Using awk to find min and max? - awk

I have a large file that contains many types of lines. One of the types is lines of this form:
The lines all start with ATOM, and the 7th-9th fields are the x, y, and z values of the specified atom. How can I use awk to find all ATOM lines and then calculate the min and max of the x, y, and z values?
This is my file: http://pastebin.com/EqA2SUMy
One of the types is lines of this form:
ATOM 1 N ASP A 435 7.397 28.376 121.784 1.00 34.35 N
ATOM 2 CA ASP A 435 8.023 27.301 122.545 1.00 30.66 C
ATOM 3 C ASP A 435 8.170 27.721 124.009 1.00 31.39 C
ATOM 4 O ASP A 435 9.078 28.509 124.284 1.00 38.78 O
Can anyone show me how to do this please?

#!awk -f
BEGIN {
min7 = min8 = min9 = 1000
}
$1 == "ATOM" {
if ($7 < min7)
min7 = $7
if ($8 < min8)
min8 = $8
if ($9 < min9)
min9 = $9
if ($7 > max7)
max7 = $7
if ($8 > max8)
max8 = $8
if ($9 > max9)
max9 = $9
}
END {
print min7, min8, min9
print max7, max8, max9
}

Related

Making AWK code more efficient when evaluating sets of records

I have a file with 5 fields of content. I am evaluating 4 lines at a time in the file. So, records 1-4 are evaluated as a set. Records 5-8 are another set. Within each set, I want to extract the time from field 5 when field 4 has the max value. If there are duplicate values in field 4, then evaluate the maximum value in field 2 and use the time in field 5 associated with the max value in field 2.
For example, in the first 4 records, there is a duplicate max value in field 4 (value of 53). If that is true, I need to look at field 2 and find the maximum value. Then print the time associated with the max value in field 2 with the time in field 5.
The Data Set is:
00 31444 8.7 24 00:04:32
00 44574 12.4 25 00:01:41
00 74984 20.8 53 00:02:22
00 84465 23.5 53 00:12:33
01 34748 9.7 38 01:59:28
01 44471 12.4 37 01:55:29
01 74280 20.6 58 01:10:24
01 80673 22.4 53 01:55:49
The desired Output for records 1 through 4 is 00:12:33
The desired output for records 5 through 8 is 01:10:24
Here is my answer:
Evaluate Records 1 through 4
awk 'NR==1,NR==4 {if(max <= $4) {max = $4; time = $5} else if(max == $4) {max = $2; time = $5};next}END {print time}' test.txt test.txt
Output is: 00:12:33
Evaluate Records 5 through 8
awk 'NR==5,NR==8 {if(max <= $4) {max = $4; time = $5} else if(max == $4) {max = $2; time = $5};next}END {print time}' test.txt test.txt
Output is 01:10:24
Any suggestions on how to evaluate the record ranges more efficiently without having to write an awk statement for each set of records?
Thanks
Based on your sample input, the fact there's 4 lines for each key (first field) seems to be irrelevant and what you really want is to just produce output for each key so consider sorting the input by your desired comparison fields (field 4 then field 2) then printing the first desired output (field 5) value seen for each block per key (field 1):
$ sort -n -k1,1 -k4,4r -k2,2r file | awk '!seen[$1]++{print $5}'
00:12:33
01:10:24
This awk code
NR % 4 == 1 {max4 = $4; max2 = $2}
$4 > max4 || $4 == max4 && $2 >= max2 {max4 = $4; max2 = $2; val5 = $5}
NR % 4 == 0 {printf "lines %d-%d: %s\n", (NR - 3), NR, val5}
outputs
lines 1-4: 00:12:33
lines 5-8: 01:10:24
Looking at the data, you might want to group sets by $1 instead of hardcoding 4 lines:
awk '
function emit(nr) {printf "lines %d-%d: %s\n", nr - 3, nr, val5}
$1 != setId {
if (NR > 1) emit(NR - 1)
setId = $1
max4 = $4
max2 = $2
}
$4 > max4 || $4 == max4 && $2 >= max2 {max4 = $4; max2 = $2; val5 = $5}
END {emit(NR)}
' data
an awk-based solution that utilizes a synthetic ascii-string-comparison key combining $4 and $5, while avoiding any %-modulo operations :
mawk '
BEGIN { CONVFMT = "%020.f" (__=___=____=_____="")
_+=_+=++_ } { ____= __!=(__=__==$((_____=(+$_ "")"(" $NF)^!_) \
? __ : $!!_) || ____<_____ ? _____ : ____
} _==++___ {
printf(" group %-*s [%*.f, %-*.f] :: %s\n", --_*--_, "\"" (__) "\"", _+_,
NR-++_, ++_, NR, substr(____, index(____, "(")+_^(_____=____=___=""))) }'
group "00" [ 1, 4 ] :: 00:12:33
group "01" [ 5, 8 ] :: 01:10:24

