired Output
/abc/cde/go/ftg133333KALI.jpg
/abt/cte/come/ftg24555KALI.jpg
/abc/cde/go/ftg133333KALI.gif
/abc/cde/go/ftg24555KALI.pdf
COMMENT
Line 1,2 & 5 have the same 1st,2nd and 3rd field, with same file extension
".jpg" so only line 1 should be in the output.
Line 3 is in the output even though it has same 1st,2nd and 3rd field with
1,2 and 5, because the extension is different ".gif".
Line 4 has different 1st, 2nd and 3rd field, hence it in output.
Line 6 is in the output even though it has same 1st,2nd and 3rd field with
1,2 and 5, because the extension is different ".pdf".
$ awk '{ # using awk
n=split($0,a,/\//) # split by / to get all path components
m=split(a[n],b,".") # split last by . to get the extension
}
m>1 && !seen[a[2],a[3],a[4],b[m]]++ { # if ext exists and is unique with 3 1st dirs
for(i=2;i<=n;i++) # loop component parts and print
printf "/%s%s",a[i],(i==n?ORS:"")
}' file
Output:
/abc/cde/go/ftg133333.jpg
/abc/cde/go/ftg133333.gif
/abt/cte/come/ftg24555.jpg
/abc/cde/go/ftg24555.pdf
I split by / separately from .s in case there are .s in dir names.
Missed the KALI part:
$ awk '{
n=split($0,a,/\//)
m=split(a[n],b,".")
}
m>1&&!seen[a[2],a[3],a[4],b[m]]++ {
for(i=2;i<n;i++)
printf "/%s",a[i]
for(i=1;i<=m;i++)
printf "%s%s",(i==1?"/":(i==m?"KALI.":".")),b[i]
print ""
}' file
Output:
/abc/cde/go/ftg133333KALI.jpg
/abc/cde/go/ftg133333KALI.gif
/abt/cte/come/ftg24555KALI.jpg
/abc/cde/go/ftg24555KALI.pdf
Using awk:
$ awk -F/ '{ split($5, ext, "\\.")
if (!(($2,$3,$4,ext[2]) in files)) files[$2,$3,$4,ext[2]]=$0
}
END { for (f in files) {
sub("\\.", "KALI.", files[f])
print files[f]
}}' input.txt
/abt/cte/come/ftg24555KALI.jpg
/abc/cde/go/ftg133333KALI.gif
/abc/cde/go/ftg24555KALI.pdf
/abc/cde/go/ftg133333KALI.jpg
another awk
$ awk -F'[./]' '!a[$2,$3,$4,$NF]++' file
/abc/cde/go/ftg133333.jpg
/abc/cde/go/ftg133333.gif
/abt/cte/come/ftg24555.jpg
/abc/cde/go/ftg24555.pdf
assumes . doesn't exist in directory names (not necessarily true in general).
I have a text file: file.txt, with several thousand lines. It contains a lot of junk lines which I am not interested in, so I use the cut command to regex for the lines I am interested in first. For each entry I am interested in, it will be listed twice in the text file: Once in a "definition" section, another in a "value" section. I want to retrieve the first value from the "definition" section, and then for each entry found there find it's corresponding "value" section entry.
The first entry starts with ' gl_ ', while the 2nd entry would look like ' "gl_ ', starting with a '"'.
This is the code I have so far for looping through the text document, which then retrieves the values I am interested in and appends them to a .csv file:
while read -r line
do
if [[ $line == gl_* ]] ; then (param=$(cut -d'\' -f 1 $line) | def=$(cut -d'\' -f 2 $line) | type=$(cut -d'\' -f 4 $line) | prompt=$(cut -d'\' -f 8 $line))
while read -r glline
do
if [[ $glline == '"'$param* ]] ; then val=$(cut -d'\' -f 3 $glline) |
"$project";"$param";"$val";"$def";"$type";"$prompt" >> /filepath/file.csv
done < file.txt
done < file.txt
This seems to throw some syntax errors related to unexpected tokens near the first 'done' statement.
