aNumber bNumber startDate cost balanceAfter trafficCase Operator unknown3 MainAmount BALANCEBEFORE
22676239633 433 2014-07-02 10:16:48.000 0,00 0.20 0 Short Code 397224944 0.0000 0.2000
22677277255 76919167 2014-07-02 10:16:51.000 1,00 92.60 0 Airtel 126268625 0.0000 92.6000
22676777508 76701575 2014-07-02 10:16:55.000 1,00 217.00 0 Airtel 4132186103 0.0000 217.0000
22665706841 433 2014-07-02 10:16:57.000 0,00 69.50 0 Short Code 4133821554 0.0000 69.5000
22665799922 70110055 2014-07-03 10:16:45.000 20,00 0.50 0 Telmob 126260244 20.0000 0.5000
22676239633 433 2014-07-03 10:16:48.000 0,00 0.20 0 Short Code 397224944 0.0000 0.2000
22677277255 76919167 2014-07-04 10:16:51.000 1,00 92.60 0 Airtel 126268625 0.0000 92.6000
22676777508 76701575 2014-07-04 10:16:55.000 1,00 217.00 0 Airtel 4132186103 0.0000 217.0000
22665706841 433 2014-07-05 10:16:57.000 0,00 69.50 0 Short Code 4133821554 0.0000 69.5000
Here is a sample of the data I have. I want to sum up cost, balanceAfter, MainAmount and BALANCEBEFORE at each time the date changed but my concern is I have date combined with time and my decimal separator is dot instead of comma so my awk script can't perform the operation.
Can I have an AWK script which will first extract only the date so in the end I will have an output looking like:
Date Cost balanceAfter MainAmount BALANCEBEFORE
02/07/2014 2,00 379,3 0 379,3
03/07/2014 20,00 0,7 20 0,7
04/07/2014 2,00 309,6 0 309,6
05/07/2014 0,00 69,5 0 69,5
HERE IS MY AWK SCRIPT
awk -F 'NR==1 {header=$0; next} {a[$3]+=$4 a[$3]+=$5 a[$3]+=$9 a[$3]+=$10} END {for (i in a) {printf "%d\t%d\n", i, a[i]}; tot+=a[i]};' out.txt>output.doc
EDIT: Avoid pre-processing step as per Etan Reisner's suggestion to use $NF to work around differing numbers of tokens in Operator column.
$ cat data.txt
aNumber bNumber startDate cost balanceAfter trafficCase Operator unknown3 MainAmount BALANCEBEFORE
22676239633 433 2014-07-02 10:16:48.000 0,00 0.20 0 Short Code 397224944 0.0000 0.2000
22677277255 76919167 2014-07-02 10:16:51.000 1,00 92.60 0 Airtel 126268625 0.0000 92.6000
22676777508 76701575 2014-07-02 10:16:55.000 1,00 217.00 0 Airtel 4132186103 0.0000 217.0000
22665706841 433 2014-07-02 10:16:57.000 0,00 69.50 0 Short Code 4133821554 0.0000 69.5000
22665799922 70110055 2014-07-03 10:16:45.000 20,00 0.50 0 Telmob 126260244 20.0000 0.5000
22676239633 433 2014-07-03 10:16:48.000 0,00 0.20 0 Short Code 397224944 0.0000 0.2000
22677277255 76919167 2014-07-04 10:16:51.000 1,00 92.60 0 Airtel 126268625 0.0000 92.6000
22676777508 76701575 2014-07-04 10:16:55.000 1,00 217.00 0 Airtel 4132186103 0.0000 217.0000
22665706841 433 2014-07-05 10:16:57.000 0,00 69.50 0 Short Code 4133821554 0.0000 69.5000
$ cat so2.awk
NR > 1 {
cost = $5;
balanceAfter = $6;
mainAmount = $(NF - 1);
balanceBefore = $NF;
sub(",", ".", cost);
sub(",", ".", balanceAfter);
sub(",", ".", mainAmount);
sub(",", ".", balanceBefore);
dateCost[$3] += cost;
dateBalanceAfter[$3] += balanceAfter;
dateMainAmount[$3] += mainAmount;
dateBalanceBefore[$3] += balanceBefore;
}
END {
printf("%s\t%s\t%s\t%s\t%s\n", "Date", "Cost", "BalanceAfter", "MainAmount", "BalanceBefore");
for (i in dateCost) {
printf("%s\t%f\t%f\t%f\t%f\n", i, dateCost[i], dateBalanceAfter[i], dateMainAmount[i], dateBalanceBefore[i]);
