I'm working with GWAS data.
Using p-link command I was able to get SNPslist, SNPs.map, SNPs.ped.
Here are the data files and commands I have for 2 SNPs (rs6923761, rs7903146):
$ cat SNPs.map
0 rs6923761 0 0
0 rs7903146 0 0
$ cat SNPs.ped
6 6 0 0 2 2 G G C C
74 74 0 0 2 2 A G T C
421 421 0 0 2 2 A G T C
350 350 0 0 2 2 G G T T
302 302 0 0 2 2 G G C C
bash commands I used:
echo -n IID > SNPs.csv
cat SNPs.map | awk '{printf ",%s", $2}' >> SNPs.csv
echo >> SNPs.csv
cat SNPs.ped | awk '{printf "%s,%s%s,%s%s\n", $1, $7, $8, $9, $10}' >> SNPs.csv
cat SNPs.csv
Output:
IID,rs6923761,rs7903146
6,GG,CC
74,AG,TC
421,AG,TC
350,GG,TT
302,GG,CC
This is about 2 SNPs, so I can see manually their position so I added and called using the above command. But now I have 2000 SNPs IDs and their values. Need help with bash command which can parse over 2000 SNPs in the same way.
One awk idea that replaces all of the current code:
awk '
BEGIN { printf "IID" }
# process 1st file:
FNR==NR { printf ",%s", $2; next }
# process 2nd file:
FNR==1 { print "" } # terminate 1st line of output
{ printf $1 # print 1st column
for (i=7;i<=NF;i=i+2) # loop through columns 7-NF, incrementing index +2 on each pass
printf ",%s%s", $i, $(i+1) # print (i)th and (i+1)th columns
print "" # terminate line
}
' SNPs.map SNPs.ped
NOTE: remove comments to declutter code
This generates:
IID,rs6923761,rs7903146
6,GG,CC
74,AG,TC
421,AG,TC
350,GG,TT
302,GG,CC
You can use --recodeA flag in plink to have your IID as rows and SNPs as columns.
Related
The idea is that you have 3 text files lets name it A B C where you only have a unique column with strings (doesn't matter the content in this example). What you want is to make a join function between these three, so you'll have a join for A - B another one for B - C and a last one for A - C as if it is a permutation.
Let's make a graphic example.
The individual code would be
join -1 1 -2 1 A.txt B.txt > AB.txt
and so on for the other 2
Imagine A has
100
101
102
104
B has
101
103
104
105
C has
100
103
104
105
So A - B comparison (AB.txt) would be:
101
104
A - C comparison (AC.txt):
100
104
B - C comparison (BC.txt):
103
105
And you'll have three output file named after the comparisons AB.txt, AC.txt and BC.txt
A solution might look like this:
#!/usr/bin/env bash
# Read positional parameters into array
list=("$#")
# Loop over all but the last element
for ((i = 0; i < ${#list[#]} - 1; ++i)); do
# Loop over the elements starting with the first after the one i points to
for ((j = i + 1; j < ${#list[#]}; ++j)); do
# Run the join command and redirect to constructed filename
join "${list[i]}" "${list[j]}" > "${list[i]%.txt}${list[j]%.txt}".txt
done
done
Notice that the -1 1 -2 1 is the default behaviour for join and can be skipped.
The script has to be called with the filenames as the parameters:
./script A.txt B.txt C.txt
A function that does nothing but generate the possible combinations of two among its arguments:
#!/bin/bash
combpairs() {
local a b
until [ $# -lt 2 ]; do
a="$1"
for b in "${#:2}"; do
echo "$a - $b"
done
shift
done
}
combpairs A B C D E
A - B
A - C
A - D
A - E
B - C
B - D
B - E
C - D
C - E
D - E
I would put the files in an array, and use the index like this:
files=(a.txt b.txt c.txt) # or files=(*.txt)
for ((i=0; i<${#files[#]}; i++)); do
f1=${files[i]} f2=${files[i+1]:-$files}
join -1 1 -2 1 "$f1" "$f2" > "${f1%.txt}${f2%.txt}.txt"
done
Using echo join to debug (and quoting >), this is what would be executed:
join -1 1 -2 1 a.txt b.txt > ab.txt
join -1 1 -2 1 b.txt c.txt > bc.txt
join -1 1 -2 1 c.txt a.txt > ca.txt
Or for six files:
join -1 1 -2 1 a.txt b.txt > ab.txt
join -1 1 -2 1 b.txt c.txt > bc.txt
join -1 1 -2 1 c.txt d.txt > cd.txt
join -1 1 -2 1 d.txt e.txt > de.txt
join -1 1 -2 1 e.txt f.txt > ef.txt
join -1 1 -2 1 f.txt a.txt > fa.txt
LC_ALL=C; files(*.txt) would use all .txt files in the current directory, sorted by name, which may be relevant.