Example of text that needs to be parsed, and paired:
gl_one\User Defined\1\String\1\\1\Some Text
gl_two\User Defined\1\String\1\\1\Some Text also
gl_three\User Defined\1\Time\1\\1\Datetime now
some\junk
"gl_one\1\Value1
some\junk
"gl_two\1\Value2
"gl_three\1\Value3
So effectively, the while loop reads each line until it hits the first line that starts with 'gl_', which then stores that value (ie. gl_one) as a variable 'param'.
It then starts the nested while loop that looks for the line that starts with a ' " ' in front of the gl_, and is equivalent to the 'param' value. In other words, the
script should couple the lines gl_one and "gl_one, gl_two and "gl_two, gl_three and "gl_three.
The text file is large, and these are settings that have been defined this way. I need to collect the values for each gl_ parameter, to save them together in a .csv file with their corresponding "gl_ values.
Wanted regex output stored in variables would be something like this:
first while loop:
$param = gl_one, $def = User Defined, $type = String, $prompt = Some Text
second while loop:
$val = Value1
Then it stores these variables to the file.csv, with semi-colon separators.
Currently, I have an error for the first 'done' statement, which seems to indicate an issue with the quotation marks. Apart from this,
I am looking for general ideas and comments to the script. I.e, not entirely sure I am looking for the quotation mark parameters "gl_ correctly, or if the
semi-colons as .csv separators are added correctly.
Edit: Overall, the script runs now, but extremely slow due to the inner while loop. Is there any faster way to match the two lines together and add them to the .csv file?
Any ideas and comments?
This will generate a file containing the data you want:
cat file.txt | grep gl_ | sed -E "s/\"//" | sort | sed '$!N;s/\n/\\/' | awk -F'\' '{print $1"; "$5"; "$7"; "$NF}' > /filepath/file.csv
It uses grep to extract all lines containing 'gl_'
then sed to remove the leading '"' from the lines that contain one [I have assumed there are no further '"' in the line]
The lines are sorted
sed removes the return from each pair of lines
awk then prints
the required columns according to your requirements
Output routed to the file.
LANG=C sort -t\\ -sd -k1,1 <file.txt |\
sed '
/^gl_/{ # if definition
N; # append next line to buffer
s/\n"gl_[^\\]*//; # if value, strip first column
t; # and start next loop
}
D; # otherwise, delete the line
' |\
awk -F\\ -v p="$project" -v OFS=\; '{print p,$1,$10,$2,$4,$8 }' \
>>/filepath/file.csv
sort lines so gl_... appears immediately before "gl_... (LANG fixes LC_TYPE) - assumes definition appears before value
sed to help ensure matching definition and value (may still fail if duplicate/missing value), and tidy for awk
awk to pull out relevant fields
Im new to bash and trying to extract a list of patterns from file:
File1.txt
ABC
BDF
GHJ
base.csv (tried comma separated and tab delimited)
line 1,,,,"hfhf,ferf,ju,ABC"
line 2 ,,,,,"ewy,trggt,gtg,ABC,RFR"
line 3 .."himk,n,hn.ujj., BDF"
etc
Suggested output is smth like
ABC
line 1..
line 2..(whole lines)
BDF
line 3..
and so on for each pattern from file 1
the code i tried was:
#!/bin/bash
for i in *.txt -# cycle through all files containing pattern lists
do
for q in "$i"; # # cycle through list
do
echo $q >>output.${i};
grep -f "${q}" base.csv >>output.${i};
echo "\n";
done
done
But output is only filename and then some list of strings without pattern names, e.g.
File1.txt
line 1...
line 2...
line 3..
so i don`t know to what pattern belongs each string and have to check and assign manually. Can you please point out my errors? Thanks!
grep can process multiple files in one go, and then has the attractive added bonus of indicating which file it found a match in.
grep -f File1.txt base.csv >output.txt
It's not clear what you hope for the inner loop to do; it will just loop over a single token at a time, so it's not really a loop at all.
If you want the output to be grouped per pattern, here's a for loop which looks for one pattern at a time:
while read -r pat; do
echo "$pat"
grep "$pat" *.txt
done <File1.txt >output.txt
But the most efficient way to tackle this is to write a simple Awk script which processes all the input files at once, and groups the matches before printing them.
