Selecting specific rows of a tab-delimited file using bash (linux) - r

I have a directory lot of txt tab-delimited files with several rows and columns, e.g.
File1
Id Sample Time ... Variant[Column16] ...
1 s1 t0 c.B481A:p.G861S
2 s2 t2 c.C221C:p.D461W
3 s5 t1 c.G31T:p.G61R
File2
Id Sample Time ... Variant[Column16] ...
1 s1 t0 c.B481A:p.G861S
2 s2 t2 c.C21C:p.D61W
3 s5 t1 c.G1T:p.G1R
and what I am looking for is to create a new file with:
all the different variants uniq
the number of variants repeteated
and the file location
i.e.:
NewFile
Variant Nº of repeated Location
c.B481A:p.G861S 2 File1,File2
c.C221C:p.D461W 1 File1
c.G31T:p.G61R 1 File1
c.C21C:p.D61W 1 File2
c.G1T:p.G1R 1 File2
I think using a basic script in bash with awk sort and uniq it will work, but I do not know where to start. Or if using Rstudio or python(3) is easier, I could try.
Thanks!!

Pure bash. Requires version 4.0+
# two associative arrays
declare -A files
declare -A count
# use a glob pattern that matches your files
for f in File{1,2}; do
{
read header
while read -ra fields; do
variant=${fields[3]} # use index "15" for 16th column
(( count[$variant] += 1 ))
files[$variant]+=",$f"
done
} < "$f"
done
for variant in "${!count[#]}"; do
printf "%s\t%d\t%s\n" "$variant" "${count[$variant]}" "${files[$variant]#,}"
done
outputs
c.B481A:p.G861S 2 File1,File2
c.G1T:p.G1R 1 File2
c.C221C:p.D461W 1 File1
c.G31T:p.G61R 1 File1
c.C21C:p.D61W 1 File2
The order of the output lines is indeterminate: associative arrays have no particular ordering.

Pure bash would be hard I think but everyone has some awk lying around :D
awk 'FNR==1{next}
{
++n[$16];
if ($16 in a) {
a[$16]=a[$16]","ARGV[ARGIND]
}else{
a[$16]=ARGV[ARGIND]
}
}
END{
printf("%-24s %6s %s\n","Variant","Nº","Location");
for (v in n) printf("%-24s %6d %s\n",v,n[v],a[v])}' *

Related

Merge and remove redundant lines *among* files

I need to merge several files, removing redundant lines among files, while keeping redundant lines within files. A schematic representation of my files is the following:
File1.txt
1
2
3
3
4
5
6
File2.txt
6
7
8
8
9
File3.txt
9
10
10
11
The desired output would be:
1
2
3
3
4
5
6
7
8
8
9
10
10
11
I would prefer to get a solution either in awk, or in bash or in R language. I searched the web for solutions and, though there were plenty of them* (please find some examples below), there were all removing duplicated lines regardless of the fact that they were located within or outside files.
Thanks in advance.
Arturo
Examples of previous solutions removing redundant lines both within and outside files:
https://unix.stackexchange.com/questions/50103/merge-two-lists-while-removing-duplicates
https://unix.stackexchange.com/questions/457320/combine-text-files-and-delete-duplicate-lines
https://unix.stackexchange.com/questions/350520/awk-combine-two-big-files-and-remove-duplicated-lines
https://unix.stackexchange.com/questions/257467/merging-2-files-and-keeping-the-one-duplicate
With your shown samples, could you please try following. This will NOT remove redundant lines within files but will remove them file wise.
awk '
FNR==1{
for(key in current){
total[key]
}
delete current
}
!($0 in total)
{
current[$0]
}
' file1.txt file2.txt file3.txt
Explanation: Adding detailed explanation for above.
awk ' ##Starting awk program from here.
FNR==1{ ##Checking condition if its first line(of each file) then do following.
for(key in current){ ##Traverse through current array here.
total[key] ##placing index of current array into total(for all files) one.
}
delete current ##Deleting current array here.
}
!($0 in total) ##If current line is NOT present in total then do following.
{
current[$0] ##Place current line into current array.
}
' file1.txt file2.txt file3.txt ##Mentioning Input_file names here.
Here's a trick adding on to https://stackoverflow.com/a/15385080/3358272 using diff and its output format. There is likely a presumption of "sorted" here, untested.
out=$(mktemp -p .)
tmpout=$(mktemp -p .)
trap 'rm -f "${out}" "${tmpout}"' EXIT
for F in ${#} ; do
{ cat "${out}" ;
diff --changed-group-format='%>' --unchanged-group-format='' "${out}" "${F}" ;
} > "${tmpout}"
mv "${tmpout}" "${out}"
done
cat "${out}"
Output:
$ ./question.sh F*
1
2
3
3
4
5
6
7
8
8
9
10
10
11
$ diff <(./question.sh F*) Output.txt
(Per markp-fuso's comment, if File3.txt had two 9s, this would preserve both.)