Changing a list of values in Awk

I am trying to change values in the following list:
A 0.702
B 0.868
C 3.467
D 2.152
If the second column is less than 0.5 I would like to change to -2, between 0.5-1 to -1, between 1-1.5 to 1 and if > 1.5 then to 2.
When I try the following:
awk '$2<0.9 || $2>2' | awk '{if ($2 < 0.5) print $1,-2;}{if($2>0.5 || $2<1) print $1,-1;}{if($2>1 || $2<1.5) print $1,1;}{if($2>2) print $1,2;}'
I get the following:
A -1
A 1
B -1
B 1
C 1
C 2
D 1
D 2
I know I am missing something but for the life of me I can't figure out what - any help gratefully recieved.
If you have multiple if statements and the current value can match multiple statements, you can print multiple outputs.
If you only want to print the output of the first match, you would have to prevent running the if statements that follow.
You can use a single awk and define non overlapping matches with greater than and && lower than.
Note that using only > and < you will not for example 0.5
awk '{
if($2 < 0.5) print($1, -2)
if($2 > 0.5 && $2<1) print($1,-1)
if($2 > 1 && $2<1.5) print($1, 1)
if($2 > 1.5) print($1 ,2)
}
' file
Output
A -1
B -1
C 2
D 2
With your shown samples only. Adding one more solution with using ternary operators for condition checking(for Fun :) ).
awk '{print (NF?($2>1.5?($1 OFS 2):($2>1?($1 OFS 1):($2>0.5?($1 OFS "-1"):($1 OFS "-2")))):"")}' Input_file
Better readable form of above awk code. Since its a one-liner so breaking it up into multi form for better readability here.
awk '
{
print \
(\
NF\
?\
($2>1.5\
?\
($1 OFS 2)\
:\
($2>1\
?\
($1 OFS 1)\
:\
($2>0.5\
?\
($1 OFS "-1")\
:\
($1 OFS "-2")\
)\
)\
)\
:\
""\
)
}
' Input_file
Explanation: Simple explanation would be using ternary operators to perform conditions and accordingly printing values(since its happening in print function).
Another. Replace <s with <=s where needed:
$ awk '{
if($2<0.5) # from low to higher sets the lower limit
$2=-2
else if($2<1) # so only upper limit needs to be tested
$2=-1
else if($2<1.5)
$2=1
else
$2=2
}1' file
Output:
A -1
B -1
C 2
D 2
Probably overkill for your needs but here's a data-driven approach using GNU awk for arrays of arrays and +/-inf:
$ cat tst.awk
BEGIN {
range["-inf"][0.5] = -2
range[0.5][1] = -1
range[1][1.5] = 1
range[1.5]["+inf"] = 2
}
{
val = ""
for ( beg in range ) {
for ( end in range[beg] ) {
if ( (beg+0 < $2) && ($2 <= end+0) ) {
val = range[beg][end]
}
}
}
print $1, val
}
$ awk -f tst.awk file
A -1
B -1
C 2
D 2
I'm assuming above that "between" excludes the start of the range but includes the end of it. You could make it slightly more efficient with:
for ( beg in range ) {
if ( beg+0 < $2 ) {
for ( end in range[beg] ) {
if ( $2 <= end+0 ) {
val = range[beg][end]
}
}
}
}
but I just like having the range comparison all on 1 line and there's only 1 end for every begin so it doesn't make much difference.
UPDATE 1 : new equation should cover nearly all scenarios :
1st half equation handles the sign +/-
2nd half handles the magnitude of the binning
mawk '$NF = (-++_)^(+(__=$NF)<_) * ++_^(int(__+_--^-_)!=_--)'
X -1.25 -2
X -1.00 -2
X -0.75 -2
X -0.50 -2
X -0.25 -2
X 0.00 -2
X 0.25 -2
X 0.50 -1
X 0.75 -1
X 1.00 1
X 1.25 1
X 1.50 2
X 1.75 2
X 2.00 2
X 2.25 2
X 2.50 2
==============================
this may not cover every possible scenario, but if u want a single liner to cover the samples shown :
mawk '$NF = 4 < (_=int(2*$NF)-2)^2 ? 1+(-3)^(_<-_) :_'
A -1
B -1
C 2
D 2