An additional concern is anchoring. grep "ABC" will find a match in 123DEABCXYZ; is this something you want to avoid? You can improve the regex, or, again, turn to Awk which gives you more control over where exactly to look for a match in a structured line.
awk '# Read patterns into memory
NR==FNR { a[++i] = $1; next }
# Loop across patterns
{ for(j=1; j<=i; ++j)
if($0 ~ a[j]) {
print FILENAME ":" FNR ":" $0 >>output.a[j]
next }
}' File1.txt base.csv
You're not actually reading the files, you're just handling the filenames. Try this:
#!/bin/bash
for i in *.txt # cycle through all files containing pattern lists
do
while read -r q # read file line by line
do
echo "$q" >>"output.${i}"
grep -f "${q}" base.csv >>"output.${i}"
echo "\n"
done < "${i}"
done
Here is one that separates (with split, comma-separatd with quotes and spaces stripped off) words from file2 to an array (word[]) and stores the record names (line 1 etc.) to it comma-separated:
awk '
NR==FNR {
n=split($0,tmp,/[" ]*(,|$)[" ]*/) # split words
for(i=2;i<=n;i++) # after first
if(tmp[i]!="") # non-empties
word[tmp[i]]=word[tmp[i]] (word[tmp[i]]==""?"":",") tmp[1] # hash rownames
record[tmp[1]]=$0 # store records
next
}
($1 in word) { # word found
n=split(word[$1],tmp,",") # get record names
print $1 ":" # output word
for(i=1;i<=n;i++) # and records
print record[tmp[i]]
}' file2 file1
Output:
ABC:
line 1,,,,"hfhf,ferf,ju,ABC"
line 2 ,,,,,"ewy,trggt,gtg,ABC,RFR"
BDF:
line 3 .."himk,n,hn.ujj., BDF"
Thank you for your kind help, my friends.
Tried both variants above but kept getting various errors ( "do" expected) or misbehavior ( gets names of pattern blocks, eg ABC, BDF, but no lines.
Gave up for a while and then eventually tried another way
While base goal were to cycle through pattern list files, search for patterns in huge file and write out specific columns from lines found - i simply wrote
for *i in *txt # cycle throughfiles w/ patterns
do
grep -F -f "$i" bigfile.csv >> ${i}.out1 #greps all patterns from current file
cut -f 2,3,4,7 ${i}.out1>> ${i}.out2 # cuts columns of interest and writes them out to another file
done
I'm aware that this code should be improved using some fancy pipeline features, but it works perfectly as is, hope it`ll help somebody in similar situation. You can easily add some echoes to write out pattern list names as i initially requested
I have 2 files refer.txt and parse.txt
refer.txt contains the following
julie,remo,rob,whitney,james
parse.txt contains
remo/hello/1.0,remo/hello2/2.0,remo/hello3/3.0,whitney/hello/1.0,julie/hello/2.0,julie/hello/3.0,rob/hello/4.0,james/hello/6.0
Now my output.txt should list the files in parse.txt based on the order specified in refer.txt
ex of output.txt should be:
julie/hello/2.0,julie/hello/3.0,remo/hello/1.0,remo/hello2/2.0,remo/hello3/3.0,rob/hello/4.0,whitney/hello/1.0,james/hello/6.0
i have tried the following code:
sort -nru refer.txt parse.txt
but no luck.
please assist me.TIA
You can do that using gnu-awk:
awk -F/ -v RS=',|\n' 'FNR==NR{a[$1] = (a[$1])? a[$1] "," $0 : $0 ; next}
{s = (s)? s "," a[$1] : a[$1]} END{print s}' parse.txt refer.txt
Output:
julie/hello/2.0,julie/hello/3.0,remo/hello/1.0,remo/hello2/2.0,remo/hello3/3.0,rob/hello/4.0,whitney/hello/1.0,james/hello/6.0
Explanation:
-F/ # Use field separator as /
-v RS=',|\n' # Use record separator as comma or newline
NR == FNR { # While processing parse.txt
a[$1]=(a[$1])?a[$1] ","$0:$0 # create an array with 1st field as key and value as all the
