I need some help in fixing my code to process a tab-delimited data set. Example data is:
#ID type
A 3
A Ct
A Ct
A chloroplast
B Ct
B Ct
B chloroplast
B chloroplast
B 4
C Ct
C Ct
C chloroplast
For each unique element in column#1, I would like to count elements that matches the pattern "Ct" and those that don't match.
So expected output is
#ID count_for_matches count_for_unmatched
A 2 2
B 2 3
C 2 1
I can get the counts to pattern matches with this
awk '$2~/Ct/{x++};$2!~/Ct/{y++}END{print x,y}
And I know I could do the processing for each item by defining column#1 as an array like
awk '{a[$1]++}END{for (i in a) print i}'
But I cannot combine both pieces for a functional code. I tried some combinations like
awk '{a[$1]++}END{for (i in a){$2~/Ct/{x++};$2!~/Ctt/{y++}}END{print i,x,y}}}'
But I am obviously making some errors and I cannot figure out based on forum answers how to fix this. Perhaps $2 values should be stored with a[$1]? Would appreciate if someone can point out the errors!
$ cat tst.awk
BEGIN { FS=OFS="\t" }
NR==1 { next }
!seen[$1]++ { keys[++numKeys] = $1 }
$2=="Ct" { matches[$1]++; next }
{ unmatched[$1]++ }
END {
print "#ID", "count_for_matches", "count_for_unmatched"
for (keyNr=1; keyNr<=numKeys; keyNr++) {
key = keys[keyNr]
print key, matches[key]+0, unmatched[key]+0
}
}
$ awk -f tst.awk file
#ID count_for_matches count_for_unmatched
A 2 2
B 2 3
C 2 1
here is another minimalist version
$ awk 'NR==1{print $1,"count_for_matches","count_for_unmatches";next}
$2=="Ct"{m[$1]++}
{a[$1]++}
END{for(k in a) print k, m[k], a[k]-m[k]}' file |
column -t
#ID count_for_matches count_for_unmatches
A 2 2
B 2 3
C 2 1
Related
I have this small geo location dataset.
37.9636140,23.7261360
37.9440840,23.7001760
37.9637190,23.7258230
37.9901450,23.7298770
From a random location.
For example this one 37.97570, 23.66721
I need to create a bash command with awk that returns the distances with simple euclidean distance.
This is the command i use
awk -v OFMT=%.17g -F',' -v long=37.97570 -v lat=23.66721 '{for (i=1;i<=NR;i++) distances[i]=sqrt(($1 - long)^2 + ($2 - lat)^2 ); a[i]=$1; b[i]=$2} END {for (i in distances) print distances[i], a[i], b[i]}' filename
When I run this command i get this weird result which is not correct, could someone explain to me what am I doing wrong?
➜ awk -v OFMT=%.17g -F',' -v long=37.97570 -v lat=23.66721 '{for (i=1;i<=NR;i++) distances[i]=sqrt(($1 - long)^2 + ($2 - lat)^2 ); a[i]=$1; b[i]=$2} END {for (i in distances) print distances[i], a[i], b[i]}' filename
44,746962127881936 37.9440840 23.7001760
44,746962127881936 37.9901450 23.7298770
44,746962127881936 37.9636140 23.7261360
44,746962127881936
44,746962127881936 37.9637190 23.7258230
Updated.
Appended the command that #jas provided, I included od -c as #mark-fuso suggetsted.
The issue now is that I get different results from #jas
Command output which showcases the new issue.
awk -v OFMT=%.17g -F, -v long=37.97570 -v lat=23.66721 '
{distance=sqrt(($1 - long)^2 + ($2 - lat)^2 ); print distance, $1, $2}
' file
1,1820150904705098 37.9636140 23.7261360
1,1820150904705098 37.9440840 23.7001760
1,1820150904705098 37.9637190 23.7258230
1,1820150904705098 37.9901450 23.7298770
od -c that shows the content of the input file.
od -c file
0000000 3 7 . 9 6 3 6 1 4 0 , 2 3 . 7 2
0000020 6 1 3 6 0 \n 3 7 . 9 4 4 0 8 4 0
0000040 , 2 3 . 7 0 0 1 7 6 0 \n 3 7 . 9
0000060 6 3 7 1 9 0 , 2 3 . 7 2 5 8 2 3
0000100 0 \n 3 7 . 9 9 0 1 4 5 0 , 2 3 .
