I want to pull all rows from a text file in linux which contain a specific number (in this case 9913) in a specific column (column 4). This is a tab-delimited file, so I am calling this a column, though I am not sure it is.
In some cases, there is only one number in column 4, but in other lines there are multiple numbers in this column (ex. 9913; 4444; 5555). I would like to get any rows for which the number 9913 appears in the 4th column (whether or not it is the only number or in a list). How do I put all lines which contain the number 9913 in column 4 and put them in their own file?
Here is an example of what I have tried:
cat file.txt | grep 9913 > newFile.txt
result is a mixture of the following:
CDR1as CDR1as ENST00000003100.8 9913 AAA-GGCAGCAAGGGACUAAAA (files that I want)
CDR1as CDR1as ENST00000399139.1 9606 GUCCCCA................(file ex. I don't want)
I do not get any results when calling a specific column. Shown by the helper below, the code is not recognizing the columns I think, and I get blank files when using awk.
awk '$4 == "9913"' file.txt > newfile.txt
will give me no transfer of data to a new file.
Thanks
This is one way of doing it
awk '$4 == "9913" {print $0}' file.txt > newfile.txt
or just
awk '$4 == "9913"' file.txt > newfile.txt
Related
I am trying to filter a text file with columns based on two conditions. Due to the size of the file, I cannot use the column numbers (as there are thousands and are unnumbered) but need to use the column names. I have searched and tried to come up with multiple ways to do this but nothing is returned to the command line.
Here are a few things I have tried:
awk '($colname1==2 && $colname2==1) { count++ } END { print count }' file.txt
to filter out the columns based on their conditions
and
head -1 file.txt | tr '\t' | cat -n | grep "COLNAME
to try and return the possible column number related to the column.
An example file would be:
ID ad bd
1 a fire
2 b air
3 c water
4 c water
5 d water
6 c earth
Output would be:
2 (count of ad=c and bd=water)
with your input file and the implied conditions this should work
$ awk -v c1='ad' -v c2='bd' 'NR==1{n=split($0,h); for(i=1;i<=n;i++) col[h[i]]=i}
$col[c1]=="c" && $col[c2]=="water"{count++} END{print count+0}' file
2
or you can replace c1 and c2 with the values in the script as well.
to find the column indices you can run
$ awk -v cols='ad bd' 'BEGIN{n=split(cols,c); for(i=1;i<=n;i++) colmap[c[i]]}
NR==1{for(i=1;i<=NF;i++) if($i in colmap) print $i,i; exit}' file
ad 2
bd 3
or perhaps with this chain
$ sed 1q file | tr -s ' ' \\n | nl | grep -E 'ad|bd'
2 ad
3 bd
although may have false positives due to regex match...
You can rewrite the awk to be more succinct
$ awk -v cols='ad bd' '{while(++i<=NF) if(FS cols FS ~ FS $i FS) print $i,i;
exit}' file
ad 2
bd 3
As I mentioned in an earlier comment, the answer at https://unix.stackexchange.com/a/359699/133219 shows how to do this:
awk -F'\t' '
NR==1 {
for (i=1; i<=NF; i++) {
f[$i] = i
}
}
($(f["ad"]) == "c") && ($(f["bd"]) == "water") { cnt++ }
END { print cnt+0 }
' file
2
I'm assuming your input is tab-separated due to the tr '\t' in the command in your question that looks like you're trying to convert tabs to newlines to convert column names to numbers. If I'm wrong and they're just separated by any chains of white space then remove -F'\t' from the above.
Use miller toolkit to manipulate tab-delimited files using column names. Below is a one-liner that filters a tab-delimited file (delimiter is specified using --tsv) and writes the results to STDOUT together with the header. The header is removed using tail and the lines are counted with wc.
mlr --tsv filter '$ad == "c" && $bd == "water"' file.txt | tail -n +2 | wc -l
Prints:
2
SEE ALSO:
miller manual
Note that miller can be easily installed, for example, using conda, like so:
conda create --name miller miller
For years it bugged me there is no succinct way in Unix to do this sort of thing, although miller is a pretty good tool for this. Recently I wrote pick to choose columns by name, and additionally modify, combine and add them by name, as well as filtering rows by clauses using column names. The solution to the above with pick is
pick -h #ad=c #bd=water < data.txt | wc -l
By default pick prints the header of the selected columns, -h is to omit it. To print columns you simply name them on the command line, e.g.
pick ad water < data.txt | wc -l
Pick has many modes, all of them focused on manipulating columns and selecting/filtering rows with a minimal amount of syntax.
I have a csv file which looks like below:
2212,A1,
2212,A1,128
2307,B1,
2307,B1,107
how can i copy value of 3rd column in place of missing values in 3rd column of if value of first 2 column is same. e.g. first two columns of first two rows are same so automatically it should print value of 3rd column of second row in missing place of third column of first row.
expected output:
2212,A1,128
2212,A1,128
2307,B1,107
2307,B1,107
Please help as i couldn't even think of a solution and there are millions of values such like this in my file..