One in GNU awk:
$ gawk '{
a[ARGIND][$0] # hash all files to arrays
}
END { # after hashing
for(i in a) # form pairs
for(j in a)
if(i<j) { # avoid self and duplicate comparisons
f=ARGV[i] ARGV[j] ".txt" # form output filename
print ARGV[i],ARGV[j] > f # output pair info
for(k in a[i])
if(k in a[j])
print k > f # output matching records
}
}' a b c
Output, for example:
$ cat ab.txt
a b
101
104
All files are hashed in the memory in the beginning so if the files are huge, you may run out of memory.
Another variation
declare -A seen
for a in {A,B,C}; do
for b in {A,B,C}; do
[[ $a == $b || -v seen[$a$b] || -v seen[$b$a] ]] && continue
seen[$a$b]=1
comm -12 "$a.txt" "$b.txt" > "$a$b.txt"
done
done
I want to replace the second column of my first file
file 1:
2 rs58086319 0 983550 T C
2 rs56809628 0 983571 T C
2 rs7608441 0 983572 A G
2 rs114910509 0 983579 A G
2 var_chr2_983614 0 983614 T C
2 var_chr2_983624 0 983624 A G
2 rs115188027 0 983632 A C
2 var_chr2_983636 0 983636 T C
2 var_chr2_983650 0 983650 A G
2 var_chr2_983660 0 983660 T C
with the first column of my second file
file 2:
2_983550_T_C
2_983571_T_C
2_983572_A_G
2_983579_A_G
2_983614_T_C
2_983624_A_G
2_983632_A_C
2_983636_T_C
2_983650_A_G
2_983660_T_C
I've tried join and awk but somehow it doesn't seem to work. I suspect the fact that there's '_' on my second file.
Thank you
I'm a bit puzzled why you need a second file. All information of file2 seems to be encoded in file1. You could just do something like this :
awk '{$2=$1"_"$4"_"$5"_"$6}1' file1
Your file2 have only one column so with awk.
awk -v f='file2' '{getline $2 <f}1' file1
If the separator of file2 is "_"
awk -v f='file2' '{getline a <f;split(a,b,"_");$2=b[1]}1' file1
EDIT: In case you want to make _ as field separator in Input_file2 then following may help you.
awk 'FNR==NR{a[FNR]=$1;next} (FNR in a){$2=a[FNR]} 1' FS="_" file2 FS=" " file1 | column -t
Following awk may help you here.
awk 'FNR==NR{a[FNR]=$0;next} (FNR in a){$2=a[FNR]} 1' file2 file1 | column -t
I would go with paste and awk, e.g.:
paste file1 file2 | awk '{ $2 = $NF } NF--' OFS='\t'
Output:
2 2_983550_T_C 0 983550 T C
2 2_983571_T_C 0 983571 T C
2 2_983572_A_G 0 983572 A G
2 2_983579_A_G 0 983579 A G
2 2_983614_T_C 0 983614 T C
2 2_983624_A_G 0 983624 A G
2 2_983632_A_C 0 983632 A C
2 2_983636_T_C 0 983636 T C
2 2_983650_A_G 0 983650 A G
2 2_983660_T_C 0 983660 T C
I have tab delimited text files in which common rows between them are to be found based on columns 1 and 2 as key columns.
