compare lines in two files and extract common line plus more info 2

[GiovanniC]

Hi,

I'm trying to do the usual compare two files and pull out the common field, but in addition to that, I want some additional information from file two to be extracted as well. Tried a few different approaches, but think its time to ask the experts.

I've placed an example of the two files at this link

http://wwwdev.scu.edu.au/research/cpcg/question/example.doc

Basically, I want to compare the two files, pull out the common heading (which commences with '>') and also the additional information which is listed in any number of rows below this heading until the next header.

Hope someone has a solution. Many thanks,

Giovanni

 

[iribach]

man comm diff cmp sort

 

[GiovanniC]

iribach

Thanks for the very quick response and your confidence in my abilities ... but I'm afraid I'm not that far advanced to take the suggestion and put it into a workable script :-(

 

[iribach]

giovanni, parli la mia lingua ?
comm fileA fileB
gives you a 3 cols output
col1 items unique in file A
col2 items unique in file B
col3 items common in file A and B
are you on unix?

 

[GiovanniC]

iribach

I assume you asked me what language I speak ... only English unfortunately.

I can compare the two files and pull out the common item, but I don't know how to pull out the extra information from file2. I'm on UNIX.

Thanks

 

[iribach]

yes, a giovanni speaking only english is
seldom.
you have 2 ways:
use native *nix tools piping
g.e: aa|bb|cc|dd
or
write a own prog in awk, perl, c or better.

 

[GiovanniC]

I'm using gawk and I already have the scripts to compare the two files to pull out the common field. The example that I have posted in the document file shows that file2.txt has additional rows of information below the common field. It is this additional information that I am trying to capture and do not know how to write a script for.

 

[PHV]

Something like this ?
awk '
BEGIN{while((getline<"File1.txt")>0)++a[$0]}
/^>/{flg=a[$0]+0}
flg
' File2.txt
Feel free to explain better the expected result

Hope This Helps, PH.
Want to get great answers to your Tek-Tips questions? Have a look at FAQ219-2884 or FAQ222-2244

 

[GiovanniC]

Thanks PHV, I'll try it out when I get back to work in a couple of weeks - but for now, I'm off to a long awaited holiday

 

[GiovanniC]

Hi PHV,

I've just tried your suggestion but the script doesn't run. Couldn't work out what the problem was. But basically, I have two files. fileA contains the lines:

>TA0001
>TA0002
>TA0006
>TA0008
>TA0012

fileB looks like this:

>TA0001 some other information
GATAGGATTAGATCGATGATGATAGAGA
TAGATTABGATAGAGTATAGGATAGAGA
TAGATAGATATATAGATATAATATATA
>TA0002 some other information
GGATTAGATCGATGATGATATAGAGTAT
AGATTABGATAGAGTATAGGATAG
>TA0003 some other information
GATAGGATTAGATCGATGATGATAGAGA
TAGATTABGATAGAGTATAGGATAGAGA
TAGATAGATATATAGATATAATATATA
AGATTABGATAGAGTATAGGATAG
>TA0004 some other information
GATAGGATTAGATCGATGATGATAGAGA
TAGATAGATTABGA
and so on and so forth in numerical order for the tag lines.

What I want to do is, compare the individual lines from fileA (all start with '>') with the lines in fileB that start with '>'. If the line in fileA matches with $1 of a line in fileB starting with '>', I want to pick out that line from fileB and also the sequence information below that line in fileB until the next line that starts with the '>' character. I hope I am making sense.

Thanks for any help anyone can provide.

 

[mikevh]

This seems to work with the example you posted.
I don't write much awk these days, so this code may not be the most elegant.

#!gawk

# Get first file into array.
NR == FNR {
    arr[$0] = 1
    next
}
# If $1 exists in array, set mat to 1, else set it to 0.
$1 ~ />/ {
    if (arr[$1]) 
        {mat = 1} 
    else 
        {mat = 0}
}
# Print if mat is 1.
mat

[b]Output:[/b]
>TA0001 some other information
GATAGGATTAGATCGATGATGATAGAGA
TAGATTABGATAGAGTATAGGATAGAGA
TAGATAGATATATAGATATAATATATA
>TA0002 some other information
GGATTAGATCGATGATGATATAGAGTAT
AGATTABGATAGAGTATAGGATAG

HTH

 

[CaKiwi]

Try modifying PHV's script as follows:

BEGIN{while((getline<"File1.txt")>0)++a[$0]}
/^>/{flg=a[$1]}
flg

CaKiwi

 

[GiovanniC]

Thanks everyone who provided suggestions ... the combination of them has helped me solve my little problem.

Cheers