I've a CSV file containing records like below.
id,h1,h2,h3,h4,h5,h6,h7
101,zebra,1,papa,4,dog,3,apple
102,2,yahoo,5,kangaroo,7,ape
I want to sort rows into this file without header and first column. My output should like this.
id,h1,h2,h3,h4,h5,h6,h7
101,1,3,4,apple,dog,papa,zebra
102,2,5,7,ape,kangaroo,yahoo
I tried below AWK but don't know how to exclude header and first column.
awk -F"," ' {
s=""
for(i=1; i<=NF; i++) { a[i]=$i; }
for(i=1; i<=NF; i++)
{
for(j = i+1; j<=NF; j++)
{
if (a[i] >= a[j])
{
temp = a[j];
a[j] = a[i];
a[i] = temp;
}
}
}
for(i=1; i<=NF; i++){ s = s","a[i]; }
print s
}
' file
Thanks
If perl is okay:
$ perl -F, -lane 'print join ",", $.==1 ? #F : ($F[0], sort #F[1..$#F])' ip.txt
id,h1,h2,h3,h4,h5,h6,h7
101,1,3,4,apple,dog,papa,zebra
102,2,5,7,ape,kangaroo,yahoo
-F, to indicate , as input field separator, results saved in #F array
See https://perldoc.perl.org/perlrun#Command-Switches for details on other options
join "," to use , as output field separator
$.==1 ? #F for first line, print as is
($F[0], sort #F[1..$#F]) for other lines, get first field and sorted output of other fields
.. is range operator, $#F will give index of last field
you can also use (shift #F, sort #F) instead of ($F[0], sort #F[1..$#F])
For given header, sorting first line would work too, so this can simplify logic required
$ # can also use: perl -F, -lane 'print join ",", shift #F, sort #F'
$ perl -F, -lane 'print join ",", $F[0], sort #F[1..$#F]' ip.txt
id,h1,h2,h3,h4,h5,h6,h7
101,1,3,4,apple,dog,papa,zebra
102,2,5,7,ape,kangaroo,yahoo
$ # can also use: ruby -F, -lane 'print [$F.shift, $F.sort] * ","'
$ ruby -F, -lane 'print [$F[0], $F.drop(1).sort] * ","' ip.txt
id,h1,h2,h3,h4,h5,h6,h7
101,1,3,4,apple,dog,papa,zebra
102,2,5,7,ape,kangaroo,yahoo
if you have gawk use asort:
awk -v OFS="," 'NR>1{split($0, a, ",");
$1=a[1];
delete a[1];
n = asort(a, b);
for (i = 1; i <= n; i++){ $(i+1)=b[i]}};
1' file.csv
This splits the columns to array a with seperator as , for all raws except the first one.
Then assign the first value in the column in a raw with the first value in a and delete this value from a.
Now the a is sorted to b and assign value starting from 2 column. then print it.
You can just use the asort() function in awk for your requirement and start sorting them from second line on-wards. The solution is GNU awk specific because of length(array) function
awk 'NR==1{ print; next }
NR>1 { finalStr=""
arrayLength=""
delete b
split( $0, a, "," )
for( i = 2; i <= length(a); i++ )
b[arrayLength++] = a[i]
asort( b )
for( i = 1; i <= arrayLength ; i++ )
finalStr = (finalStr)?(finalStr","b[i]):(b[i])
printf( "%s", a[1]","finalStr )
printf( "\n" );
}' file
The idea is first we split the entire line with a , delimiter into the array a from which we get the elements from the 2nd field onwards to a new array b. We sort those elements in this new array and append the first column element when we print it finally.
Related
I have multi columns file and i want to extract some info in column 71.
I want to extract using tags which the value can be anything, for example i want to just extract AC=* ; AF=* , where the value can be anything .