Sample files:
file1.txt
aba 0 0
aba 0 0 1
abc 0 1
abd 1 1
xxx 0 0
file2.txt
xyz 0 0
aba 0 0 0 0
aba 0 0 0 1
xxx 0 0
abc 1 1
file3.txt
xyx 0 0
aba 0 0
aba 0 1 0
xxx 0 0 0 1
abc 1 1
The below code does the same and returns the rows only if the key column is found in all the N files (3 files in this case).
awk '
FNR == NR {
arr[$1,$2] = 1
line[$1,$2] = line[$1,$2] ( line[$1,$2] ? SUBSEP : "" ) $0
next
}
FNR == 1 { delete found }
{ if ( arr[$1,$2] && ! found[$1,$2] ) { arr[$1,$2]++; found[$1,$2] = 1 } }
END {
num_files = ARGC -1
for ( key in arr ) {
if ( arr[key] < num_files ) { continue }
split( line[ key ], line_arr, SUBSEP )
for ( i = 1; i <= length( line_arr ); i++ ) {
printf "%s\n", line_arr[ i ]
}
}
}
' *.txt > commoninall.txt
Output:
xxx 0 0
aba 0 0
aba 0 0 1
However, now I would like to get the output if 'x' files have the key columns.
For example x=2 i.e. rows which are common in two files based on key columns 1 and 2. The output in this case would be:
xyz 0 0
abc 1 1
In real scenario I do have to specify different values for x. Can anybody suggest an edit to this or a new solution.
First attempt
I think you just need to modify the END block a little, and the command invocation:
awk -v num_files=${x:-0} '
…
…script as before…
…
END {
if (num_files == 0) num_files = ARGC - 1
for (key in arr) {
if (arr[key] == num_files) {
split(line[key], line_arr, SUBSEP)
for (i = 1; i <= length(line_arr); i++) {
printf "%s\n", line_arr[i]
}
}
}
}
'
Basically, this takes a command line parameter based on $x, defaulting to 0, and assigning it to the awk variable num_files. In the END block, the code checks for num_files being zero, and resets it to the number of files passed on the command line. (Interestingly, the value in ARGC discounts any -v var=value options and either a command line script or -f script.awk, so the ARGC-1 term remains correct. The array ARGV contains awk (or whatever name you invoked it with) in ARGV[0] and the files to be processed in ARGV[1] through ARGV[ARGC-1].) The loop then checks for the required number of matches and prints as before. You can change == to >= if you want the 'or more' option.
Does it work?
I observed in a comment:
I'm not clear what you are asking. I took it that your code was working for the example with three files and producing the right answer. I simply suggested how to modify the working code to handle N files and at least M of them sharing an entry. I have just realized, while typing this, that there is a bit more work to do. An entry could be missing from the first file but present in the others and will need to be processed, therefore. It is easy to report all occurrences in every file, or the first occurrence in any file. It is harder to report all occurrences only in the first file with a key.
The response was:
It is perfectly fine to report first occurrence in any file and need not be only from the first file. However, the issue with the suggested modification is, it is producing the same output for different values of x.
That's curious: I was able to get sane output from the amended code with different values for the number of files where the key must appear. I used this shell script. The code in the awk program up to the END block is the same as in the question; the only change is in the END processing block.
#!/bin/bash
while getopts n: opt
do
case "$opt" in
(n) num_files=$OPTARG;;
(*) echo "Usage: $(basename "$0" .sh) [-n number] file [...]" >&2
exit 1;;
esac
done
shift $(($OPTIND - 1))
awk -v num_files=${num_files:-$#} '
FNR == NR {
arr[$1,$2] = 1
line[$1,$2] = line[$1,$2] (line[$1,$2] ? SUBSEP : "") $0
next
}
FNR == 1 { delete found }
{ if (arr[$1,$2] && ! found[$1,$2]) { arr[$1,$2]++; found[$1,$2] = 1 } }
END {
if (num_files == 0) num_files = ARGC - 1
for (key in arr) {
if (arr[key] == num_files) {
split(line[key], line_arr, SUBSEP)
for (i = 1; i <= length(line_arr); i++) {
printf "%s\n", line_arr[i]
}
}
}
}
' "$#"
Sample runs (data files from question):
$ bash common.sh file?.txt
xxx 0 0
aba 0 0
aba 0 0 1
$ bash common.sh -n 3 file?.txt
xxx 0 0
aba 0 0
aba 0 0 1
$ bash common.sh -n 2 file?.txt
$ bash common.sh -n 1 file?.txt
abc 0 1
abd 1 1
$
That shows different answers depending on the value specified via -n. Note that this only shows lines that appear in the first file and appear in exactly N files in total. The only key that appears in two files (abc/1) does not appear in the first file, so it is not listed by this code which stops paying attention to new keys after the first file is processed.