}
}
$ awk -f so2.awk data.txt
Date Cost BalanceAfter MainAmount BalanceBefore
2014-07-02 2.000000 379.300000 0.000000 379.300000
2014-07-03 20.000000 0.700000 20.000000 0.700000
2014-07-04 2.000000 309.600000 0.000000 309.600000
2014-07-05 0.000000 69.500000 0.000000 69.500000
This requires no pre-processing of the file:
awk '
BEGIN {print "Date Cost BalanceAfter MainAmount BalanceBefore"}
NR == 1 {next}
function showday() {
printf "%s\t%.2f\t%.1f\t%d\t%.1f\n", date, cost, bAfter, main, bBefore
}
date != $3 {
if (date) showday()
date = $3
cost = bAfter = main = bBefore = 0
}
{
sub(/,/, ".", $5)
cost += $5
bAfter += $6
main += $(NF-1)
bBefore += $NF
}
END {showday()}
' file | column -t
Date Cost BalanceAfter MainAmount BalanceBefore
2014-07-02 2.00 379.3 0 379.3
2014-07-03 20.00 0.7 20 0.7
2014-07-04 2.00 309.6 0 309.6
2014-07-05 0.00 69.5 0 69.5
Related
I have a file that looks like this:
measured 10.8 0.0000 0.0000 0.0236 0.0304 0.0383 0.0433 0.0437 0.0442 0.0452
0.0455 0.0448 0.0440 0.0423 0.0386 0.0344 0.0274 0.0000 0.0000
I want gawk to print all the numbers in one long single column like this:
0.0000
0.0000
0.0236
0.0304
0.0383
0.0433
0.0437
0.0442
0.0452
0.0455
0.0448
0.0440
0.0423
0.0386
0.0344
0.0274
0.0000
0.0000
I run the command gawk '/measured/ { printf $3"\n" $4"\n" $5"\n" $6"\n" $7"\n" $8"\n" $9"\n" $10"\n" $11"\n" $12"\n" $13"\n" $14"\n" $15"\n" $16"\n" $17"\n" $18"\n" }' filename.txt
But I just get the first row of numbers:
0.0000
0.0000
0.0236
0.0304
0.0383
0.0433
0.0437
0.0442
0.0452
How do I get gawk to print the second row?
$ cat tst.awk
BEGIN { OFS = "\n" }
/measured/ { c=2; $1=$2=""; $0=$0 }
c && c-- { $1=$1; print }
$ awk -f tst.awk file
0.0000
0.0000
0.0236
0.0304
0.0383
0.0433
0.0437
0.0442
0.0452
0.0455
0.0448
0.0440
0.0423
0.0386
0.0344
0.0274
0.0000
0.0000
$ grep -A1 measured file | tr -s ' ' \\n | tail -n+4
0.0000
0.0000
0.0236
0.0304
0.0383
0.0433
0.0437
0.0442
0.0452
0.0455
0.0448
0.0440
0.0423
0.0386
0.0344
0.0274
0.0000
0.0000
with awk
$ awk -v OFS='\n' '/measured/ {p=1; for(i=3;i<=NF;i++) print $i; next}
p {$1=$1; print; exit}' file
If the number of fields is guaranteed to be as in the example, you can use the following command:
awk '{for(i=NF-8;i<=NF;i++){print $i}}' input.file
The GNU implementation of Awk allows an arbitrary regular expression as the RS record separator If the keyword measured occurs before each batch of numbers, we can use that keyword as the separator:
$ gawk 'BEGIN { RS = "measured" } { for (i = 1; i <= NF ; i++) print "field " i " = " $i }'
measured 10.8 0.0000 0.0000 0.0236 0.0304 0.0383 0.0433 0.0437 0.0442 0.0452
0.0455 0.0448 0.0440 0.0423 0.0386 0.0344 0.0274 0.0000 0.000
field 1 = 10.8
field 2 = 0.0000
field 3 = 0.0000
field 4 = 0.0236
field 5 = 0.0304
field 6 = 0.0383
field 7 = 0.0433
field 8 = 0.0437
field 9 = 0.0442
field 10 = 0.0452
field 11 = 0.0455
field 12 = 0.0448
field 13 = 0.0440
field 14 = 0.0423
field 15 = 0.0386
field 16 = 0.0344
field 17 = 0.0274
field 18 = 0.0000
field 19 = 0.000
As you can see, all the fields between the measured record separators are parsed out regardless of line breaks. Fields are separated on any mixture of spaces, tabs and newlines.