0000120 7 2 9 8 7 7 0 \n
0000130
While #jas has provided a 'fix' for the problem, thought I'd throw in a few comments about what OP's code is doing ...
Some basics ...
the awk program ({for (i=1;i<=NR;i++) ... ; b[i]=$2}) is applied against each row of the input file
as each row is read from the input file the awk variable NR keeps track of the row number (ie, NR=1 for the first row, NR=2 for the second row, etc)
on the last pass through the for loop the counter (i in this case) will have a value of NR+1 (ie, the i++ is applied on the last pass through the loop thus leaving i=NR+1)
unless there are conditional checks for each line of input the awk program will apply against every line from the input file (including blank lines - more on this below)
for (i in distances)... isn't guaranteed to process the array indices in numerical order
The awk/for loop is doing the following:
for the 1st input row (NR=1) we get for (i=1;i<=1;i++) ...
for the 2nd input row (NR=2) we get for (i=1;i<=2;i++) ...
for the 3rd input row (NR=3) we get for (i=1;i<=3;i++) ...
for the 4th input row (NR=4) we get for (i=1;i<=4;i++) ...
For each row processed by awk the program will overwrite all previous entries in the distance[] array; net result is the last row (NR=4) will place the same values in all 4 entries of the the distance[] array.
The a[i]=$1; b[i]=$2 array assignments occur outside the scope of the for loop so these will be assigned once per input row (ie, will not be overwritten) however, the array assignments are being made with i=NR+1; net result is the contents of the 1st row (NR=1) are stored in array entries a[2] and b[2], the contents of the 2nd row (NR=2) are stored in array entries a[3] and a[3], etc.
Modifying OP's code with print i, distances[i], a[i], b[i]} and running against the 4-line input file I get:
1 0.064310270672728084 # no data for 2nd/3rd columns because a[1] and b[1] are never set
2 0.064310270672728084 37.9636140 23.7261360 # 2nd/3rd columns are from 1st row of input
3 0.064310270672728084 37.9440840 23.7001760 # 2nd/3rd columns are from 2nd row of input
4 0.064310270672728084 37.9637190 23.7258230 # 2nd/3rd columns are from 3rd row of input
From this we can see the first column of output is the same (ie, distance[1]=distance[2]=distance[3]=distance[4]), while the 2nd and 3rd columns are the same as the input columns except they are shifted 'down' by one row.
That leaves us with two outstanding issues ...
why does OP show 5 lines of output?
why is the first column consist of the garbage 44,746962127881936?
I was able to reproduce this issue by adding a blank line on the end of my input file:
$ cat geo.dat
37.9636140,23.7261360
37.9440840,23.7001760
37.9637190,23.7258230
37.9901450,23.7298770
<<=== blank line !!
Which generates the following with OP's awk code:
44.746962127881936
44.746962127881936 37.9636140 23.7261360
44.746962127881936 37.9440840 23.7001760
44.746962127881936 37.9637190 23.7258230
44.746962127881936 37.9901450 23.7298770
NOTES:
this order is different from OP's sample output and is likely due to OP's awk version not processing for (i in distances)... in numerical order; OP can try something like for (i=1;i<=NR;i++)... or for (i=1;i in distances; i++)... (though the latter will not work correcly for a sparsely populated array)
OPs output (in the question; in comment to #jas' answer) shows a comma (,) in place of the period (.) for the first column so I'm guessing OP's env is using a locale that switches the comma/period as thousands/decimal delimiter (though the input data is based on an 'opposite' locale)
Notice we finally get to see the data from the 4th line of input (shifted 'down' and displayed on line 5) but the first column has what appears to be a nonsensical value ... which can be tracked back to applying the following against a blank line:
sqrt(($1 - long)^2 + ($2 - lat)^2 )
sqrt(( - long)^2 + ( - lat)^2 ) # empty line => $1 = $2 = undefined/empty
sqrt(( - 37.97570)^2 + ( - 23.66721^2 )
sqrt( 1442.153790 + 560.136829 )
sqrt( 2002.290619 )
44.746952... # contents of 1st column
To 'fix' this issue the OP can either a) remove the blank line from the input file or b) add some logic to the awk script to only perform calculations if the input line has (numeric) values in fields #1 & #2 (ie, $1 and $2 are not empty); it's up to the coder to decide on how much validation to apply (eg, are the fields numeric, are the fields within the bounds of legitimate long/lat values, etc).