Rewrite
However, here's a rewrite, using some of the same ideas, but working more thoroughly.
#!/bin/bash
# SO 30428099
# Given that the key for a line is the first two columns, this script
# lists all appearances in all files of a given key if that key appears
# in N different files (where N defaults to the number of files). For
# the benefit of debugging, it includes the file name and line number
# with each line.
usage()
{
echo "Usage: $(basename "$0" .sh) [-n number] file [...]" >&2
exit 1
}
while getopts n: opt
do
case "$opt" in
(n) num_files=$OPTARG;;
(*) usage;;
esac
done
shift $(($OPTIND - 1))
if [ "$#" = 0 ]
then usage
fi
# Record count of each key, regardless of file: keys
# Record count of each key in each file: key_file
# Count of different files containing each key: files
# Accumulate line number, filename, line for each key: lines
awk -v num_files=${num_files:-$#} '
{
keys[$1,$2]++;
if (++key_file[$1,$2,FILENAME] == 1)
files[$1,$2]++
#printf "%s:%d: Key (%s,%s); keys = %d; key_file = %d; files = %d\n",
# FILENAME, FNR, $1, $2, keys[$1,$2], key_file[$1,$2,FILENAME], files[$1,$2];
sep = lines[$1,$2] ? RS : ""
#printf "B: [[\n%s\n]]\n", lines[$1,$2]
lines[$1,$2] = lines[$1,$2] sep FILENAME OFS FNR OFS $0
#printf "A: [[\n%s\n]]\n", lines[$1,$2]
}
END {
#print "END"
for (key in files)
{
#print "Key =", key, "; files =", files[key]
if (files[key] == num_files)
{
#printf "TAG\n%s\nEND\n", lines[key]
print lines[key]
}
}
}
' "$#"
Sample output (given the data files from the question):
$ bash common.sh file?.txt
file1.txt 5 xxx 0 0
file2.txt 4 xxx 0 0
file3.txt 4 xxx 0 0 0 1
file1.txt 1 aba 0 0
file1.txt 2 aba 0 0 1
file2.txt 2 aba 0 0 0 0
file2.txt 3 aba 0 0 0 1
file3.txt 2 aba 0 0
file3.txt 3 aba 0 1 0
$ bash common.sh -n 2 file?.txt
file2.txt 5 abc 1 1
file3.txt 5 abc 1 1
$ bash common.sh -n 1 file?.txt
file1.txt 3 abc 0 1
file3.txt 1 xyx 0 0
file1.txt 4 abd 1 1
file2.txt 1 xyz 0 0
$ bash common.sh -n 3 file?.txt
file1.txt 5 xxx 0 0
file2.txt 4 xxx 0 0
file3.txt 4 xxx 0 0 0 1
file1.txt 1 aba 0 0
file1.txt 2 aba 0 0 1
file2.txt 2 aba 0 0 0 0
file2.txt 3 aba 0 0 0 1
file3.txt 2 aba 0 0
file3.txt 3 aba 0 1 0
$ bash common.sh -n 4 file?.txt
$
You can fettle this to give the output you want (probably missing file name and line number). If you only want the lines from the first file containing a given key, you only add the information to lines when files[$1,$2] == 1. You can separate the recorded information with SUBSEP instead of RS and OFS if you prefer.
Can't you simply use uniq to search for repeated lines in you files?
Something like:
cat file1.txt file2.txt file3.txt | uniq -d
For your complete scenario, you could use uniq -c to get the number of repetition for each line, and filter this with grep.
I have a 5-column file:
PS 6 15 0 1
PS 1 17 0 1
PS 4 18 0 1
that I would like to get it in this 7-column format:
PS.15 PS 6 N 1 0 1
PS.17 PS 1 P 1 0 1
PS.18 PS 4 N 1 0 1
To create 6 of the 7 columns requires just grabbing directly (and sometimes applying small arithmetic) from columns in the original file. However, to create one column (column 4) requires an if-else statement.