Note that because measured appears first, we get an empty record. The output you see above is, effectively, from the second record. The first record is the whitespcae before measured, which contains no fields.
In other words, he record separator is really expected to be a terminator, except that it can be missing after the last record.
I have a file
splice_region_variant,intron_variant A1CF 1
3_prime_UTR_variant A1CF 18
intron_variant A1CF 204
downstream_gene_variant A1CF 22
synonymous_variant A1CF 6
missense_variant A1CF 8
5_prime_UTR_variant A2M 1
stop_gained A2M 1
missense_variant A2M 15
splice_region_variant,intron_variant A2M 2
synonymous_variant A2M 2
upstream_gene_variant A2M 22
intron_variant A2M 308
missense_variant A4GNT 1
intron_variant A4GNT 21
5_prime_UTR_variant A4GNT 3
3_prime_UTR_variant A4GNT 7
This file is sorted by $2
for each occurrence of an unique element in $2, I wanna transform in a column each unique occurrence of an element in $1, with corresponding value in $3, or 0 if the record is not there. So that I have:
splice_region_variant,intron_variant 3_prime_UTR_variant intron_variant downstream_gene_variant synonymous_variant missense_variant 5_prime_UTR_variant stop_gained upstream_gene_variant
A1CF 1 18 204 22 6 8 0 0 0
A2M 2 0 308 0 2 15 1 1 22
A4GNT 0 7 21 0 0 22 3 0 0
test file:
a x 2
b,c x 4
dd x 3
e,e,t x 5
a b 1
cc b 2
e,e,t b 1
This is what I'm getting:
a b,c dd e,e,t cc
x 5 2 4 3
b 1 2 1
EDIT: This might be doing it but doesn't output 0s in blank fields
'BEGIN {FS = OFS = "\t"}
NR > 1 {data[$2][$1] = $3; blocks[$1]}
END {
PROCINFO["sorted_in"] = "#ind_str_asc"
# header
printf "gene"
for (block in blocks) {
printf "%s%s", OFS, block
}
print ""
# data
for (ts in data) {
printf "%s", ts
for (block in blocks) {
printf "%s%s", OFS, data[ts][block]
}
print ""
}
}' file
modified from https://unix.stackexchange.com/questions/424642/dynamic-transposing-rows-to-columns-using-awk-based-on-row-value
If you want to print 0 if a certain value is absent, you could do something like this:
val = data[ts][block] ? data[ts][block] : 0;
printf "%s%s", OFS, val
I am trying to sum the last 12 values in a field in a particular csv file, but AWK is failing to correctly sum the values. If I output the data to a new file then run the same AWK statement against the new file it works.
Here are the contents of the original file. The fields are separated by ";"
I want to sum the values in the 3rd field
...$ tail -12 OriginalFile.csv...
02/02/2020 10:30:00;50727.421;0.264;55772.084;0.360;57110.502;0.384
02/02/2020 10:35:00;50727.455;0.408;55772.126;0.504;57110.548;0.552
02/02/2020 10:40:00;50727.489;0.408;55772.168;0.504;57110.593;0.540
02/02/2020 10:45:00;50727.506;0.204;55772.193;0.300;57110.621;0.336
02/02/2020 10:50:00;50727.541;0.420;55772.236;0.516;57110.667;0.552
02/02/2020 10:55:00;50727.566;0.300;55772.269;0.396;57110.703;0.432
02/02/2020 11:00:00;50727.590;0.288;55772.300;0.372;57110.737;0.408
02/02/2020 11:05:00;50727.605;0.180;55772.321;0.252;57110.762;0.300
02/02/2020 11:10:00;50727.621;0.192;55772.344;0.276;57110.786;0.288
02/02/2020 11:15:00;50727.659;0.456;55772.389;0.540;57110.835;0.588
02/02/2020 11:20:00;50727.681;0.264;55772.417;0.336;57110.866;0.372
02/02/2020 11:25:00;50727.704;0.276;55772.448;0.372;57110.900;0.408
I used the following code to print the original value and the summed value of field 3 for each record, but it just returns the same output for the summed value for each line
...$ awk 'BEGIN { FS = ";" } ; { sum += $3 } { print $3, sum }' OriginalFile.csv|tail -12...
