How to count a matching pattern in one line? - shell

Question

enter code hereI have a fasta file containing sequences
>lcl|QCYY01003067.1_cds_ROT65593.1_2
ATGCGTCTCCCCTTTAGAGAGTTCTCTCTAGCTACGTA
>lcl|QCYY01003067.1_cds_ROT65593.1_3
ATCTCTNNNNNNNNNNATATCCCCTTTNNNNNCTCTCT
>lcl|QCYY01003067.1_cds_ROT65593.1_4
ATCTCTNNNNNNNNNNATATCCCCTTCTCGGGGCCCC
I wanted to count the number of 'N' and also the number of patterns occurring in each line. No need to include header (>lcl|QCYY01003067.1_cds_ROT65593.1_2 )
eg:-
line 2=0,0
line 4=15,2
line 6=10,1
How to improve this code:
grep -n '[{N}]' <filename> | cut -d : -f 1 | uniq -c

Answer 1

Another awk:
$ awk 'NR%2==0{printf "line %d=%d,%d\n",NR,gsub(/N/,"N"),gsub(/N+/,"")}' file
Output:
line 2=0,0
line 4=15,2
line 6=10,1
Explained:
$ awk '
NR%2==0 { # process even records
printf "line %d=%d,%d\n",NR,gsub(/N/,"N"),gsub(/N+/,"") # count with gsub
}' file
gsub(/N/,"N") counts the amount of Ns in the record (returns the amount of replacements). gsub(/N+/,"") counts the number of consecutive strings of Ns. Notice, that "" removes those Ns from the record so if you need to later further process the data, use gsub(/N+/,"&") instead.
Updated:
The version I wrote for your already-deleted next question.
I added an extra line to your data which demonstrates the question I asked in the comments (is ...N\nNN.. one (NNN) or two (N,NN) patterns of your definition):
...
>seq4
ATCTCTNNNNNNNNNNATATCCCCTTCTCGGGGCCNNN
NNNNNTTTTTCTCTCTCGCGCTCGTCGAAAAATGCCCC
This one is for GNU awk (for using RT):
$ gawk '
BEGIN {
RS=">seq[^\n]+"
}
NR>1 {
# gsub(/\n/,"") # UNCOMMENT THIS IF NEWLINE SEPARATED PATTERN IS ONE PATTERN
printf "%s=%d,%d\n",rt,gsub(/N/,"N"),gsub(/N+/,"")
}
{
rt=RT
}' file
Output (pay special attention to the seq4):
>seq1=0,0
>seq2=15,2
>seq3=15,2
>seq4=18,3
or if you uncomment the gsub(/\n/,"") to remove the newline separating strings, the output is:
>seq1=0,0
>seq2=15,2
>seq3=15,2
>seq4=18,2
One-liner (with the one gsub uncommented):
$ awk 'BEGIN{RS=">seq[^\n]+"}NR>1{gsub(/\n/,"");printf "%s=%d,%d\n",rt,gsub(/N/,"N"),gsub(/N+/,"")}{rt=RT}' file

Answer 2

Could you please try following.
awk '
!/^>/{
while(match($0,/N+/)){
count++
total+=length(substr($0,RSTART,RLENGTH))
$0=substr($0,RSTART+RLENGTH)
}
printf("%s %d=%d,%d\n","line",FNR,total,count)
count=total=""
}
' Input_file
Output will be as follows.
line 2=0,0
line 4=15,2
line 6=10,1
Explanation: Adding detailed explanation for above code here.
awk ' ##Starting awk program from here.
!/^>/{ ##Checking condition if a line is NOT starting from > then do following.
while(match($0,/N+/)){ ##Running a while loop which will run till a match found for N characters continuous occurrence.
count++ ##Doing increment to variable count with 1 each time cursor comes here.
total+=length(substr($0,RSTART,RLENGTH)) ##Creating total variable which is keep adding its own value along with length of matched regex, where regex is looking for continuous occurrence of N character in current line.
$0=substr($0,RSTART+RLENGTH) ##Resetting value of current line to have only REST of line which starts from very next character of matched regex. So that we can skip previous matched regex and look for others in rest of the line.
} ##Closing BLOCK for above mentioned while loop here.
printf("%s %d=%d,%d\n","line",FNR,total,count) ##Printing values line,FNR,total,count variables here.
count=total="" ##Nullifying variables count and total here, so that previous values should NOT be added to current values of it.
}
' Input_file ##Mentioning Input_file name here.