deleting repetitive columns in unix

I would like to delete multiple repetitive columns from a huge file (about 1 million).
The columns that I want to delete has the same column names: A and others has different unique name. Say:
A B2 A B3
1.1 AA 1.2 AA
2.1 AB 4.3 CT
2.2 AC 6.4 GT
so column headers are A, B2, A, B3,... .
How could I delete the columns named as A's from the data.
Another in awk:
$ awk '
NR==1 {
split($0,a)
for(i in a)
if(a[i]=="A")
delete a[i]
}
{
for(i=1;i<=NF;i++)
printf "%s",(i in a?$i OFS:"")
printf ORS
}' file
B2 B3
AA AA
AB CT
AC GT
I'm not sure I'm understanding your question correctly, but here an (GNU) awk solution to delete all duplicate columns (keeping only the first occurrence):
#!/usr/bin/awk -f
NR==1 {
seen[$1] = 1
cols[0] = 1
for (i=2; i<=NF; i++) {
if (!($i in seen)) {
seen[$i] = 1
cols[length(cols)] = i
}
}
}
{
for (i=0; i<length(cols); i++)
printf $(cols[i]) " "
printf "\n"
}
For the first line (NR==1), we find all non-duplicate columns (preserving the order), and for all the other lines, we just print out the columns (fields) we selected before (cols array holds column/field indexes we wish to keep).
$ ./filter.awk file
A B2 B3
1.1 AA AA
2.1 AB CT
2.2 AC GT
cut -d' ' -f $(head -1 filename|tr ' ' '\n'|awk '{if(!seen[$0]++) print NR}'|paste -s -d ',') filename
this will work like a charm.
The question is solved by the James Brown code.
I added
!/usr/bin/awk -f
to the first line of his code and correct tiny typo at the end of the code (simply additional -'- deleted).
I am sorry, I did not have time to try all other suggestions
with my best wishes

Grep to count occurrences of file A in file B

I have two files, file A may be in file B and I would like to count for each line in file A, how many times it occurs in file B. For example:
File A:
GAGGACAGACTACTAAAGCC
CTTGCCGCAGATTATCAGAG
CCAGCTTGATGTGTCCTGTG
TGATAGGCAGTGGAACACTG
File B:
NTCTTGAGGAAAGGACGAATCTGCGGAGGACAGACTACTAAAGCCGTTTGAGAGCTAGAACGAGCAAGTTAAGAGA
TCTTGAGGAAAGGACGAAACTCCGGAGGACAGACTACTAAAGCCGTTTTAGAGCTAGAAAGCGCAAGTTAAACGAC
NTCTTGAGGAAAGGACGAATCTGCGCTTGCCGCAGATTATCAGAGGTATGAGAGCTAGAACGAGCAAGTTAAGAGC
TCTTGAGGAAAGGACGAAAGTGCGCTTGCCGCAGATTATCAGAGGTTTTAGAGCTAGAAAGAGCAAGTTAAAATAA
GATCTAGTGGAAAGGACGATTCTCCGCTTGCCGCAGATTATCAGAGGTTGTAGAGCTAGAACTAGCAAGTGACAAG
ATCTTGAGGAAAGGACGAATCTGCGCTTGCCGCAGATTATCAGAGGTTTGAGAGCTAGAACTAGCAAGTTAATAGA
CGATCAAGTGGAAGGACGATTCTCCGTGATAGGCAGTGGAACACTGGATGTAGAGCTAGAAATAGCAAGTGAGCAG
ATCTAGAGGAAAGGACGAATCTCCGTGATAGGCAGTGGAACACTGGTATGAGAGCTAGAACTAGCAAGTTAATAGA
TCTTGAGGAAAGGACGAAACTCCGTGATAGGCAGTGGAACACTGGTTTTAGAGCTAGAAAGCGCAAGTTAAAAGAC
And the output should be File C:
2 GAGGACAGACTACTAAAGCC
4 CTTGCCGCAGATTATCAGAG
0 CCAGCTTGATGTGTCCTGTG
3 TGATAGGCAGTGGAACACTG
I would like to do this using grep and I've tried a few variations of -c,o,f but I can't seem to get the right output.
How can I achieve this?
Try this
for i in `cat a`; do echo "$i `grep $i -c b`"; done
In this case if line from file A occurred several times in one line of file B then this will be count as one occurrence. If you want to count such occurrences but without its overlapping use this
for i in `cat a`; do printf $i; grep $i -o b | wc -l; done
And maybe this variant would be quicker
cat b | grep "`cat a`" -o | sort | uniq -c
#!/usr/bin/perl
open A, "A"; # open file "A" to handle A
open B, "B"; # open file "B" to handle B
chomp(#keys = <A>); # read keys to array, strip line-feeds
#counts{#keys} = (0) x #keys; # initialize hash counts for keys
while(<B>){ # iterate file handle B line by line
foreach $k (#keys){ # iterate keys array
if (/$k/) { # if key matches line
$counts{$k}++; # increase count for key by one
}
}
}
print "$counts{$_} $_\n" for (keys %counts);
Linux command to compare files:
comm FileA FileB
comm produces three-column output. Column one contains lines unique to FileA, column two contains lines unique to FileB, and column three contains lines common to both files.

