My input:
Position A B C D No
1 0 0 0 0 0
2 1 0 1 0 0
3 0 6 0 0 0
4 0 0 0 0 0
5 0 5 0 0 0
I have a TSV file, like the above, where I wish to sum the rows of numbers in the ABCD columns only, not the Position column.
Desired output would have a TSV, two columns with Position and Sum in the first row,
Position Sum
1 0
2 2
3 6
4 0
5 5
So far I have:
awk 'BEGIN{print"Position\tSum"}{if(NR==1)next; sum=$2+$3+$4+$5 printf"%d\t%d\n",$sum}' infile.tsv > outfile.tsv
You were very close, try this:
awk 'BEGIN{print"Position\tSum"}{if(NR==1)next; sum=$2+$3+$4+$5; printf "%d\t%d\n",$1,sum; }' infile.tsv > outfile.tsv
But I say it's way cleaner with newlines and spaces:
awk '
BEGIN {
print"Position\tSum";
}
{
if (NR==1) {
next;
}
sum = $2 + $3 + $4 + $5 + $6;
printf "%d\t%d\n", $1, sum;
}'
a minimalist script can be
$ awk '{print $1 "\t" (NR==1?"Sum":$2+$3+$4+$5)}' file
Could you please try following, what you were trying to hard code field numbers which will not work in many cases so I am coming with a loop approach(where we are skipping first field and taking sum of all fields then).
awk 'FNR==1{print $1,"sum";next} {for(i=2;i<NF;i++){sum+=$i};print $1,sum;sum=""}' Input_file
Change awk to awk 'BEGIN{OFS="\t"} rest part same of code in case you need output in TAB form.
Related
I am trying to make a script (and a loop) to extract matching lines to print them into a new file. There are 2 conditions: 1st is that I need to print the value of the 2nd and 4th columns of the map file if the 2nd column of the map file matches with the 4th column of the test file. The 2nd condition is that when there is no match, I want to print the value in the 2nd column of the test file and a zero in the second column.
My test file is made this way:
8 8:190568 0 190568
8 8:194947 0 194947
8 8:197042 0 197042
8 8:212894 0 212894
My map file is made this way:
8 190568 0.431475 0.009489
8 194947 0.434984 0.009707
8 19056880 0.395066 112.871160
8 101908687 0.643861 112.872348
1st attempt:
for chr in {21..22};
do
awk 'NR==FNR{a[$2]; next} {if ($4 in a) print $2, $4 in a; else print $2, $4 == "0"}' map_chr$chr.txt test_chr$chr.bim > position.$chr;
done
Result:
8:190568 1
8:194947 1
8:197042 0
8:212894 0
My second script is:
for chr in {21..22}; do
awk 'NR == FNR { ++a[$4]; next }
$4 in a { print a[$2], $4; ++found[$2] }
END { for(k in a) if (!found[k]) print a[k], 0 }' \
"test_chr$chr.bim" "map_chr$chr.txt" >> "position.$chr"
done
And the result is:
1 0
1 0
1 0
1 0
The result I need is:
8:190568 0.009489
8:194947 0.009707
8:197042 0
8:212894 0
This awk should work for you:
awk 'FNR==NR {map[$2]=$4; next} {print $4, map[$4]+0}' mapfile testfile
190568 0.009489
194947 0.009707
197042 0
212894 0
This awk command processes mapfile first and stores $2 as key with $4 as a value in an associative array named as map.
Later when it processes testfile in 2nd block we print $4 from 2nd file with the stored value in map using key as $4. We add 0 in stored value to make sure that we get 0 when $4 is not present in map.
I have a file with numbers and I want to sum numbers from two lines and this for each column, then in my last step I want to filter out pairs of lines that has a count bigger or equal than 3 of '0' sum counts. I write a small example to make it clear:
This is my file (without the comments ofc), it contains 2 pairs of lines (=4 lines) with 5 columns.
2 6 0 8 9 # pair 1.A
0 1 0 5 1 # pair 1.B
0 2 0 3 0 # pair 2.A
0 0 0 0 0 # pair 2.B
And I need to sum up pairs of lines so I get something like this (intermediate step)
2 7 0 13 10 # sum pair 1, it has one 0
0 2 0 3 0 # sum pair 2, it has three 0
Then I want to print the original lines, but only those which the sum of 0 (of the sum of the two lines) is lower than 3, therefore I should get printed this:
2 6 0 8 9 # pair 1.A
0 1 0 5 1 # pair 1.B
Because the sum of the second pair of lines has three 0, then it should be excluded
So from the first file I need to get the last output.