One last design-related comment ... as demonstrated in jas' answer there is no need for any of the arrays (which in turn reduces memory usage) when all desired output can generated 'on-the-fly' while processing each line of the input file.
Awk takes care of the looping for you. The code will be run in turn for each line of the input file:
$ awk -v OFMT=%.17g -F, -v long=37.97570 -v lat=23.66721 '
{distance=sqrt(($1 - long)^2 + ($2 - lat)^2 ); print distance, $1, $2}
' file
0.060152679674309095 37.9636140 23.7261360
0.045676346307474212 37.9440840 23.7001760
0.059824979147508742 37.9637190 23.7258230
0.064310270672728084 37.9901450 23.7298770
EDIT:
OP is getting different results. I notice in OP's output that there are commas instead of decimal points when printing the distance. This points to a possible issue with the locale setting.
OP confirms that the locale was set for greek, causing the difference in output.
I know it may sounds that there are 2000 answer to this question online but I found none for this specific case (ex. -vFPAT of this and other answers) cause I need to be with split. I have to split a CSV file with awk in which there may be some values inside double quotes. I need to tell the split function to ignore , if inside "" in order to get an array of the elements.
Here what I tried based on other answers as example
cat try.txt
Hi,I,"am,your",father
maybe,you,knew,it
but,"I,wanted",to,"be,sure"
cat tst.awk
BEGIN {}
{
n_a = split($0,a,/([^,]*)|("[^"]+")/);
for (i=1; i<=n_a; i++) {
collecter[NR][i]=a[i];
}
}
END {
for (i=1; i<=length(collecter); i++)
{
for (z=1; z<=length(collecter[i]);z++)
{
printf "%s\n", collecter[i][z];
}
}
}
but no luck:
awk -f tst.awk try.txt
,
,
,
,
,
,
,
,
,
I tried other regex expression based on other similar answer but none works for this particular case.
Please note: double quoted fields mat and may not be present, may be more than one, and without fixed position/length!
Thanks in advance for any help!
gnu awk has a function called patsplit that lets you do a split using an FPAT pattern:
$ awk '{ print "RECORD " NR ":"; n=patsplit($0, a, "([^,]*)|(\"[^\"]+\")"); for (i=1;i<=n;++i) {print i, "|" a[i] "|"}}' file
RECORD 1:
1 |Hi|
2 |I|
3 |"am,your"|
4 |father|
RECORD 2:
1 |maybe|
2 |you|
3 |knew|
4 |it|
RECORD 3:
1 |but|
2 |"I,wanted"|
3 |to|
4 |"be,sure"|
If Python is an alternative, here is a solution:
try.txt:
Hi,I,"am,your",father
maybe,you,knew,it
but,"I,wanted",to,"be,sure"
Python snippet:
import csv
with open('try.txt') as f:
reader = csv.reader(f, quoting=csv.QUOTE_ALL)
for row in reader:
print(row)
The code snippet above will result in:
['Hi', 'I', 'am,your', 'father']
['maybe', 'you', 'knew', 'it']
['but', 'I,wanted', 'to', 'be,sure']
I have a number of files (N>1000) with qtl summary data e.g. lets assume the first file is made of six lines (in reality they are all GWAs/imputed files with >10M SNPs)
cat QTL.1.txt
Chr Rs BP beta se pvalue
11 rs11224233 134945522 0.150216 0.736939 0.962375
11 rs4616056 134945709 0.129518 0.371824 0.910326
11 rs11823417 134945710 0.103462 0.41737 0.845826
11 rs80294507 134945765 0.150336 0.735363 0.961403
11 rs61907173 134946034 0.104531 0.158224 0.884548
11 rs147621717 134946277 0.105365 0.196168 0.86476
I would like to filter each of these datasets based on chromosome and positions of a list of genes (my list has 100 genes but now lest assume it has 2); therefore creating N_QTL*N_Genes files. I would like to go through each gene/position for each QTL. The Chromosome, positions and name of the genes are stored in four arrays and I would like to read iteratively these arrays and save the output for each qtl file for each gene.
