Shell Programming and Scripting

what do you think is happening here?

Code:

o[i[++ic] = $1,$2,$3] =$1

Code:

o[i[++ic] = $1,$2,$3] =$1

$1,$2,$3 are being stored in array o, I think? Thank you

or should that be

Code:

o[i[++ic] = $1,$2,$3] ={[$1,$2,$3]}

.

Hello cmccabe,

You could split the arrays like as follows to make it easier.
o[i[++ic] = $1,$2,$3] =$1 could be written as:

Code:

i[++ic] = $1,$2,$3   
o[i[ic]]=$1

Following is the explanation too for o[i[++ic] = $1,$2,$3] =$1(Only for understanding I have split it into 2 steps).

Code:

i[++ic] = $1,$2,$3       
array named i whose value is increasing number of variable named i and it's value is $1,$2,$3.
o[i[++ic] = $1,$2,$3] =$1
array named o whose index is value of array i (whose index is increasing value if variable named ic(each time it will be increased by 1.)) and it's value is the value of field 1st.

Thanks,
R. Singh

Thanks you, but I am getting a syntax error... do I need to enclose the array in {}? Thank you .

Code:

awk '
BEGIN {    FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
i[++ic] = $1,$2,$3
o[i[++ic] = $1,$2,$3] =$1
}
{    if($2 in o)
o[$2] = $1 OFS $2 OFS $4 OFS $5 OFS $50 OFS $51 OFS $52 OFS $53
}
END {    for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' match.txt M28189_val
awk: cmd. line:8: i[++ic] = $1,$2,$3
awk: cmd. line:8:             ^ syntax error

Hi cmccabe,
Let us go back to post #1 in this thread where you said that you were matching field #1 in file1 with field #2 in file2. Then let us go to post #6 where your new data has all numeric values in field #1 in file1 and all alphabetic values in field #2 in file2. Do you think that part of your problem might be that there are no matching fields?

In my code, the indexes in the array i[] are input line numbers and the values assigned to elements in array i[] are the keys (the field #1 value in file1 which will also be the field #2 value in matching lines in file2) used to lookup values in the array o[]. Since there are no cases in any of your sample input where field #2 in file2 matches fields 1, 2, AND 3 in file1; you get an empty output line for each line in the starting contents of file1.

Given that the format of your input files no longer matches the format described in post #1 in this thread, I have no idea what you are trying to do with the new index values you are using. Maybe if you go back to the start and describe the contents of both input files, the keys used to match lines in the two files, and the fields to be included in the updated file1 for lines that have no matching line in file2 and the fields to be included in the updated file1 for lines that do have a matching line in file2.

If keys in file1 are not unique and you do not want identical output for those lines that have a matching key in file2, you need to clearly describe what output is supposed to be produced for each line in file1 with an identical key.

And, for the record, the standard way to assign a multi-dimensional index value to an array element would be:

Code:

o[i[++ic] = $1 SUBSEP $2 SUBSEP $3] = "whatever you want to print if no match is found for the 3 fields in file2 that match the 1st 3 fields of file1"

Here are a few lines of the tab-delimited input that I use (the actual files are several million lines).

file1

Code:

Match:
68521889    C    T
167099158    A    G
18122506    G    A

Basically, I just am trying to use $1,$2, and $3 as the unique key, and use that to lookup in file2, also tab-delimeted. I apologize for the confusion and appreciate the help. Since my files are rather large I was trying to be brief, but I can see that's no help

awk

Code:

awk '
BEGIN {    FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 FS $2 FS $3] =$1
}
{    if($2 in o)
o[$2] = $1 OFS $2 OFS $4 OFS $5 OFS $50 OFS $51 OFS $52 OFS $53
}
END {    for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' file1 file2

The awk runs but the result is just $1 of file1

Hello cmccabe,

Off course it will give an error because it is allowed to seperate variables inside the array's index not while defining their values(though I am not at all sure what you are trying to do here), so in case you want to save an array's value like above then you could do following like:

Code:

i[++ic] = $1","$2","$3

I would like to request you here, please rephrase your requirement here as it is not clear at all this time what you are trying to do(for me at least), Solutions were given for your previous reuirement, so now if you have a different requirement then please rephrase it with sample Input_file and all rules with expected output too, I hope this helps you.

Thanks,
R. Singh