If you first sort the file in reverse order, the rows with data preceed the empty rows:
$ sort -r file
2307,B1,107
2307,B1,
2212,A1,128
2212,A1,
Then use following awk to process the output of sort:
$ sort -r file | awk 'NR>1 && match(prev,$0) {$0=prev} {prev=$0} 1'
2307,B1,107
2307,B1,107
2212,A1,128
2212,A1,128
awk -F, '{a[$1FS$2]++;b[$1FS$2]=$NF}END{for (i in b) {for(j=1;j<=a[i];j++) print i FS b[i]}}' file
I've tried many combinations of grep and awk commands to process text from file.
This is a list of customers of this type:
John,Mills,81,Crescent,New York,NY,john#mills.com,19/02/1954
I am trying to separate these records into two categories, MEN and FEMALES.
I have a list of some 5000 Female Names , all in plain text , all in one file.
How can I "grep" the first column ( since I am only matching first names) but still printing the entire customer record ?
I found it easy to "cut" the first column and grep --file=female.names.txt, but this way it's not going to print the entire record any longer.
I am aware of the awk option but in that case I don't know how to read the female names from file.
awk -F ',' ' { if($1==" ???Filename??? ") print $0} '
Many thanks !
You can do this with Awk:
awk -F, 'NR==FNR{a[$0]; next} ($1 in a)' female.names.txt file.csv
Would print the lines of your csv file that contain first names of any found in your file female.names.txt.
awk -F, 'NR==FNR{a[$0]; next} !($1 in a)' female.names.txt file.csv
Would output lines not found in female.names.txt.
This assumes the format of your female.names.txt file is something like:
Heather
Irene
Jane
Try this:
grep --file=<(sed 's/.*/^&,/' female.names.txt) datafile.csv
This changes all the names in the list of female names to the regular expression ^name, so it only matches at the beginning of the line and followed by a comma. Then it uses process substitution to use that as the file to match against the data file.
Another alternative is Perl, which can be useful if you're not super-familiar with awk.
#!/usr/bin/perl -anF,
use strict;
our %names;
BEGIN {
while (<ARGV>) {
chomp;
$names{$_} = 1;
}
}
print if $names{$F[0]};
To run (assume you named this file filter.pl):
perl filter.pl female.names.txt < records.txt
So, I've come up with the following:
Suppose, you have a file having the following lines in a file named test.txt:
abe 123 bdb 532
xyz 593 iau 591
Now you want to find the lines which include the first field having the first and last letters as vowels. If you did a simple grep you would get both of the lines but the following will give you the first line only which is the desired output:
egrep "^([0-z]{1,} ){0}[aeiou][0-z]+[aeiou]" test.txt
Then you want to the find the lines which include the third field having the first and last letters as vowels. Similary, if you did a simple grep you would get both of the lines but the following will give you the second line only which is the desired output:
egrep "^([0-z]{1,} ){2}[aeiou][0-z]+[aeiou]" test.txt
The value in the first curly braces {1,} specifies that the preceding character which ranges from 0 to z according to the ASCII table, can occur any number of times. After that, we have the field separator space in this case. Change the value within the second curly braces {0} or {2} to the desired field number-1. Then, use a regular expression to mention your criteria.
I have two files which are of following format.
File1: - It contains 4 column. First field is ID in text format and rest of columns are also some text values.
id1 val12 val13 val14
id2 val22 val23 val24
id3 val32 val33 val34
File2 - In file two I only have IDs.
id1
id2
Output
id3 val32 val33 val34
My question is: How to find rows from first file whose ID(first field) does not appear in second file. Size of both files in pretty large with file1 containing 42 million rows, size 8GB and file2 contains 33 million IDs. Order of IDs in two files might not be same.
Assuming the two files are sorted by id, then something like
join "-t " -j 1 -v 1 file1 file2
should do it.
You could do like this with awk:
awk 'FNR == NR { h[$1] = 1; next } !h[$1]' file2 file1
The first block gathers ids from file2 into the h hash. The last part (!h[$1]) executes the default block ({ print $0 }) if the id wasn't present in file2.
I don't claim that this is the "best" way to do it because best can include a number of trade-off criteria, but here's one way:
You can do this with the -f option to specify File2 as the file containing search patterns to grep:
grep -v -f File2 File1 > output
And as #glennjackman suggests:
One way to force the id to match at the beginning of the line:grep -vf <(sed 's/^/^/' File2) File1
I have several text files whose lines are tab-delimited.
The second column contains incorrect data.
How do I change everything in the second column to a specific text string?
awk ' { $2="<STRING>"; print } ' <FILENAME>
cat INFILE | perl -ne '$ln=$_;#x=split(/","/); #a=split(/","/, $ln,8);#b=splice(#a,0,7); $l=join("\",\"", #b); $r=join("\",\"", splice(#x,8)); print "$l\",\"10\",\"$r"'
This is an example that changes the 10th column to "10". I prefer this as I don't have to count the matching parenthesis like in the sed technique.
A simple and cheap hack:
cat INFILE | sed 's/\(.*\)\t\(.*\)\t\(.*\)/\1\tREPLACEMENT\t\3/' > OUTFILE
testing it:
echo -e 'one\ttwo\tthree\none\ttwo\tthree' | sed 's/\(.*\)\t\(.*\)\t\(.*\)/\1\tREPLACEMENT\t\3/'
takes in
one two three
one two three
and produces
one REPLACEMENT three
one REPLACEMENT three