In this file the lines can be split into different records with a name (starting with >) and the encoded information/sequence (001010...) associated with the header. Now, I need to add some code to the header according to the following file:
head -n 5 code.txt
>KF1.8.1;code=D0:B;D1:P;D2:E;D3:C;D4:H;D5:S_(1);
>DF1.6.1;code=D0:B;D1:D;D2:F;D3:C;D4:F;D5:S_(1);
>XC1.3.7;code=D0:A;D1:D;D2:E;D3:C;D4:H;D5:H;
>GG5.1.1;code=D0:A;D1:D;D2:E;D3:C;D4:F;D5:H;
>HK1.2.2;code=D0:A;D1:F;D2:F;D3:C;D4:H;D5:K_[23];
It works because awk has associative arrays, you can do ARRAY["something"]="ABCD". And NR==FNR means 'do this only for the first file listed'. So it reads the entire list into an associative array, then reads through the huge file hunting for relevant lines, substituting where appropriate, then printing everything.
Just a side note: Many shells (for instance bash and zsh) have associative arrays too. Problem is that the OP did not specify whether he wants to restrict his solution to a particular shell, as the code snippet he wrote would be compliant to several shells.
---------- Post updated at 08:54 AM ---------- Previous update was at 08:35 AM ----------
Dear Corona,
Thanks for the help and the explanation. I'm am not sure I understand the solution completely.
A[$1]=$0 means I read everything from the first file provided - because I use -F ";" the line in the first file is split up /^>/ && ($1 in A) is this the if statement - if the line starts with a ">" sign and $1 is somewhere in the arry - why $1 ? Is it not file two or is it everything after ";" meant for file two?
Would be great if you would find the time to explain me the awk array a bit more. I really appreciate your help.
Could you please go through following and let me know if this helps you.
awk -F';' ##### Making field separator as ";"
'NR==FNR ##### Checking NR==FNR condition here, this condition will be TRUE when first file code.txt is getting read.
{ A[$1]=$0 ; ##### Making an aray named A with index $1 and keeping it's value as current line.
next } ; ##### putting next keyword from built-in awk's keyword it will skip all next statements then.
/^>/ && ($1 in A) ##### Checking here 2 conditions, 1st condition if any line starts from ">" and first field or that line is present in array A. If both conditions are TRUE then perform the following statements.
{ $1=A[$1] } ##### Making first field as array A's value whose index is $1.
1 ##### Mentioning 1 here, so awk works on condition then action part, when condition is TRUE then action will happen. So here by mentioning 1 we are making condition as TRUE and no action mentioned so default action will happen which is printing of the current line.
' code.txt seq.txt ##### Mentioning the Input_files here too.