What I have done so far doesnt work and I know awk is not the best way to do this:
declare -a array1
declare -a array2
declare -a array3
declare -a array4
array1=(11 11) #chromosome
array2=(134945709 134945765) #start gene position
array3=(134946034 134946277) #end gene position
array4=(A B) # gene name
for qtl in 1; do # in reality it would be for qtl in 1 1000
for ((i=0; i<${#array1[#]}; i++)); do
cat QTL.$qtl.txt | awk '$1=='array1[$i]' && $3>='array2[$i]' &&
$3<='array3[$i]' {print$0}' > Gene.${array4[$i]}_QTL.$qtl.txt;
done;
done
within awk $1 is the chromosome and $3 the position- so therefore filtering based on these.
So my expected output for QTL.1.txt for Gene A would be
cat Gene.A_QTL.1.txt
Chr Rs BP beta se pvalue
11 rs4616056 134945709 0.129518 0.371824 0.910326
11 rs11823417 134945710 0.103462 0.41737 0.845826
11 rs80294507 134945765 0.150336 0.735363 0.961403
11 rs61907173 134946034 0.104531 0.158224 0.884548
And for QTL.1.txt for Gene B would be
cat Gene.B_QTL.1.txt
Chr Rs BP beta se pvalue
11 rs80294507 134945765 0.150336 0.735363 0.961403
11 rs61907173 134946034 0.104531 0.158224 0.884548
11 rs147621717 134946277 0.105365 0.196168 0.86476
I end up with empty files as probably the way I ask these columns to be filtered based on the values of the arrays doesnt work.
Any help very much appreciated!
Thank you in advance
Mixing bash and awk for parsing files is not always the best way forward.
Here a solution with awk only.
Assume you have the information assigned to your bash array in a file:
$ cat info
11 134945765 154945765 Gene1
12 134945522 174945522 Gene2
You could use the following awk script to perform a lookup with the data file:
awk 'NR==FNR{
for(i=2;i<=NF;i++)
a[$1,i]=$i
next
}
a[$1,2]<=$3 && a[$1,3]>=$3{
print $0 > a[$1,4]"_QTL"
}' info QTL.1.txt
This will create a file with the following content:
$ cat Gene1_QTL
11 rs80294507 134945765 0.150336 0.735363 0.961403
11 rs61907173 134946034 0.104531 0.158224 0.884548
11 rs147621717 134946277 0.105365 0.196168 0.86476
Maybe not exactly what you're looking at, but yet I hope this is helpful...
You might want to do the following if multiple genes are located in the same chromosome (using gene name instead of chr as Key):
awk 'NR==FNR{
chr[$4]=$1;
start[$4]=$2;
end[$4]=$3;
}
NR!=FNR{
for (var in chr){
name=var"_"FILENAME;
if(chr[var]==$1 && start[var] <=$3 && end[var]>=$3){
print $0 > name;
}
}
}' info QTL
Hello Everyone,
I have two files File1 and File2 which has the following data.