AWK: Help on transforming data table

I have the following file called in.txt:
2020-01-01 fruit banana 3.4
2020-03-02 alcohol smirnov 26.99
2020-03-10 fruit orange 4.20
2020-04-03 fruit orange 4.20
2021-09-01 alcohol beer 6.00
2021-08-03 fruit mango 6.99
2022-01-01 fruit orange 4.30
2022-03-04 alcohol beer 6.00
2022-03-03 alcohol beer 6.00
2022-04-01 fruit mango 7.20
I want to transform the file so it reads something like this:
2020-01-01 2021-01-01 2022-01-01
-2020-12-31 -2021-12-31 -2022-12-31
fruit banana 3.40 0.00 0.00
orange 8.40 0.00 4.30
mango 0.00 6.99 7.20
Subt 11.80 6.99 11.50
alcohol beer 0.00 6.00 12.00
smirnov 26.99 0.00 0.00
Subt 26.99 6.00 12.00
Total 38.59 12.99 23.50
I have started writing the following script but am stuck on how to approach this. How can I display totals columns side by side. The other problem is that this is just dummy data. I have many different categories other than fruit and alcohol and it seems wrong to write if statements and for-loops for each one. Also how can I print fruit and alcohol out just once rather than for every iteration of column 3 and bring the date range to the top. Help is much appreciated.
#!/usr/bin/env bash
awk '
BEGIN{
FS=OFS="\t";
}
{
if ($2 ~ fruit && $1 >= "2020-01-01" && $1 <= "2020-12-31") {
a[$3]+=$4;
sa+=$4;
}
}
END {
PROCINFO["sorted_in"]="#ind_str_asc";
for (i in a) {
print "fruit", i, a[i]
}
}
' "${#:--}"
Would you please try the following:
#!/bin/bash
awk '
{
year = substr($1, 1, 4) # extract year
if (from == "" || from > year) from = year # first (smallest) year
if (to == "" || to < year) to = year # last (largest) year
if ($3 in category == 0) {
category[$3] = $2 # map item to category
list[$2] = list[$2] fs[$2] $3 # csv of items
fs[$2] = "," # delimiter for csv
}
sum[$3,year] += $4 # sum of the item in the year
subt[$2,year] += $4 # sum of the category in the year
ttl[year] += $4 # sum in the year
}
END {
format1 = "%-10s%-10s" # format for the left cells
format2 = "%-16s" # format for the header
format3 = "%-16.2f" # format for the amounts
# print upper header
printf(format1, "", "")
for (y = from; y <= to; y++) {
printf(format2, y "-01-01")
}
print ""
# print second header
printf(format1, "", "")
for (y = from; y <= to; y++) {
printf(format2, "-" y "-12-31")
}
print ""
for (cat in list) { # loop over the categories ("fruit" and "alcohol")
n = split(list[cat], item, ",") # split into items
for (i = 1; i <= n; i++) { # loop over the items
printf(format1, i == 1 ? cat : "", item[i])
for (y = from; y <= to; y++) { # loop over years
printf(format3, sum[item[i],y]) # append the sum of the year
}
print "" # finally break the line
}
print "" # insert blank line
printf(format1, "Subt", "")
for (y = from; y <= to; y++) {
printf(format3, subt[cat,y]) # append the subtotal
}
print "\n"
}
printf(format1, "Total", "")
for (y = from; y <= to; y++) {
printf(format3, ttl[y]) # append the total amount
}
print ""
}
' in.txt
Output with the provided input:
2020-01-01 2021-01-01 2022-01-01
-2020-12-31 -2021-12-31 -2022-12-31
alcohol smirnov 26.99 0.00 0.00
beer 0.00 6.00 12.00
Subt 26.99 6.00 12.00
fruit banana 3.40 0.00 0.00
orange 8.40 0.00 4.30
mango 0.00 6.99 7.20
Subt 11.80 6.99 11.50
Total 38.79 12.99 23.50
Please forgive me the order of items are not same as the OP's.
Using GNU awk for arrays of arrays:
$ cat tst.awk
BEGIN { OFS="\t" }
{
sub(/-.*/,"",$1)
minYear = ( NR==1 || $1 < minYear ? $1 : minYear )