Specifically, to create new columns 1, 2, 3, I use:
cat File | awk '{print $1"."$3"\t"$1"\t"$2}'
and to create new columns 5, 6,7, I use:
cat testFileB | awk '{print $4+$5"\t"$4/($4+$5)"\t"$5/($4+$5)}'
and to create new column 4, I use:
cat testFileB | awk '{if ($2 == 1 || $2 == 2 || $2 == 3) print "P"; else print "N";}'
These three statements work fine independently and get me what I want (the correct values for the columns that are all separated by tabs). However, when I try to apply them simultaneously (create all 7 columns at once), I can only do so with unwanted new lines (instead of tabs) before and after column 4 (the if/else statement column):
For instance, my attempt to simultaneously create columns 1, 2, 3, 4:
cat File | awk '{print $1"."$3"\t"$1"\t"$2; if ($2 == 1 || $2 == 2 || $2 == 3) print "P"; else print "N";}'
results in unwanted new lines before column 4:
PS.15 PS 6
N
PS.17 PS 1
P
PS.18 PS 4
Similarly, my attempt to simultaneously create columns 4, 5, 6, 7:
cat File | awk '{if ($2 == 1 || $2 == 2 || $2 == 3) print "P"; else print "N"; print $4+$5"\t"$4/($4+$5)"\t"$5/($4+$5)}'
results in unwanted new lines after column 4:
N
1 0 1
P
1 0 1
N
1 0 1
Is there a solution so that I can create all 7 columns at once, and there are only tabs between them (no new lines)?
If you don't want automatic line feeds, you can just use printf instead of print. I'm not quite sure if you want a tab separating the N1 or not, but that's easy enough to adjust;
cat testfile | awk '{printf "%s.%s\t%s\t%s\t",$1,$3,$1,$2; if ($2 == 1 || $2 == 2 || $2 == 3) printf "P"; else printf "N"; print $4+$5"\t"$4/($4+$5)"\t"$5/($4+$5)}'
PS.15 PS 6 N1 0 1
PS.17 PS 1 P1 0 1
PS.18 PS 4 N1 0 1
Simply set your OFS (instead of repeating a \t all across the line), and use the ternary operator to print P or N:
$ awk -v OFS='\t' '{s=$4+$5;print $1"."$3,$1,$2,($2~/^[123]$/?"P":"N"),s,$4/s,$5/s}' file
PS.15 PS 6 N 1 0 1
PS.17 PS 1 P 1 0 1
PS.18 PS 4 N 1 0 1
Given a file with data like this (ie stores.dat file)
sid|storeNo|latitude|longitude
2tt|1|-28.0372000t0|153.42921670
9|2t|-33tt.85t09t0000|15t1.03274200
What is the command that would return the number of occurrences of the 't' character per line?
eg. would return:
count lineNum
4 1
3 2
6 3
Also, to do it by count of occurrences by field what is the command to return the following results?
eg. input of column 2 and character 't'
count lineNum
1 1
0 2
1 3
eg. input of column 3 and character 't'
count lineNum
2 1
1 2
4 3
To count occurrence of a character per line you can do:
awk -F'|' 'BEGIN{print "count", "lineNum"}{print gsub(/t/,"") "\t" NR}' file
count lineNum
4 1
3 2
6 3
To count occurrence of a character per field/column you can do:
column 2:
awk -F'|' -v fld=2 'BEGIN{print "count", "lineNum"}{print gsub(/t/,"",$fld) "\t" NR}' file
count lineNum
1 1
0 2
1 3
column 3:
awk -F'|' -v fld=3 'BEGIN{print "count", "lineNum"}{print gsub(/t/,"",$fld) "\t" NR}' file
count lineNum
2 1
1 2
4 3
gsub() function's return value is number of substitution made. So we use that to print the number.
NR holds the line number so we use it to print the line number.
For printing occurrences of particular field, we create a variable fld and put the field number we wish to extract counts from.
grep -n -o "t" stores.dat | sort -n | uniq -c | cut -d : -f 1
gives almost exactly the output you want:
4 1
3 2
6 3
Thanks to #raghav-bhushan for the grep -o hint, what a useful flag. The -n flag includes the line number as well.
To count occurences of a character per line:
$ awk -F 't' '{print NF-1, NR}' input.txt
4 1
3 2
6 3
this sets field separator to the character that needs to be counted, then uses the fact that number of fields is one greater than number of separators.
