Hello I wrote a perl code to match two files. But when the input file is very large, it runs very very long time. How I can shorter the running time by change some code? Thanks in advance for any great help! Best, Yue 

open(IN1,"tmp12") || die "Cannot open this file";

@lines1 = <IN1>;

open(IN2,"donor_82_01.csv") || die "Cannot open this file";

@lines2 = <IN2>;


open(OUT,">tmp12_01") || die "Cannot open this file";

for $item1(@lines1){

    chomp $item1;


    #print OUT $item1,"\t";

@tmp1=split(/\t+/, $item1);


for $item2(@lines2){

    chomp $item2;

@tmp2=split(/\,+/, $item2);

        if ($tmp1[1] eq $tmp2[0]){

            print OUT $tmp1[0],",",$item2;

            last;    

        }

    $i++
}


print OUT "\n";


}


close(IN1);

close(IN2);

close(OUT);

[download]

The file of tmp12 is:


A1BG    ENSG00000121410
A1BG-AS1    ENSG00000268895
A1CF    ENSG00000148584
A2M    ENSG00000175899
A2M-AS1    ENSG00000245105
A2ML1    ENSG00000166535
A2ML1-AS1    ENSG00000256661
A2ML1-AS2    ENSG00000256904
A3GALT2    ENSG00000184389
A4GALT    ENSG00000128274
A4GNT    ENSG00000118017
AAAS    ENSG00000094914
AACS    ENSG00000081760
AADAC    ENSG00000114771
AADACL2    ENSG00000197953
AADACL2-AS1    ENSG00000242908
AADACL3    ENSG00000188984
AADACL4    ENSG00000204518
AADAT    ENSG00000109576
AAGAB    ENSG00000103591
AAK1    ENSG00000115977
AAMDC    ENSG00000087884
AAMP    ENSG00000127837
AANAT    ENSG00000129673
AAR2    ENSG00000131043
AARD    ENSG00000205002
AARS1    ENSG00000090861
AARS2    ENSG00000124608
AARSD1    ENSG00000266967
AASDH    ENSG00000157426
AASDHPPT    ENSG00000149313
AASS    ENSG00000008311
AATBC    ENSG00000215458
AATF    ENSG00000275700
AATK    ENSG00000181409
ABALON    ENSG00000281376
ABAT    ENSG00000183044
ABCA1    ENSG00000165029
ABCA10    ENSG00000154263
ABCA12    ENSG00000144452
ABCA13    ENSG00000179869
ABCA2    ENSG00000107331
ABCA3    ENSG00000167972
ABCA4    ENSG00000198691
ABCA5    ENSG00000154265
ABCA6    ENSG00000154262
ABCA7    ENSG00000064687
ABCA8    ENSG00000141338
ABCA9    ENSG00000154258

[download]

The file of donor_82_01.csv is:

,AAACCTGAGCGTTTAC-1,AAACCTGAGTCGCCGT-1,AAACCTGGTAGGACAC-1,AAACCTGGTGCC
+TTGG-1,AAACCTGGTTCAGCGC-1
ENSG00000148584,0,0,0,0,0
ENSG00000237613,0,0,0,0,0
ENSG00000186092,0,0,0,0,0
ENSG00000118017,0,0,0,0,0
ENSG00000239945,0,0,0,0,0
ENSG00000205002,0,0,0,0,0
ENSG00000090861,0,0,0,0,0
ENSG00000279928,0,0,0,0,0
ENSG00000181409,0,1,0,1,0
ENSG00000228463,0,0,0,0,0
ENSG00000236743,0,0,0,0,0
ENSG00000165029,0,0,0,0,0
ENSG00000144452,0,0,0,0,0
ENSG00000278566,0,0,0,0,0
ENSG00000179869,0,0,0,0,0
ENSG00000235146,0,0,0,0,0
ENSG00000154262,0,0,0,0,0
ENSG00000141338,0,0,0,0,0
ENSG00000154258,0,0,0,0,0

[download]

In reply to match two files by yueli711

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.