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awk split and awk calculation in the same command

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# 1  
Old 03-22-2016
awk split and awk calculation in the same command
I am trying to run the awk below. My question is when I split the input, then run anotherawk to perform a calculation using that splitas the input there are no issues. When I try to combine them the output is not correct, is the split not working or did I do it wrong? Thank you Smilie.

input
Code:
 
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    1    15
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    2    16
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    3    16
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    4    14
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    5    17

after the split awk '{split($5,a,"-"); print $1,$2,$3,$4,a[1]}' input > split

split (uses the - in $5 and prints $1,$2,$3,$4,and the split a[1]

Code:
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN

if I use that file (split) in the below awk the output is correct

output ($5 count of lines that are the same and the sum of $3-$2
Code:
AGRN 5 1100

If I try to perform the split and run the calculation in the same awk, I get the below output:

Code:
awk '{split($5,a,"-"); print $1,$2,$3,$4,a[1]} {c1[a1]++; c2[a1]+=($3-$2)}
>     END{for (e in c1) print e, c1[e], c2[e]}' split

output
Code:
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
 5 1100

# 2  
Old 03-22-2016
use a[1] instead of a1
This User Gave Thanks to rdrtx1 For This Post:
cmccabe
# 3  
Old 03-22-2016
Try c1[a[1]] instead of c1[a1]
This User Gave Thanks to Scrutinizer For This Post:
cmccabe
# 4  
Old 03-25-2016
Thank you both Smilie
# 5  
Old 05-19-2016
awk not calculating the same on input file
The below awk is producing different results since my input changed on some lines from (old input):
I can not seem to fix this and need some expert help Smilie... thank you Smilie.

awk
Code:
awk '{split($5,a,"-"); print $1,$2,$3,$4,a[1]} {c1[a[1]]++; c2[a[1]]+=($3-$2)}
     END{for (e in c1) print e, c1[e], c2[e]}' input

old input
Code:
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    1    15
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    2    16
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    3    16
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    4    14
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    5    17

output -- this is correct
Code:
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
AGRN 5 1100

using the awk on the attached fille:


out.txt (attachment) -- does not count $5 or subtract each $3-$2 as it did before

Code:
chr7 121738788 121738930 chr7:121738788-121738930 AASS
chr7 121738788 121738930 chr7:121738788-121738930 AASS
chr7 121738788 121738930 chr7:121738788-121738930 AASS
chr7 121741414 121741502 chr7:121741414-121741502 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS
chr7 121769404 121769601 chr7:121769404-121769601 AASS

NA12878_newheader_base_counts_lessthan_30reads_perbase.txt.tar.gz (570.0 KB) 
out.txt.tar.gz (86.7 KB) 
# 6  
Old 05-19-2016
Seems to work for me - when applied to a small subset of your input.
Code:
.
.
.
chr17 67160204 67160305 chr17:67160204-67160305 ABCA10
ABCA1 1 144
AASS 19 3469
ABCA10 14 1414

# 7  
Old 05-19-2016
On a small subset the awk seems to work, but using the actual input (attached, which is much larger) what the awk seems to be doing is printing the split and then the calculation below it. Do I need to perform the split separate in order not to see it in the output? Or can I print the results of the split in one file then use that file to output the calculations? Thank you Smilie.


Code:
. . . 
chr17 67160204 67160305 chr17:67160204-67160305 ABCA10  -- up to here is split 
ABCA1 1 144 
AASS 19 3469 
ABCA10 14 1414

Last edited by cmccabe; 05-19-2016 at 01:56 PM.. Reason: added details
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