maxYear = ( NR==1 || $1 > maxYear ? $1 : maxYear )
items[$2][$3]
vals[$1][$2][$3] += $4
typeTots[$1][$2] += $4
yearTots[$1] += $4
}
END {
printf "%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%s", OFS, year
}
print ""
for ( type in items ) {
itemCnt = 0
for ( item in items[type] ) {
printf "%s%s%s", (itemCnt++ ? "" : type), OFS, item
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%0.2f", OFS, vals[year][type][item]
}
print ""
}
printf "Subt%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%0.2f", OFS, typeTots[year][type]
}
print ORS
}
printf "Total%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%0.2f", OFS, yearTots[year]
}
print ""
}
$ awk -f tst.awk in.txt
2020 2021 2022
alcohol beer 0.00 6.00 12.00
smirnov 26.99 0.00 0.00
Subt 26.99 6.00 12.00
fruit orange 8.40 0.00 4.30
mango 0.00 6.99 7.20
banana 3.40 0.00 0.00
Subt 11.80 6.99 11.50
Total 38.79 12.99 23.50
or if you really want specific date ranges instead of just the year in the header:
$ cat tst.awk
BEGIN { OFS="\t" }
{
sub(/-.*/,"",$1)
minYear = ( NR==1 || $1 < minYear ? $1 : minYear )
maxYear = ( NR==1 || $1 > maxYear ? $1 : maxYear )
items[$2][$3]
vals[$1][$2][$3] += $4
typeTots[$1][$2] += $4
yearTots[$1] += $4
}
END {
printf "%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%s-01-01", OFS, year
}
print ""
printf "%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s-%s-12-31", OFS, year
}
print ""
for ( type in items ) {
itemCnt = 0
for ( item in items[type] ) {
printf "%s%s%s", (itemCnt++ ? "" : type), OFS, item
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%0.2f", OFS, vals[year][type][item]
}
print ""
}
printf "Subt%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%0.2f", OFS, typeTots[year][type]
}
print ORS
}
printf "Total%s", OFS
for ( year=minYear; year<=maxYear; year++ ) {
printf "%s%0.2f", OFS, yearTots[year]
}
print ""
}
$ awk -f tst.awk in.txt | column -s$'\t' -t
2020-01-01 2021-01-01 2022-01-01
-2020-12-31 -2021-12-31 -2022-12-31
alcohol beer 0.00 6.00 12.00
smirnov 26.99 0.00 0.00
Subt 26.99 6.00 12.00
fruit orange 8.40 0.00 4.30
mango 0.00 6.99 7.20
banana 3.40 0.00 0.00
Subt 11.80 6.99 11.50
Total 38.79 12.99 23.50
I believe the following piece of awk code is a good start. The remaining part to do is just some cleanup and some extra code for the sums.
BEGIN{
# how many divisions per year
n=1
# initialisation of some variables
tmax=0;tmin=999999; ymax=qmax=0;ymin=9999;qmin=99
}
# convert date to quarter,trim,half
{ y=$1+0; q=(substr($1,6,7)+0)%n}
# compute min max time
(y*100+q < tmin) { ymin=y;qmin=q;tmin=y*100+q }
(y*100+q > tmax) { ymax=y;qmax=q;tmax=y*100+q }
# Create arrays that keep track of everything
# a : prices by year,q,category and element
# b : just a list of categories, eg fruit
# c : just a list of elements and the category it belongs to.
{ a[y,q,$2,$3]=$4; b[$2]; c[$3]=$2 }
END{
# loop over categories (eg fruit)
for(i in b) {
# loop over elemnts
for(j in c) {
# exclude elements that do not belong to category
if (i!=c[j]) continue
s=i OFS j;
# loop over the time
for (y=ymin;y<=ymax;y++) {
for (q=0;q<n;++q) {
if (y*100+q < tmin) continue
if (y*100+q > tmax) continue
s=s OFS a[y,q,i,j]+0
}
}
print s
}
}
}
This currently outputs:
alcohol beer 0 6 6
alcohol smirnov 26.99 0 0
fruit orange 4.2 0 4.3
fruit mango 0 6.99 7.2
fruit banana 3.4 0 0

awk equivalents for tidyverse concepts (melt and spread)