I found similar question and gave it a try but it didn't work
Extract columns with values matching a specific pattern
Column 71 looks like this:
AC=14511;AC_AFR=382;AC_AMR=1177;AC_Adj=14343;AC_EAS=5;AC_FIN=427;AC_Het=11813;AC_Hom=1265;AC_NFE=11027;AC_OTH=97;AC_SAS=1228;AF=0.137;AN=106198;AN_AFR=8190;AN_AMR=10424;AN_Adj=99264;AN_EAS=7068;AN_FIN=6414;AN_NFE=51090;AN_OTH=658;AN_SAS=15420;BaseQRankSum=1.73;ClippingRankSum=-1.460e-01;DB;DP=1268322;FS=0.000;GQ_MEAN=190.24;GQ_STDDEV=319.67;Het_AFR=358;Het_AMR=1049;Het_EAS=5;Het_FIN=399;Het_NFE=8799;Het_OTH=83;Het_SAS=1120;Hom_AFR=12;Hom_AMR=64;Hom_EAS=0;Hom_FIN=14;Hom_NFE=1114;Hom_OTH=7;Hom_SAS=54;InbreedingCoeff=0.0478;MQ=60.00;MQ0=0;MQRankSum=0.037;NCC=270;POSITIVE_TRAIN_SITE;QD=21.41;ReadPosRankSum=0.212;VQSLOD=4.79;culprit=MQ;DP_HIST=30|3209|1539|1494|30007|7938|4130|2038|1310|612|334|185|97|60|31|25|9|11|7|33,0|66|339|1048|2096|2665|2626|1832|1210|584|323|179|89|54|31|22|7|9|4|15;GQ_HIST=84|66|56|82|3299|568|617|403|250|319|436|310|28566|2937|827|834|451|186|217|12591,15|15|13|16|25|11|22|28|18|38|52|31|65|76|39|83|93|65|97|12397;CSQ=T|ENSG00000186868|ENST00000334239|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11502.1|ENSP00000334886|TAU_HUMAN|B4DSE3_HUMAN|UPI0000000C16||||2/8||ENST00000334239.8:c.134-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000570299|Transcript|intron_variant&non_coding_transcript_variant||||||rs754512|1||1|MAPT|HGNC|6893|processed_transcript||||||||||2/6||ENST00000570299.1:n.262-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000340799|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS45716.1|ENSP00000340438|TAU_HUMAN||UPI000004EEE6||||3/10||ENST00000340799.5:c.221-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000262410|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11501.1|ENSP00000262410|TAU_HUMAN||UPI0000EE80B7||||4/13||ENST00000262410.5:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000446361|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11500.1|ENSP00000408975|TAU_HUMAN||UPI000004EEE5||||2/9||ENST00000446361.3:c.134-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000574436|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11499.1|ENSP00000460965|TAU_HUMAN||UPI000002D754||||3/10||ENST00000574436.1:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000571987|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11501.1|ENSP00000458742|TAU_HUMAN||UPI0000EE80B7||||3/12||ENST00000571987.1:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000415613|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS45715.1|ENSP00000410838|TAU_HUMAN||UPI0001AE66E9||||3/13||ENST00000415613.2:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000571311|Transcript|intron_variant&NMD_transcript_variant||||||rs754512|1||1|MAPT|HGNC|6893|nonsense_mediated_decay|||ENSP00000460048||I3L2Z2_HUMAN|UPI00025A2E6E||||4/4||ENST00000571311.1:c.*176-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000535772|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS56033.1|ENSP00000443028|TAU_HUMAN|B4DSE3_HUMAN|UPI000004EEE4||||4/10||ENST00000535772.1:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000576518|Transcript|stop_gained|5499|7|3|K/*|Aag/Tag|rs754512|1||1|MAPT|HGNC|6893|protein_coding|||ENSP00000458621||I3L170_HUMAN&B4DSE3_HUMAN|UPI0001639A7C|||1/7|||ENST00000576518.1:c.7A>T|ENSP00000458621.1:p.Lys3Ter|T:0.1171|||||||||15792962|||||POSITION:0.00682261208576998&ANN_ORF:-255.6993&MAX_ORF:-255.6993|PHYLOCSF_WEAK|ANC_ALLELE|LC,T|ENSG00000186868|ENST00000420682|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS45716.1|ENSP00000413056|TAU_HUMAN||UPI000004EEE6||||2/9||ENST00000420682.2:c.221-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000572440|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2790|||||rs754512|1||1|MAPT|HGNC|6893|retained_intron|||||||||1/1|||ENST00000572440.1:n.2790A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000351559|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11499.1|ENSP00000303214|TAU_HUMAN||UPI000002D754||||4/11||ENST00000351559.5:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000344290|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding|YES|CCDS45715.1|ENSP00000340820|TAU_HUMAN||UPI0001AE66E9||||4/14||ENST00000344290.5:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000347967|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding|||ENSP00000302706|TAU_HUMAN|B4DSE3_HUMAN|UPI0000173D91||||4/10||ENST00000347967.5:c.32-100A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000431008|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS56033.1|ENSP00000389250|TAU_HUMAN|B4DSE3_HUMAN|UPI000004EEE4||||3/9||ENST00000431008.3:c.308-94A>T||T:0.1171|||||||||15792962||||||||
The code that i tried:
awk '{
for (i = 1; i <= NF; i++) {
if ($i ~ /AC|AF/) {
printf "%s %s ", $i, $(i + 1)
}
}
print ""
}'
I keep getting syntax error.