# records with keys julie, remo, rob etc.
}
{ # while processing the second file refer.txt
s = (s)?s "," a[$1]:a[$1] # aggregate all values by reading key from 2nd file
}
END {print s } # print all the values
In pure native bash (4.x):
# read each file into an array
IFS=, read -r -a values <parse.txt
IFS=, read -r -a ordering <refer.txt
# create a map from content before "/" to comma-separated full values in preserved order
declare -A kv=( )
for value in "${values[#]}"; do
key=${value%%/*}
if [[ ${kv[$key]} ]]; then
kv[$key]+=",$value" # already exists, comma-separate
else
kv[$key]="$value"
fi
done
# go through refer list, putting full value into "out" array for each entry
out=( )
for value in "${ordering[#]}"; do
out+=( "${kv[$value]}" )
done
# print "out" array in comma-separated form
IFS=,
printf '%s\n' "${out[*]}" >output.txt
If you're getting more output fields than you have input fields, you're probably trying to run this with bash 3.x. Since associative array support is mandatory for correct operation, this won't work.
tr , "\n" refer.txt | cat -n >person_id.txt # 'cut -n' not posix, use sed and paste
cat person_id.txt | while read person_id person_key
do
print "$person_id" > $person_key
done
tr , "\n" parse.txt | sed 's/(^[^\/]*)(\/.*)$/\1 \1\2/' >person_data.txt
cat person_data.txt | while read foreign_key person_data
do
person_id="$(<$foreign_key)"
print "$person_id" " " "$person_data" >>merge.txt
done
sort merge.txt >output.txt
A text book data processing approach, a person id table, a person data table, merged on a common key field, which is the first name of the person:
[person_key] [person_id]
- person id table, a unique sortable 'id' for each person (line number in this instance, since that is the desired sort order), and key for each person (their first name)
[person_key] [person_data]
- person data table, the data for each person indexed by 'person_key'
[person_id] [person_data]
- a merge of the 'person_id' table and 'person_data' table on 'person_key', which can then be sorted on person_id, giving the output as requested
The trick is to implement an associative array using files, the file name being the key (in this instance 'person_key'), the content being the value. [Essentially a random access file implemented using the filesystem.]
This actually adds a step to the otherwise simple but not very efficient task of grepping parse.txt with each value in refer.txt - which is more efficient I'm not sure.
NB: The above code is very unlikely to work out of the box.
NBB: On reflection, probably a better way of doing this would be to use the file system to create a random access file of parse.txt (essentially an index), and to then consider refer.txt as a batch file, submitting it as a job as such, printing out from the parse.txt random access file the data for each of the names read in from refer.txt in turn:
# 1) index data file on required field
cat person_data.txt | while read data
do
key="$(print "$data" | sed 's/(^[^\/]*)/\1/')" # alt. `cut -d'/' -f1` ??
print "$data" >>./person_data/"$key"
done
# 2) run batch job
cat refer_data.txt | while read key
do
print ./person_data/"$key"
done
However having said that, using egrep is probably just as rigorous a solution or at least for small datasets, I would most certainly use this approach given the specific question posed. (Or maybe not! The above could well prove faster as well as being more robust.)
Command
while read line; do
grep -w "^$line" <(tr , "\n" < parse.txt)
done < <(tr , "\n" < refer.txt) | paste -s -d , -
Key points
For both files, newlines are translated to commas using the tr command (without actually changing the files themselves). This is useful because while read and grep work under the assumption that your records are separated by newlines instead of commas.
while read will read in every name from refer.txt, (i.e julie, remo, etc.) and then use grep to retrieve lines from parse.txt containing that name.
The ^ in the regex ensures matching is only performed from the start of the string and not in the middle (thanks to #CharlesDuffy's comment below), and the -w option for grep allows whole-word matching only. For example, this ensures that "rob" only matches "rob/..." and not "robby/..." or "throb/...".
The paste command at the end will comma-separate the results. Removing this command will print each result on its own line.