0.264 2.00198e+09
0.408 2.00198e+09
0.408 2.00198e+09
0.204 2.00198e+09
0.420 2.00198e+09
0.300 2.00198e+09
0.288 2.00198e+09
0.180 2.00198e+09
0.192 2.00198e+09
0.456 2.00198e+09
0.264 2.00198e+09
0.276 2.00198e+09
If I output the contents of the file into a different file, the same code works as expected
...$ tail -12 OriginalFile.csv > testfile2.csv...
...$ awk 'BEGIN { FS = ";" } ; { sum += $3 } { print $3, sum }' testfile2.csv...
0.264 0.264
0.408 0.672
0.408 1.08
0.204 1.284
0.420 1.704
0.300 2.004
0.288 2.292
0.180 2.472
0.192 2.664
0.456 3.12
0.264 3.384
0.276 3.66
How can I get the correct output from the original file without having to create a new file?
As #Shawn's excellent comment points out, the order in which you pipe in your data is the problem. By the time you reach the 12th line from the end, sum is already 2.00198e+09; adding many small fractions is not significant, so it seems like it is "the same output".
Simply:
tail -12 OriginalFile.csv | awk 'BEGIN { FS = ";" } ; { sum += $3 } { print $3, sum }'
How can I tell gawk to use two different delimiters so that I can separate some columns, but select others using the tab-delimited format of my file?
> cat broad_snps.tab
chrsnpID rsID freq_bin snp_maf gene_count dist_nearest_gene_snpsnap dist_nearest_gene_snpsnap_protein_coding dist_nearest_gene dist_nearest_gene_located_within loci_upstream loci_downstream ID_nearest_gene_snpsnap ID_nearest_gene_snpsnap_protein_coding ID_nearest_gene ID_nearest_gene_located_within HGNC_nearest_gene_snpsnap HGNC_nearest_gene_snpsnap_protein_coding flag_snp_within_gene flag_snp_within_gene_protein_coding ID_genes_in_matched_locus friends_ld01 friends_ld02 friends_ld03 friends_ld04 friends_ld05 friends_ld06 friends_ld07 friends_ld08 friends_ld09 -1
10:10001753 10:10001753 7 0.07455 0 98932.0 1045506.0 98932.0 inf 9986766 10039928 ENSG00000224788 ENSG00000048740 ENSG00000224788 CELF2 False False 253.0 103.0 55.0 40.0 35.0 33.031.0 20.0 0.0 -1
10:10001794 10:10001794 41 0.4105 0 98891.0 1045465.0 98891.0 inf 9964948 10071879 ENSG00000224788 ENSG00000048740 ENSG00000224788 CELF2 False False 365.0 299.0 294.0 266.0 168.0 138.58.0 45.0 0.0 -1
10:100023489 10:100023489 10 0.1054 1 4518.0 4518.0 4518.0 4518.0 100023489 100023489 ENSG00000138131 ENSG00000138131 ENSG00000138131 ENSG00000138131 LOXL4 LOXL4 True True ENSG00000138131 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1
10:100025128 10:100025128 45 0.4543 1 2879.0 2879.0 2879.0 2879.0 100025128 100025128 ENSG00000138131 ENSG00000138131 ENSG00000138131 ENSG00000138131 LOXL4 LOXL4 True True ENSG00000138131 112.0 70.0 3.0 0.0 0.0
The output I want:
chr10 10001752 10001753 CELF2
chr10 10001793 10001794 CELF2
chr10 100023488 100023489 LOXL4
chr10 100025127 100025128 LOXL4
chr10 10002974 10002975 LOXL4
The command I am currently using:
cat broad_snps.tab | tail -n+2 | gawk -vOFS="\t" -vFS=":" '{ print "chr"$1, ($2 - 1), $2}' | gawk -vOFS="\t" '{print $1, $2, $3}' > broad_SNPs.bed
Returns this:
chr10 10001752 10001753 10
chr10 10001793 10001794 10
chr10 100023488 100023489 10
chr10 100025127 100025128 10
chr10 10002974 10002975 10
chr10 10003391 10003392 10
chr10 100038815 100038816 10
chr10 10008001 10008002 10
chr10 100093012 100093013 10
I'd like to be able to use the ":" delimiter to split up the first column, but I need to use "\t" to pick out the gene ID.