I have some text logs that I need to parse and format into CSV.
I have a working R script but it is slow once file sizes increase and this problem seems like a good candidate for a speed up using awk (or other commandline tools?) as I understand.
I have not done much with awk, and the issue I am having is translating how I think about processing in R to how awk scripting is done.
Example truncated input data (Scrap.log):
; these are comment lines
; *******************************************************************************
; \\C:\Users\Computer\Folder\Folder\Scrap.log
!!G 99999 % % % % % % % % CURRENT XYZ ABC STATE1 STATE2
_START Header1 Header2 Header3 Header4 Header5 Header6 Header7
10 12.23 1.91 6.63 1.68 50.03 0.50 13.97
11 11.32 1.94 6.64 1.94 50.12 0.58 15.10
12 12.96 2.15 6.57 2.12 55.60 0.62 16.24
13 11.43 2.18 6.60 2.36 50.89 0.68 17.39
14 14.91 2.32 6.64 2.59 56.09 0.73 18.41
15 13.16 2.38 6.53 2.85 51.62 0.81 19.30
16 15.02 2.50 6.67 3.05 56.22 0.85 20.12
!!G 99999 % % % % % % % % CURRENT XYZ ABC STATE1 STATE2
_START Header8 Header9 Header10 Header11 Header12 Header13 Header14
10 22.03 24.41 15.01 51.44 44.28 16.57 11.52
11 21.05 24.62 15.62 51.23 45.42 16.47 11.98
12 20.11 24.64 16.38 52.16 46.59 16.54 12.42
13 24.13 24.93 17.23 52.34 47.72 16.51 12.88
14 27.17 24.95 18.06 52.79 48.72 16.45 13.30
15 22.87 25.04 19.27 53.01 49.50 16.47 13.63
16 23.08 25.22 20.12 53.75 50.64 16.55 14.03
Expected output (truncated):
HH1,HH2,HH3,HH4,HH5,HH6,HH7,HH8,HH9,HH10,HH11,HH12,HH13,HH14,START,HeaderName,Value
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header1,12.23
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header2,1.91
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header3,6.63
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header4,1.68
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header5,50.03
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header6,0.5
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,10,Header7,13.97
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header1,11.32
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header2,1.94
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header3,6.64
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header4,1.94
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header5,50.12
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header6,0.58
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,11,Header7,15.1
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header1,12.96
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header2,2.15
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header3,6.57
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header4,2.12
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header5,55.6
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header6,0.62
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,12,Header7,16.24
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,13,Header1,11.43
99999,CURRENT,XYZ,ABC,STATE1,STATE2,%,%,%,%,%,%,%,%,13,Header2,2.18
...
My general steps in the R script:
add a single header row with new names at the top of file
spread the top row (starting with !!G) to each row
melt the header column (_START) from wide to long format
Pieces I have working in awk so far include:
how to grab and print the header lines
awk '/_START/ {header = $0; print header}' Scrap.log
How to write a single row with the new header values
awk ' BEGIN{ ORS=" "; for (counter = 1; counter <= 14; counter++) print "HH",counter;}'
I know each block is separated by a newline and starts with a !!G, so can write a match on that. Unsure if a split-apply-combine type of thinking works well in awk?
awk '/!!G/,/\n/ {print}' Scrap.log
alternatively, I tried setting RS/FS parameters like:
awk ' BEGIN{RS="\n";FS=" ";}/^!!G/{header=$0;print header}/[0-9]/{print $2}END{}' Scrap.log
I then get stuck on iterating over the rows and fields to do the melt step as well as combining the capture groups correctly.
How do I combine all these pieces to get to the CSV format?
I think the following:
awk '
BEGIN{
# output the header line
print "HH1,HH2,HH3,HH4,HH5,HH6,HH7,HH8,HH9,HH10,HH11,HH12,HH13,HH14,START,HeaderName,Value"
}
# ignore comment lines
/;/{next}
/!!G/{
valcnt = 1
# save and shuffle the values
val[valcnt++] = $2
val[valcnt++] = $11
val[valcnt++] = $12
val[valcnt++] = $13
val[valcnt++] = $14
val[valcnt++] = $15
val[valcnt++] = $3
val[valcnt++] = $4
val[valcnt++] = $5
val[valcnt++] = $6
val[valcnt++] = $7
val[valcnt++] = $8
val[valcnt++] = $9
val[valcnt++] = $10
next
}
/_START /{
# these are headers - save them to head, to be reused later
for (i = 2; i <= NF; ++i) {
# fun fact: its indexed on NF
head[i] = $i
}
next
}
# this function is redundant, but its just easier for me to think about the code
function output(firstval, header, value, \
cur, i) {
cur = valcnt
val[cur++] = firstval
val[cur++] = header
val[cur++] = value
# output val as csv
for (i = 1; i < cur; ++i) {
printf "%s%s", val[i], i != cur - 1 ? "," : "\n"
}
}
/[0-9]+/{
for (i = 2; i <= NF; ++i) {
# add these 3 to all the other values and output them
# ie. add first column, the header from header and the value
output($1, head[i], $i)
}
}
'
Should output what you want. Tested on repl.