output wanted :
AC=14511;AF=0.137
Whenever you have name=value pairs, it's usually simplest to first create an array that maps names to values (n2v[] below) and then you can just access the values by their names.
$ cat file
AC=1;AC_AFR=2;AF=3 AC=4;AC_AFR=5;AF=6
$ cat tst.awk
{
delete n2v
split($2,tmp,/[;=]/)
for (i=1; i in tmp; i+=2) {
n2v[tmp[i]] = tmp[i+1]
}
prt("AC")
prt("AF")
}
function prt(name) { print name, "=", n2v[name] }
$ awk -f tst.awk file
AC = 4
AF = 6
Just change $2 to $71 for your real input.
Something like this should do it (in Gnu awk due to switch):
$ awk '{split($71,a,";");for(i in a )if(a[i]~/^AF/) print a[i]}' foo
AF=0.137
You split the field $71 by ;s, loop thru the array you split to looking for desired match. For multiple matches use switch:
$ awk '{
split($0,a,";");
for(i in a )
switch(a[i]) {
case /^AF=/:
b=b a[i] OFS;
break;
case /^AC=/:
b=b a[i] OFS;
break
}
sub(/.$/,"\n",b);
printf b
}' foo
AC=14511 AF=0.137
EDIT: Now it buffers output to a variable and prints it in the end. You can control the separator with OFS.
I'm an absolute beginner to awk and would like some help with this.
I have this data:
FOO|BAR|1234|A|B|C|D|
FOO|BAR|1234|E|F|G|H|
FOO|BAR|5678|I|J|K|L|
FOO|BAR|5678|M|N|O|P|
FOO|BAR|5678|Q|R|S|T|
Desired output:
FOO|BAR|1234|A|B|C|D|E|F|G|H|
FOO|BAR|5678|I|J|K|L|M|N|O|P|Q|R|S|T|
Basically I have to append some fields to the lines where column 3 matches.
Appreciate any responses, thanks a lot!
Another way:
awk -F"|" '$3 in a{
a[$3]=a[$3]"|"$4"|"$5"|"$6"|"$7;
next
}
{ a[$3]=$0
}
END {
for ( i in a) {
print a[i]
}
}'
$ awk -f chain.awk < data
FOO|BAR|1234|A|B|C|D|E|F|G|H|
FOO|BAR|5678|I|J|K|L|M|N|O|P|Q|R|S|T|
$ cat chain.awk
BEGIN {FS = "|"}
$3==old {for(i = 4; i <= NF; i++) saved = saved (i>4?"|":"") $i}
$3!=old {if(old) print saved ; saved = $0 ; old = $3}
END {print saved}
$
BEGIN we set the field separator
$3==old we append the fields $4 ... $NF to the saved data, joining the fields with | except for the first one (note that there is a last, null field)
$3!=old we print the saved data (except for the first record, when old is false) and we restart the mechanism
END we still have saved data in our belly, we have to print it
If we have an input:
TargetIDs,CPD,Value,SMILES
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
95,CPD-3333333,-1,c1ccccc1N
Now we would like to separate the duplicates and non-duplicates based on the fourth column (smiles)
duplicate:
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
non-duplicate
95,CPD-3333333,-1,c1ccccc1N
Now the following attempt could do separate the duplicate without any problem. However, the first occurrence of the duplicate will still be included into the non-duplicate file.