Compare 2 files in unix file1(2M numbers/rows/lines) , file2(2,000,480 numbers/rows/lines)

How can I compare this 2 big files in unix.
I've already tried using 'grep -Fxvf file1.txt file2.txt | wc -l' but the output is 2,000,480 and when switching file1 and file2 the output is 1,999,999.
How can I get the output of '480' because that's what i am expecting.
I've also tried using diff/cmp commands but the output is too complicated.
I think you want an absolute value of a difference in line numbers in 2 files. You can achieve it easily with awk and get a decent result. You'd read numbers of lines in an array and later subtract the array values in the END block. For pure shell it'd have to get more complex. Imagine you get some test data generated (10 and 14 line files):
$ seq 1 10 > ten
$ seq 1 14 > fourteen
And then you do:
$ ( wc -l ten ; wc -l fourteen ) | awk '{ print $1}' | sort -rn | xargs -J % echo % - p | dc
The result:
4
But much better way would be do just do it in 3 lines (get word count for file1, then file2 and then subtract)

Finding common elements from one file in a column of another file and output the entire row of the latter

I needed to extract all hits from one list (list.txt) which can be found in one of the columns of another (here in Data.txt) into a third (output.txt).
Data.txt (tab delimited)
some_data more_data other_data here yet_more_data etc
A B 2 Gee;Whiz;Hello 13 12
A B 2 Gee;Whizz;Hi 56 32
E 4 Btm;Lol 16 2
T 3 Whizz 13 3
List.txt
Gee
Whiz
Lol
Ideally output.txt looks like
some_data more_data other_data here yet_more_data etc
A B 2 Gee;Whiz;Hello 13 12
A B 2 Gee;Whizz;Hi 56 32
E 4 Btm;Lol 16 2
So I tried a shell script
for ids in List.txt
do
grep $ids Data.txt >> output.txt
done
except I typed out everything (cut and paste actually) in List.txt in said script.
Unfortunately it gave me an output.txt including the last line, I assume as 'Whizz' contains 'Whiz'.
I also tried cat Data.txt | egrep -F "List.txt" and that resulted in grep: conflicting matchers specified -- I suppose that was too naive of me. The actual files: List.txt contains a sorted list of 985 words, Data.txt has 115576 rows with 17 columns.
Some help/guidance would be much appreciated thanks.
Try something like this:
for ids in List.txt
do
grep "[TAB;]$ids[TAB;]" Data.txt >> output.txt
done
But it has two drawbacks:
"Data.txt" is scanned multiple times
You can get one line multiple times.
If it is problem try two step version:
cat List.txt | sed -e "s/.*/[TAB;]\0[TAB;]/g" > List_mod.txt
grep -f List_mod.txt Data.txt > output.txt
Note:
TAB character can be inserted by combination Ctrl-V following by Tab key in command line, and Tab character in editor. You have to check if your edit does not change tab to series of spaces.
The UNIX tool for general text processing is "awk":
awk '
NR==FNR { list[$0]; next }
{
for (word in list) {
if ($0 ~ "[\t;]" word "[\t;]") {
print
next
}
}
}
' List.txt Data.txt > output.txt

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