Taking similar consecutive rows and appending them into one longer row with AWK

I've got a big 7-column text file with sorted rows like this:
gi|352964122|gb|JH286168.1| 00884 C C 14 1.00 u
gi|352964122|gb|JH286168.1| 00884 C C 26 0.76 p
gi|352964122|gb|JH286168.1| 00884 C C 33 0.89 f
gi|352964122|gb|JH286168.1| 00885 G G 14 1.00 u
gi|352964122|gb|JH286168.1| 00885 A A 30 0.84 f
gi|352964122|gb|JH286168.1| 00886 T T 31 0.81 f
What I'm needing to do is, if the first two columns are the same in consecutive rows, append the rest of the columns to the first row. There can be 1, 2, or 3 "similar" rows, and I need placeholders to keep columns intact if less than 3. So the above would look like this:
gi|352964122|gb|JH286168.1| 00884 C C 14 1.00 u C C 26 0.76 p C C 33 0.89 f
gi|352964122|gb|JH286168.1| 00885 G G 14 1.00 u - - - ------------ G G 33 0.89 f
gi|352964122|gb|JH286168.1| 00886 T T 31 0.81 f - - - ---- - - - ------ - - -- ----- - -
I've tried many approaches with AWK but can't quite get it. How might this be done?
I'm unsure about how you get your second row but this might match at least how I understand the goal:
awk '
{
head=$1 " " $2
tail=$3 " " $4 " " $5 " " $6 " "$7
if(previous!=head) {
if(previous!="") printf("%s %s %s %s\n",previous,p[1],p[2],p[3])
previous=head
i=1
p[i]=tail
p[2]=p[3]="- - - -"
} else {
i=i+1
p[i]=tail
}
}
END { printf("%s %s %s %s\n",previous,p[1],p[2],p[3]) }'
Output:
gi|352964122|gb|JH286168.1| 00884 C C 14 1.00 u C C 26 0.76 p C C 33 0.89 f
gi|352964122|gb|JH286168.1| 00885 G G 14 1.00 u A A 30 0.84 f - - - -
gi|352964122|gb|JH286168.1| 00886 T T 31 0.81 f - - - - - - - -
This should do it:
(Edit: I didn't notice you needed placeholders. I'll look into it....)
awk '
$1 == last1 && $2 == last2 {
printf " %s %s %s %s %s",$3,$4,$5,$6,$7;
last1 = $1; last2 = $2;
next;
}
{
$1 = $1; # normalize spacing
printf "%s%s", NR==1?"":"\n", $0;
last1 = $1; last2 = $2;
}
END { print ""; }
' file
$ cat tst.awk
BEGIN { maxRecs = 3 }
function prta( i, dflt) {
dflt = a[1]
gsub(/[^[:space:]]+/,"-",dflt)
printf "%s ", key
for (i=1; i<=maxRecs; i++) {
printf "%s%s", (i in a ? a[i] : dflt), (i<maxRecs ? OFS : ORS)
delete a[i]
}
numRecs = 0
}
{ key = $1 FS $2 }
prev && (key != prev) { prta() }
{
$1 = $1
sub(/([^[:space:]]+[[:space:]]+){2}/,"")
a[++numRecs] = $0
prev = key
}
END { prta() }
$
$ awk -f tst.awk file
gi|352964122|gb|JH286168.1| 00885 C C 14 1.00 u C C 26 0.76 p C C 33 0.89 f
gi|352964122|gb|JH286168.1| 00886 G G 14 1.00 u A A 30 0.84 f - - - - -
gi|352964122|gb|JH286168.1| 00886 T T 31 0.81 f - - - - - - - - - -