BEGIN { FS = ","; f1="a"; f2="b"}
{
# Keep count of the fields in fourth column
count[$4]++;
# Save the line the first time we encounter a unique field
if (count[$4] == 1)
first[$4] = $0;
# If we encounter the field for the second time, print the
# previously saved line
if (count[$4] == 2)
print first[$4] > f1 ;
# From the second time onward. always print because the field is
# duplicated
if (count[$4] > 1)
print > f1;
if (count[$4] == 1) #if (count[$4] - count[$4] == 0) <= change to this doesn't work
print first[$4] > f2;
duplicate output results from the attempt:
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
non-duplicate output results from the attempt
TargetIDs,CPD,Value,SMILES
95,CPD-3333333,-1,c1ccccc1N
95,CPD-1111111,-2,c1ccccc1
May I know if any guru might have comments/solutions? Thanks.
I would do this:
awk '
NR==FNR {count[$2] = $1; next}
FNR==1 {FS=","; next}
{
output = (count[$NF] == 1 ? "nondup" : "dup")
print > output
}
' <(cut -d, -f4 input | sort | uniq -c) input
The process substitution will pre-process the file and perform a count on the 4th column. Then, you can process the file and decide if that line is "duplicated".
All in awk: Ed Morton shows a way to collect the data in a single pass. Here's a 2 pass solution that's virtually identical to my example above
awk -F, '
NR==FNR {count[$NF]++; next}
FNR==1 {next}
{
output = (count[$NF] == 1 ? "nondup" : "dup")
print > output
}
' input input
Yes, the input file is given twice.
$ cat tst.awk
BEGIN{ FS="," }
NR>1 {
if (cnt[$4]++) {
dups[$4] = nonDups[$4] dups[$4] $0 ORS
delete nonDups[$4]
}
else {
nonDups[$4] = $0 ORS
}
}
END {
print "Duplicates:"
for (key in dups) {
printf "%s", dups[key]
}
print "\nNon Duplicates:"
for (key in nonDups) {
printf "%s", nonDups[key]
}
}
$ awk -f tst.awk file
Duplicates:
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
Non Duplicates:
95,CPD-3333333,-1,c1ccccc1N
This solution only works if the duplicates are grouped together.
awk -F, '
function fout( f, i) {
f = (cnt > 1) ? "dups" : "nondups"
for (i = 1; i <= cnt; ++i)
print lines[i] > f
}
NR > 1 && $4 != lastkey { fout(); cnt = 0 }
{ lastkey = $4; lines[++cnt] = $0 }
END { fout() }
' file
Little late
My version in awk
awk -F, 'NR>1{a[$0":"$4];b[$4]++}
END{d="\n\nnondupe";e="dupe"
for(i in a){split(i,c,":");b[c[2]]==1?d=d"\n"i:e=e"\n"i} print e d}' file
Another built similar to glenn jackmans but all in awk
awk -F, 'function r(f) {while((getline <f)>0)a[$4]++;close(f)}
BEGIN{r(ARGV[1])}{output=(a[$4] == 1 ? "nondup" : "dup");print >output} ' file
I need to use an awk script to extract some information from a file.
I have a title line which has 11 field and I split it to an array called titleList.
Student Number:Name:Lab1:Lab2:Lab3:Lab4:Lab5:Lab6:Exam1:Exam2:Final
After finding a proper line I need to print the fields which proceeds by the titles for example if the result is :
92839342:Robert Bloomingdale:9:26:18:22:9:12:25:39:99
I must print it in this way:
Student Number:92839342 Name:Robert Bloomingdale Lab1:9 Lab2:26 Lab3:18
Lab4:22 Lab5:9 Lab6:12 Exam1:25 Exam2:39 Final:99
I use a for loop to manage it:
for (i=0 ;i<=NF ;i++)
{
printf "%s %s %s %s",titleList[i],":",$i," "
}
everything look good except the result which has 2 problems:
first there is an extra space between each result and second the last field of the searched line is missing
Student Number : 92839342 Name : Robert Bloomingdale Lab1 : 9 Lab2 : 26
Lab3:18 Lab4 : 22 Lab5 : 9 Lab6 : 12 Exam1 : 25 Exam2 : 39 Final
what should I do?
is there any problem with \n at the end of the search result?
