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Full Discussion: Comparing two files
Top Forums Shell Programming and Scripting Comparing two files Post 302382983 by genehunter on Sunday 27th of December 2009 10:13:10 PM
Old 12-27-2009
Quote:
Originally Posted by danmero
Base on original data sample:
Code:
# cat f1
CHR             SNP   A1   A2          MAF  NCHROBS
    0   SNP_A-8414268    A    G       0.1522     5354
   1      rs12565286    C    G      0.04139     5340
   1       rs2980319    A    T       0.1503     5362
   1       rs2980300    T    C       0.1773     5346
   1       rs6603781    A    G       0.1149     5346
# cat f2
CHR             SNP   A1   A2          MAF  NCHROBS
   1       rs2980319    A    T       0.1503     4252
   1       rs2980300    T    C       0.1273     4546
   1       rs6603781    G    A       0.0249     4546
# # awk 'NR==FNR{$1=$1;a[$2]=$0;b[$2]=$3;next}b[$2]==$3||b[$2]==$4{print $2 > "nonambig.txt"}$1!~"[A-Z]"{$1=a[$2];print}' f1 f2
1 rs2980319 A T 0.1503 5362 rs2980319 A T 0.1503 4252
1 rs2980300 T C 0.1773 5346 rs2980300 T C 0.1273 4546
1 rs6603781 A G 0.1149 5346 rs6603781 G A 0.0249 4546
# cat nonambig.txt
SNP
rs2980319
rs2980300
rs6603781

Can you kindly help by interpreting this code, that will help me understand it. It would be very helpful and I would appreciate it very much.
Code:
 awk 'NR==FNR{$1=$1;a[$2]=$0;b[$2]=$3;next}b[$2]==$3||b[$2]==$4{print $2 > "nonambig.txt"}$1!~"[A-Z]"{$1=a[$2];print}' f1 f2

 

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Msgcat(3pm)						User Contributed Perl Documentation					       Msgcat(3pm)

NAME
Locale::Msgcat - Perl extension for blah blah blah SYNOPSIS
use Locale::Msgcat; $cat = new Locale::Msgcat; $rc = $cat->catopen(name, oflag); $msg = $cat->catgets(set_number, message_number, string); $rc = $cat->catclose(); DESCRIPTION
The Locale::Msgcat module allows access to the message catalog functions which are available on some systems. A new Locale::Msgcat object must first be created for each catalog which has to be open at a given time. The catopen operation opens the catalog whose name is given as argument. The oflag can be either 0 or NL_CAT_LOCALE (usually 1) which is the recommended value. The catgets message retrieves message_number for the set_number message set, and if not found returns string. The catclose function should be used when access to a catalog is not needed anymore. EXAMPLES
use Locale::Msgcat; $cat = new Locale::Msgcat; unless ($cat->catopen("whois.cat", 1)) { print STDERR "Can't open whois catalog. "; exit(1); } printf "First message, first set : %s ", $cat->catgets(1, 1, "not found"); unless ($cat->catclose()) { print STDERR "Can't close whois catalog. "; exit(1); } The above example would print the first message from the first message set found in the whois catalog, or if not found it would print "not found". AUTHOR
Christophe Wolfhugel, wolf@pasteur.fr SEE ALSO
catopen(3), catclose(3), catgets(3), perl(1). perl v5.14.2 1999-11-15 Msgcat(3pm)
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