So far what I have been able to do is to sum pairs of lines, count zeros, and identify those with a count lower than 3 of 0 but I don't know how to print the two lines that contributed to the SUM, I am only able to print one of the two lines (the last one). This is the awk I am using:
awk '
NR%2 { split($0, a); next }
{ for (i=1; i<=NF; i++) if (a[i]+$i == 0) SUM +=1;
if (SUM < 3) print $0; SUM=0 }' myfile
(That's what I get now)
0 1 0 5 1 # pair 1.B
Thanks!
Another variation, could be useful to avoid loop iterations in some input cases:
awk '!(NR%2){ zeros=0; for(i=1;i<=NF;i++) { if(a[i]+$i==0) zeros++; if(zeros>=3) next }
print prev ORS $0 }{ split($0,a); prev=$0 }' file
The output:
2 6 0 8 9
0 1 0 5 1
Well, after digging a little bit more I found that it was rather simple to print the previous line (I was complicating myself)
awk '
NR%2 { split($0, a) ; b=$0; next }
{ for (i=1; i<=NF; i++) if (a[i]+$i == 0) SUM +=1;
if (SUM < 3) print b"\n"$0; SUM=0}' myfile
So I just have to save the first line in a variable b and print when the condition is favorable.
Hope it can help other people too
$ cat tst.awk
!(NR%2) {
split(prev,p)
zeroCnt = 0
for (i=1; i<=NF; i++) {
zeroCnt += (($i + p[i]) == 0 ? 1 : 0)
}
if (zeroCnt < 3) {
print prev ORS $0
}
}
{ prev = $0 }
$ awk -f tst.awk file
2 6 0 8 9
0 1 0 5 1
We want to subset a text file on rows and columns, where rows and columns numbers are read from a file. Excluding header (row 1) and rownames (col 1).
inputFile.txt Tab delimited text file
header 62 9 3 54 6 1
25 1 2 3 4 5 6
96 1 1 1 1 0 1
72 3 3 3 3 3 3
18 0 1 0 1 1 0
82 1 0 0 0 0 1
77 1 0 1 0 1 1
15 7 7 7 7 7 7
82 0 0 1 1 1 0
37 0 1 0 0 1 0
18 0 1 0 0 1 0
53 0 0 1 0 0 0
57 1 1 1 1 1 1
subsetCols.txt Comma separated with no spaces, one row, numbers ordered. In real data we have 500K columns, and need to subset ~10K.
1,4,6
subsetRows.txt Comma separated with no spaces, one row, numbers ordered. In real data we have 20K rows, and need to subset about ~300.
1,3,7
Current solution using cut and awk loop (Related post: Select rows using awk):
# define vars
fileInput=inputFile.txt
fileRows=subsetRows.txt
fileCols=subsetCols.txt
fileOutput=result.txt
# cut columns and awk rows
cut -f2- $fileInput | cut -f`cat $fileCols` | sed '1d' | awk -v s=`cat $fileRows` 'BEGIN{split(s, a, ","); for (i in a) b[a[i]]} NR in b' > $fileOutput
Output file: result.txt
1 4 6
3 3 3
7 7 7
Question:
This solution works fine for small files, for bigger files 50K rows and 200K columns, it is taking too long, 15 minutes plus, still running. I think cutting the columns works fine, selecting rows is the slow bit.
Any better way?
Real input files info:
# $fileInput:
# Rows = 20127
# Cols = 533633
# Size = 31 GB
# $fileCols: 12000 comma separated col numbers
# $fileRows: 300 comma separated row numbers
More information about the file: file contains GWAS genotype data. Every row represents sample (individual) and every column represents SNP. For further region based analysis we need to subset samples(rows) and SNPs(columns), to make the data more manageable (small) as an input for other statistical softwares like r.
System:
$ uname -a
Linux nYYY-XXXX ZZZ Tue Dec 18 17:22:54 CST 2012 x86_64 x86_64 x86_64 GNU/Linux
Update: Solution provided below by #JamesBrown was mixing the orders of columns in my system, as I am using different version of awk, my version is: GNU Awk 3.1.7
Even though in If programming languages were countries, which country would each language represent? they say that...
Awk: North Korea. Stubbornly resists change, and its users appear to be unnaturally fond of it for reasons we can only speculate on.