You can correct the amount of extra whitespace between fields by correcting the printf statement:
awk -F ":" 'NR == 1 { split($0, array, FS) } NR >= 2 { for (i=1; i<=NF; i++) printf "%s:%s ", array[i], $i; printf "\n" }' file.txt
Contents of file.txt:
Student Number:Name:Lab1:Lab2:Lab3:Lab4:Lab5:Lab6:Exam1:Exam2:Final
92839342:Robert Bloomingdale:9:26:18:22:9:12:25:39:99
Results:
Student Number:92839342 Name:Robert Bloomingdale Lab1:9 Lab2:26 Lab3:18 Lab4:22 Lab5:9 Lab6:12 Exam1:25 Exam2:39 Final:99
EDIT:
Also, your missing the last value because the file you're working with probably has windows newline endings. To fix this, run: dos2unix file.txt before running your awk code. Alternatively, you can set awk's record separater so that it understands newline endings:
awk 'BEGIN { RS="\r\n"; FS=":" } NR == 1 { split($0, array, FS) } NR >= 2 { for (i=1; i<=NF; i++) printf "%s:%s ", array[i], $i; printf "\n" }' file.txt
EDIT:
The above requires GNU awk, split() splits on the FS by default so no need to use that as an arg, it's common to use "next" rather than specifying opposite conditions, and it's common to use print "" instead of printf "\n" so you use the ORS setting rather than hard-coding it's value in output statements. So, the above should be tweaked to:
gawk 'BEGIN { RS="\r\n"; FS=":" } NR == 1 { split($0, array); next } { for (i=1; i<=NF; i++) printf "%s:%s ", array[i], $i; print "" }' file.txt
I am in need of reorganizing a large CSV file. The first column, which is currently a 6 digit number needs to be split up, using commas as the field separator.
For example, I need this:
022250,10:50 AM,274,22,50
022255,11:55 AM,275,22,55
turned into this:
0,2,2,2,5,0,10:50 AM,274,22,50
0,2,2,2,5,5,11:55 AM,275,22,55
Let me know what you think!
Thanks!
It's a lot shorter in perl:
perl -F, -ane '$,=","; print split("",$F[0]), #F[1..$#F]' <file>
Since you don't know perl, a quick explanation. -F, indicates the input field separator is the comma (like awk). -a activates auto-split (into the array #F), -n implicitly wraps the code in a while (<>) { ... } loop, which reads input line-by-line. -e indicates the next argument is the script to run. $, is the output field separator (it gets set iteration of the loop this way, but oh well). split has obvious purpose, and you can see how the array is indexed/sliced. print, when lists as arguments like this, uses the output field separator and prints all their fields.
In awk:
awk -F, '{n=split($1,a,""); for (i=1;i<=n;i++) {printf("%s,",a[i])}; for (i=2;i<NF;i++) {printf("%s,",$i)}; print $NF}' <file>
I think this might work. The split function (at least in the version I am running) splits the value into individual characters if the third parameter is an empty string.
BEGIN{ FS="," }
{
n = split( $1, a, "" );
for ( i = 1; i <= n; i++ )
printf("%s,", a[i] );
sep = "";
for ( i = 2; i <= NF; i++ )
{
printf( "%s%s", sep, $i );
sep = ",";
}
printf("\n");
}
here's another way in awk
$ awk -F"," '{gsub(".",",&",$1);sub("^,","",$1)}1' OFS="," file
0,2,2,2,5,0,10:50 AM,274,22,50
0,2,2,2,5,5,11:55 AM,275,22,55
Here's a variation on a theme. One thing to note is it prints the remaining fields without using a loop. Another is that since you're looping over the characters in the first field anyway, why not just do it without using the null-delimiter feature of split() (which may not be present in some versions of AWK):
awk -F, 'BEGIN{OFS=","} {len=length($1); for (i=1;i<len; i++) {printf "%s,", substr($1,i,1)}; printf "%s", substr($1,len,1);$1=""; print $0}' filename
As a script:
BEGIN {FS = OFS = ","}
{
len = length($1);
for (i=1; i<len; i++)
{printf "%s,", substr($1, i, 1)};
printf "%s", substr($1, len, 1)
$1 = "";
print $0
}