To count occurences in a particular column cut out that column first:
$ cut -d '|' -f 2 input.txt | awk -F 't' '{print NF-1, NR}'
1 1
0 2
1 3
$ cut -d '|' -f 3 input.txt | awk -F 't' '{print NF-1, NR}'
2 1
1 2
4 3
One possible solution using perl:
Content of script.pl:
use warnings;
use strict;
## Check arguments:
## 1.- Input file
## 2.- Char to search.
## 3.- (Optional) field to search. If blank, zero or bigger than number
## of columns, default to search char in all the line.
(#ARGV == 2 || #ARGV == 3) or die qq(Usage: perl $0 input-file char [column]\n);
my ($char,$column);
## Get values or arguments.
if ( #ARGV == 3 ) {
($char, $column) = splice #ARGV, -2;
} else {
$char = pop #ARGV;
$column = 0;
}
## Check that $char must be a non-white space character and $column
## only accept numbers.
die qq[Bad input\n] if $char !~ m/^\S$/ or $column !~ m/^\d+$/;
print qq[count\tlineNum\n];
while ( <> ) {
## Remove last '\n'
chomp;
## Get fields.
my #f = split /\|/;
## If column is a valid one, select it to the search.
if ( $column > 0 and $column <= scalar #f ) {
$_ = $f[ $column - 1];
}
## Count.
my $count = eval qq[tr/$char/$char/];
## Print result.
printf qq[%d\t%d\n], $count, $.;
}
The script accepts three parameters:
Input file
Char to search
Column to search: If column is a bad digit, it searchs all the line.
Running the script without arguments:
perl script.pl
Usage: perl script.pl input-file char [column]
With arguments and its output:
Here 0 is a bad column, it searches all the line.
perl script.pl stores.dat 't' 0
count lineNum
4 1
3 2
6 3
Here it searches in column 1.
perl script.pl stores.dat 't' 1
count lineNum
0 1
2 2
0 3
Here it searches in column 3.
perl script.pl stores.dat 't' 3
count lineNum
2 1
1 2
4 3
th is not a char.
perl script.pl stores.dat 'th' 3
Bad input
No need for awk or perl, only with bash and standard Unix utilities:
cat file | tr -c -d "t\n" | cat -n |
{ echo "count lineNum"
while read num data; do
test ${#data} -gt 0 && printf "%4d %5d\n" ${#data} $num
done; }
And for a particular column:
cut -d "|" -f 2 file | tr -c -d "t\n" | cat -n |
{ echo -e "count lineNum"
while read num data; do
test ${#data} -gt 0 && printf "%4d %5d\n" ${#data} $num
done; }
And we can even avoid tr and the cats:
echo "count lineNum"
num=1
while read data; do
new_data=${data//t/}
count=$((${#data}-${#new_data}))
test $count -gt 0 && printf "%4d %5d\n" $count $num
num=$(($num+1))
done < file
and event the cut:
echo "count lineNum"
num=1; OLF_IFS=$IFS; IFS="|"
while read -a array_data; do
data=${array_data[1]}
new_data=${data//t/}
count=$((${#data}-${#new_data}))
test $count -gt 0 && printf "%4d %5d\n" $count $num
num=$(($num+1))
done < file
IFS=$OLF_IFS
awk '{gsub("[^t]",""); print length($0),NR;}' stores.dat
The call to gsub() deletes everything in the line that is not a t, then just print the length of what remains, and the current line number.
Want to do it just for column 2?
awk 'BEGIN{FS="|"} {gsub("[^t]","",$2); print NR,length($2);}' stores.dat
You could also split the line or field with "t" and check the length of the resulting array - 1. Set the col variable to 0 for the line or 1 through 3 for columns:
awk -F'|' -v col=0 -v OFS=$'\t' 'BEGIN {
print "count", "lineNum"
}{
split($col, a, "t"); print length(a) - 1, NR
}
' stores.dat
$ cat -n test.txt
1 test 1
2 you want
3 void
4 you don't want
5 ttttttttttt
6 t t t t t t
$ awk '{n=split($0,c,"t")-1;if (n!=0) print n,NR}' test.txt
2 1
1 2
2 4
11 5
6 6
cat stores.dat | awk 'BEGIN {FS = "|"}; {print $1}' | awk 'BEGIN {FS = "\t"}; {print NF}'
Where $1 would be a column number you want to count.
perl -e 'while(<>) { $count = tr/t//; print "$count ".++$x."\n"; }' stores.dat
Another perl answer yay! The tr/t// function returns the count of the number of times the translation occurred on that line, in other words the number of times tr found the character 't'. ++$x maintains the line number count.