... whenever you see yourself piping sed, cut, grep, awk, etc, stop and say to yourself: awk can make it alone!
So in this case it is a matter of extracting the rows and columns (tweaking them to exclude the header and first column) and then just buffering the output to finally print it.
awk -v cols="1 4 6" -v rows="1 3 7" '
BEGIN{
split(cols,c); for (i in c) col[c[i]] # extract cols to print
split(rows,r); for (i in r) row[r[i]] # extract rows to print
}
(NR-1 in row){
for (i=2;i<=NF;i++)
(i-1) in col && line=(line ? line OFS $i : $i); # pick columns
print line; line="" # print them
}' file
With your sample file:
$ awk -v cols="1 4 6" -v rows="1 3 7" 'BEGIN{split(cols,c); for (i in c) col[c[i]]; split(rows,r); for (i in r) row[r[i]]} (NR-1 in row){for (i=2;i<=NF;i++) (i-1) in col && line=(line ? line OFS $i : $i); print line; line=""}' file
1 4 6
3 3 3
7 7 7
With your sample file, and inputs as variables, split on comma:
awk -v cols="$(<$fileCols)" -v rows="$(<$fileRows)" 'BEGIN{split(cols,c, /,/); for (i in c) col[c[i]]; split(rows,r, /,/); for (i in r) row[r[i]]} (NR-1 in row){for (i=2;i<=NF;i++) (i-1) in col && line=(line ? line OFS $i : $i); print line; line=""}' $fileInput
I am quite sure this will be way faster. You can for example check Remove duplicates from text file based on second text file for some benchmarks comparing the performance of awk over grep and others.
One in Gnu awk version 4.0 or later as column ordering relies on for and PROCINFO["sorted_in"]. The row and col numbers are read from files:
$ awk '
BEGIN {
PROCINFO["sorted_in"]="#ind_num_asc";
}
FILENAME==ARGV[1] { # process rows file
n=split($0,t,",");
for(i=1;i<=n;i++) r[t[i]]
}
FILENAME==ARGV[2] { # process cols file
m=split($0,t,",");
for(i=1;i<=m;i++) c[t[i]]
}
FILENAME==ARGV[3] && ((FNR-1) in r) { # process data file
for(i in c)
printf "%s%s", $(i+1), (++j%m?OFS:ORS)
}' subsetRows.txt subsetCols.txt inputFile.txt
1 4 6
3 3 3
7 7 7
Some performance gain could probably come from moving the ARGV[3] processing block to the top berore 1 and 2 and adding a next to it's end.
Not to take anything away from both excellent answers. Just because this problem involves large set of data I am posting a combination of 2 answers to speed up the processing.
awk -v cols="$(<subsetCols.txt)" -v rows="$(<subsetRows.txt)" '
BEGIN {
n = split(cols, c, /,/)
split(rows, r, /,/)
for (i in r)
row[r[i]]
}
(NR-1) in row {
for (i=1; i<=n; i++)
printf "%s%s", $(c[i]+1), (i<n?OFS:ORS)
}' inputFile.txt
PS: This should work with older awk version or non-gnu awk as well.
to refine #anubhava solution we can
get rid of searching over 10k values for each row
to see if we are on the right row by takeing advantage of the fact the input is already sorted
awk -v cols="$(<subsetCols.txt)" -v rows="$(<subsetRows.txt)" '
BEGIN {
n = split(cols, c, /,/)
split(rows, r, /,/)
j=1;
}
(NR-1) == r[j] {
j++
for (i=1; i<=n; i++)
printf "%s%s", $(c[i]+1), (i<n?OFS:ORS)
}' inputFile.txt
Python has a csv module. You read a row into a list, print the desired columns to stdout, rinse, wash, repeat.
This should slice columns 20,000 to 30,000.
import csv
with open('foo.txt') as f:
gwas = csv.reader(f, delimiter=',', quoting=csv.QUOTE_NONE)
for row in gwas:
print(row[20001:30001]
I have this ordered data by column 2 then 3 and then 1 in a space delimited file (i used linux sort to do that):
0 0 2
1 0 2
2 0 2
1 1 4
2 1 4
I want to create a new file (leaving the old file as is)
0 2 0,1,2
1 4 1,2
Basically put the fields 2 and 3 first and group the elements of field 1 (as a comma separated list) by them. Is there a way to do that by an awk, sed, bash one liner, so to avoid writing a Java, C++ app for that?
