I need to make the following script more efficient and faster. It works fine with a few lines in the file but if you are dealing with 6.0 Million lines it will take forever.
I am trying to rename the IDs in the second column of file 2. file 1 contains the conversion table.
File.1 conversion table in a tab delimited format CGP_A0000000001 AAAA CGP_A0000000002 AAAB CGP_A0000000003 AAAC CGP_A0000000004 AAAD CGP_A0000000005 AAAE CGP_A0000000006 AAAF CGP_A0000000007 AAAG CGP_A0000000008 AAAH CGP_A0000000009 AAAI CGP_A0000000010 AAAJ CGP_A0000000011 AAAK CGP_A0000000012 AAAL CGP_A0000000013 AAAM CGP_A0000000014 AAAN CGP_A0000000015 AAAO CGP_A0000000016 AAAP CGP_A0000000017 AAAQ CGP_A0000000018 AAAR CGP_A0000000019 AAAS CGP_A0000000020 AAAT CGP_A0000000021 AAAU CGP_A0000000022 AAAV
File.2 has three column and the 2nd needs to be replaced, using conver +sion table of (File1) 3998122 CGP_A0000000001 13 5877245 CGP_A0000000001 17 3637488 CGP_A0000000001 19 3998162 CGP_A0000000001 21 638421 CGP_A0000000001 23 2395226 CGP_A0000000001 25 3094278 CGP_A0000000001 27 2029460 CGP_A0000000001 29 1406937 CGP_A0000000001 31 2054853 CGP_A0000000001 35 4182290 CGP_A0000000001 37 3784069 CGP_A0000000002 13 6477860 CGP_A0000000002 17 394789 CGP_A0000000002 19 5095549 CGP_A0000000002 21 692543 CGP_A0000000002 23 5446227 CGP_A0000000002 25 1546807 CGP_A0000000002 27 1741167 CGP_A0000000002 29 1187972 CGP_A0000000002 31 1600142 CGP_A0000000002 33 1833098 CGP_A0000000002 35 1770403 CGP_A0000000003 1353 3254322 CGP_A0000000003 1355 6152600 CGP_A0000000003 1357 3195476 CGP_A0000000003 1361 3108815 CGP_A0000000003 1371 77684 CGP_A0000000003 1373 3269969 CGP_A0000000003 1375 3259137 CGP_A0000000003 1377 6502805 CGP_A0000000003 1379 5899118 CGP_A0000000003 1381 5417394 CGP_A0000000003 1383 806606 CGP_A0000000003 1385 1662014 CGP_A0000000003 1387 6490426 CGP_A0000000003 1389 6206360 CGP_A0000000003 1391
the RESULT file is the same as the second file but the the second colu +mn has the equivalent IDs from 2nd column of file 1 3998122 AAAA 13 5877245 AAAA 17 3637488 AAAA 19 3998162 AAAA 21 638421 AAAA 23 2395226 AAAA 25
#!/usr/bin/perl -w use strict; use warnings; use vars qw(%origins); if( @ARGV < 3){ print "usage: A message here\n"; exit 0; } open(INPUT1,$ARGV[0]) || die "Cannot open file \"$ARGV[0]\""; #Orginal + IDs and four letter codes open(INPUT2,$ARGV[1]) || die "Cannot open file \"$ARGV[1]\""; #Orginal + IDs in the second column open(RESULTS,">$ARGV[2]")|| die "Cannot open the Results file \"$ARGV[ +2]\""; # Origanl IDs will change to four letter code my %origins; while (<INPUT1>) { chomp; my @columns = split '\t'; $origins{$columns[0]} = $columns[1]; } close(INPUT1); while (<INPUT2>) { chomp; (my $bioC, my $contig_id , my $pip) = split("\t", $_); for my $oKey (sort keys %origins) { my $origin = $origins{$oKey}; if ($contig_id eq $oKey){ print RESULTS "$bioC\t$origin\t$pip\n"; #print "$bioC\t$origin\t$pip\n"; } } } close(INPUT2); close(RESULTS);
In reply to Make my script faster and more efficient by sesemin
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