Thanks!
awk -F'[\t:]' '{print $1, $2, $4, $17}'
I have this pdb file and I want to calculate the distance between the atom 7 and 8 ($2) with the atoms 12,14,15,17 and 18. If the distance is lower than 5 angstrons, the value should be printed
ATOM 1 N ASN p 140 38.455 18.232 -3.207 1.00 7.39 N
ATOM 2 CA ASN p 140 37.856 18.151 -4.534 1.00 7.91 C
ATOM 3 C ASN p 140 38.700 18.848 -5.595 1.00 10.75 C
ATOM 4 O ASN p 140 39.797 19.271 -5.313 1.00 9.25 O
ATOM 5 CB ASN p 140 36.435 18.715 -4.446 1.00 7.62 C
ATOM 6 CG ASN p 140 35.556 17.898 -3.501 1.00 6.82 C
ATOM 7 OD1 ASN p 140 35.269 18.315 -2.323 1.00 8.53 O
ATOM 8 ND2 ASN p 140 35.197 16.691 -3.945 1.00 5.41 N
TER 9 ASN 140
HETATM 10 C 08H p 1 29.121 15.727 -1.182 1.00 5.89 C
HETATM 11 C 08H p 1 29.763 16.230 -0.040 1.00 5.86 C
HETATM 12 N 08H p 1 31.023 16.810 -0.046 1.00 6.15 N
HETATM 13 C 08H p 1 31.533 17.872 0.633 1.00 6.24 C
HETATM 14 N 08H p 1 32.815 18.037 0.299 1.00 6.83 N
HETATM 15 N 08H p 1 33.151 17.112 -0.526 1.00 7.37 C
HETATM 16 C 08H p 1 32.058 16.349 -0.758 1.00 7.06 C
HETATM 17 O 08H p 1 31.956 15.215 -1.730 1.00 8.15 O
HETATM 18 N 08H p 1 30.979 15.691 -2.746 1.00 10.31 N
HETATM 19 C 08H p 1 29.651 15.777 -2.509 1.00 6.71 C
HETATM 20 O HOH p 170 34.699 19.032 2.134 1.00 6.42 O
Based on a similar script, I wrote this code
# usage: awk -f test.awk structure.pdb
BEGIN{print "asparagine and ligand in the structure..."; ORS=""}
$1=="ATOM" && $3~"ND2|OD1" && $4=="ASN" || $1=="HETATM" && $12~"N|O" && $4!~"HOH" {
print $2,$3,$4,$6"\n"
atm_x[$2]=$7; atm_y[$2]=$8; atm_z[$2]=$9
}
END{ ORS="\n"
for (key1 in atm_x) { list=list" "key1
for (key2 in atm_x) {
if (index(list, key2) != 0 ) continue
dx=atm_x[key1]-atm_x[key2]
dy=atm_y[key1]-atm_y[key2]
dz=atm_z[key1]-atm_z[key2]
distance=sqrt(dx^2+dy^2+dz^2)
if (distance < 5 && distance != 0 ) {
i++
candidate[i]=key1"-"key2": "distance
}
}
}
print "\nCandidates ..."
for (keys in candidate) {print candidate[keys]}
}
when I run this script I get the following result
asparagine and ligand in the structure...
7 OD1 ASN 140
8 ND2 ASN 140
12 N 08H 1
14 N 08H 1
17 O 08H 1
18 N 08H 1
Candidates ...
7-8: 2.2964
7-14: 3.60198
7-17: 4.57576
8-17: 4.19391
8-18: 4.49768
12-14: 2.19905
12-17: 2.50007
12-18: 2.92303
14-17: 3.58028
14-18: 4.25989
17-18: 1.48774
The problem is that I don't want to print the distances when the atoms have the same residue name ($4). I'm new to awk and was wondering what's the best way to handle this. Any suggestions would be appreciated!!
awk '
($1=="ATOM" && ($3=="ND2" || $3=="OD1") && $4=="ASN") || \
($1=="HETATM" && ($12=="N" || $12 =="O") && $4!="HOH") {
atom[$2] = 1
x[$2] = $7
y[$2] = $8
z[$2] = $9
name[$2] = $4
}
END {
for (a in atom) {
for (b in atom) {
if (a > b && name[a] != name[b]) {
dist = sqrt((x[a]-x[b])^2 + (y[a]-y[b])^2 + (z[a]-z[b])^2)
if (dist < 5)
printf "%s-%s: %.4f\n", a, b, dist
}
}
}
}
' pdbfile
7-17: 4.5758
7-14: 3.6020
8-17: 4.1939
8-18: 4.4977