Since the file is already ordered, you can print the line as they change:
awk '
seen==$2 FS $3 { line=line "," $1; next }
{ if(seen) print seen, line; seen=$2 FS $3; line=$1 }
END { print seen, line }
' file
0 2 0,1,2
1 4 1,2
This will preserve the order of output.
with your input and output this line may help:
awk '{f=$2 FS $3}!(f in a){i[++p]=f;a[f]=$1;next}
{a[f]=a[f]","$1}END{for(x=1;x<=p;x++)print i[x],a[i[x]]}' file
test:
kent$ cat f
0 0 2
1 0 2
2 0 2
1 1 4
2 1 4
kent$ awk '{f=$2 FS $3}!(f in a){i[++p]=f;a[f]=$1;next}{a[f]=a[f]","$1}END{for(x=1;x<=p;x++)print i[x],a[i[x]]}' f
0 2 0,1,2
1 4 1,2
awk 'a[$2, $3]++ { p = p "," $1; next } p { print p } { p = $2 FS $3 FS $1 } END { if (p) print p }' file
Output:
0 2 0,1,2
1 4 1,2
The solution assumes data on second and third column is sorted.
Using awk:
awk '{k=$2 OFS $3} !(k in a){a[k]=$1; b[++n]=k; next} {a[k]=a[k] "," $1}
END{for (i=1; i<=n; i++) print b[i],a[b[i]]}' file
0 2 0,1,2
1 4 1,2
Yet another take:
awk -v SUBSEP=" " '
{group[$2,$3] = group[$2,$3] $1 ","}
END {
for (g in group) {
sub(/,$/,"",group[g])
print g, group[g]
}
}
' file > newfile
The SUBSEP variable is the character that joins strings in a single-dimensional awk array.
http://www.gnu.org/software/gawk/manual/html_node/Multidimensional.html#Multidimensional
This might work for you (GNU sed):
sed -r ':a;$!N;/(. (. .).*)\n(.) \2.*/s//\1,\3/;ta;s/(.) (.) (.)/\2 \3 \1/;P;D' file
This appends the first column of the subsequent record to the first record until the second and third keys change. Then the fields in the first record are re-arranged and printed out.
This uses the data presented but can be adapted for more complex data.
I have a tab delimited two column data. I want to get the third based on the condition applied on second column.
if second column is not equal to zero it should print col 1 and 3 and ratio of col1/col2
if col two is zero and col one is more than 15 than it should print col 1 and col2 and the value in col1 (in col 3) else (when col1<=15 & col2 is 0) it should print col1 col2 and 0.
for example, for a file like this
1 2
4 5
6 7
14 0
18 0
the output should be
1 2 0.5
4 5 0.8
6 7 0.85
14 0 0
18 0 18
What I have tried:
awk '{if ($2!=0) print $1 "\t" $2 "\t" $1/$2; elseif($2>15) print $1 "\t" $2 "\t" $1 ; else print $1 "\t" $2 "\t" $2}'<tags| head
Obviously I am doing something wrong, please help me in getting the above code right.
Thank you
Slightly different way:
awk '{if($2!=0) $3=$1/$2; else if($1>15) $3=$1; else $3=0}1' OFS='\t' file
Determined by the order of the if clause:
awk '{$3=0} $1>15{$3=$1} $2{$3=$1/$2}1' OFS='\t' file
or the cryptic version:
awk '{$3=$2?$1/$2:$1>15?$1:0}1' OFS='\t' file
a funny but unreadable(maybe) :) one-liner:
awk '{$0=$2?$1FS$2FS$1/$2:$1>15?$1FS$2FS$1:$1FS$2FS"0"}1' file
short explaination:
a=boolean? first : second
this means assign var a, if boolean true, using value first, otherwise use value second.
I set `$0 = $2? FOO : BAR`
FOO part: $1 FS $2 FS $1/$2
BAR part: $1>15? FOO2 : BAR2
FOO2 part: $1 FS $2 FS $1
BAR2 part: $1 FS $2 FS "0"
finally, print $0
Problem in your code
chang elseif -> else if also check $1 with 15, not $2 then your oneliner works too.
Here's another alternative:
awk '!$2 { $3 = $1>15 ? $1 : 0 } $2 { $3 = $1/$2 } 1' OFS='\t' CONVFMT='%.2g'
Output:
1 2 0.5
4 5 0.8
6 7 0.86
14 0 0
18 0 18
awk '{$3=$1>=15 && $2==0?$1:$1<15 && $2==0?0:$1/$2}1' your_file