File1:
TOPIC:topic_0 30063951.0
2 19195200.0
1 7586580.0
3 2622580.0
TOPIC:topic_1 17201790.0
1 15428200.0
2 917930.0
10 670854.0
and so on..There are 15 topics and each topic have their respective weights. And the first column like 2,1,3 are the numbers which have corresponding words in file2. For example,
File 2 has:
1 i
2 new
3 percent
4 people
5 year
6 two
7 million
8 president
9 last
10 government
and so on.. There are about 10,470 lines of words. So, in short I should have the corresponding words in the first column of file1 instead of the line numbers. My output should be like:
TOPIC:topic_0 30063951.0
new 19195200.0
i 7586580.0
percent 2622580.0
TOPIC:topic_1 17201790.0
i 15428200.0
new 917930.0
government 670854.0
My Code:
import sys
d1 = {}
n = 1
with open("ap_vocab.txt") as in_file2:
for line2 in in_file2:
#print n, line2
d1[n] = line2[:-1]
n = n + 1
with open("ap_top_t15.txt") as in_file:
for line1 in in_file:
columns = line1.split(' ')
firstwords = columns[0]
#print firstwords[:-8]
if firstwords[:-8] == 'TOPIC':
print columns[0], columns[1]
elif firstwords[:-8] != '\n':
num = columns[0]
print d1[n], columns[1]
This code is running when I type print d1[2], columns[1] giving the second word in file2 for all the lines. But when the above code is printed, it is giving an error
KeyError: 10472
there are 10472 lines of words in the file2. Please help me with what I should do to rectify this. Thanks in advance!
In your first for loop, n is incremented with each line until reaching a final value of 10472. You are only setting values for d1[n] up to 10471 however, as you have placed the increment after you set d1 for your given n, with these two lines:
d1[n] = line2[:-1]
n = n + 1
Then on the line
print d1[n], columns[1]
in your second for loop (for in_file), you are attempting to access d1[10472], which evidently doesn't exist. Furthermore, you are defining d1 as an empty Dictionary, and then attempting to access it as if it were a list, such that even if you fix your increment you will not be able to access it like that. You must either use a list with d1 = [], or will have to implement an OrderedDict so that you can access the "last" key as dictionaries are typically unordered in Python.
You can either:
Alter your increment so that you do set a value for d1 in the d1[10472] position, or simply set the value for the last position after your for loop.
Depending on what you are attempting to print out, you could replace your last line with
print d1[-1], columns[1]
to print out the value for the final index position you currently have set.
I'm stumbling over myself trying to get a seemingly simple thing accomplished. I have one file, and one newline delimited string list.
File:
Dat1 Loc1
Dat2 Loc1
Dat3 Loc1
Dat4 Loc2
Dat5 Loc2
My list is something like this:
Dat1
Dat2
Dat3
Dat4
What I am trying to do is compare the list with the data file and count the number of unique Locs that appear. I am interested only in the largest count. In the example above, when comparing the list to the file, I want essentially:
Dat1 MATCHED Loc1Count = 1
Dat2 MATCHED Loc1Count = 2
Dat3 MATCHED Loc1Count = 3
Dat4 MATCHED Loc2Count = 1
Return: Loc1 if Loc1Count/Length of List > 50%
Now,
I know that awk 1 file will read a file line by line. Furthermore I know that "echo "$LIST" | awk '/search for a line that contains this/" will return the line that matches that internal string. I haven't been able to combine these ideas successfully though as nested awks, much less how to count "loc1" vs "loc2" (which, by the way, are going to be random strings, and not form-standard)
I feel like this is simple, but I'm banging my head against a wall. Any ideas? Is this sufficiently clear?
list="Dat1 Dat2 Dat3 Dat4"
awk -vli="$list" 'BEGIN{
# here list from shell is converted to awk array "list".
m=split(li,list," ")
}
{
# go through the list
for(i=1;i<=m;i++){
if($1 == list[i]){
# if Dat? is found in list, print , at the same time
print $1" matched Locount="$2" "++data[$2] # increment the count for $2 and store in loc array
loc[$2]++
}
}
}
END{
# here returns loc1 count
loc1count=loc["Loc1"]
if(( loc1count / m *100 ) > 50) {
print "Loc1 count: "loc1count
}
} ' file
output
$ ./shell.sh
Dat1 matched Locount=Loc1 1
Dat2 matched Locount=Loc1 2
Dat3 matched Locount=Loc1 3
Dat4 matched Locount=Loc2 1
Loc1 count: 3