Re^8: Compare hash with arrays and print

Thanks once again for your input!

When I try running my script with the following test set , it does not print anything in the output files, instead prints the data onto the screen!

>001.b1 gnl|ti|10009
GCTAGTGCTAGCTAGCTAGCATCGATCGAT
>002.b1 gnl|ti|10010
CAGTCAGTCGTAGTGCTAGCTGATGCTCGT
>003.b1 gnl|ti|10011
CGATCGTAGTCGTATCGATGCTGACGTAGG
>004.b1 gnl|ti|10012
CGATGCTAGTCGTAGTGCTAGTGCTATGTC
>005.b1 gnl|ti|10013
CAGTCGTAGTCGATGCTGTATCATAGCGTA
>006.b1 gnl|ti|10014
ACAGTGCTAGCTGATCGTAGCTGAGCGGAG
>007.b1 gnl|ti|10015
AGCTAGCTGATGTCGATGCTGATCGTGATG
>008.b1 gnl|ti|10016
CGATGCTGATGCTGATGCTGTAGCTATACG
>008.g1 gnl|ti|10017
GCTAGCTAGTCGTAGTCGTAGTGTCGTAGG
>009.b1 gnl|ti|10018
CGATGCTAGTCGTAGTCGTAGCTGATGCGT
>010.b1 gnl|ti|10019
CGATCGTAGTCGTAGCTGATGCTGTAGCTG
>010.g1 gnl|ti|10020
CGTAGCTGATCGTAGCGTGACTGTAGCTGG
>011.b1 gnl|ti|10021
CGTAGCTGATGCTGATCGTAGCTAGTCGAT
>011.g1 gnl|ti|10022
CAGCTGATCGTAGCTGATGCTGATGTGTGT
[download]

I thought maybe splitting the header and data might help. But as it turns out, I am not going the right way.

The output I get from the script is:

>001.b1 gnl|ti|10009
GCTAGTGCTAGCTAGCTAGCATCGATCGAT

>002.b1 gnl|ti|10010
CAGTCAGTCGTAGTGCTAGCTGATGCTCGT

>003.b1 gnl|ti|10011
CGATCGTAGTCGTATCGATGCTGACGTAGG

>004.b1 gnl|ti|10012
CGATGCTAGTCGTAGTGCTAGTGCTATGTC

>005.b1 gnl|ti|10013
CAGTCGTAGTCGATGCTGTATCATAGCGTA

>006.b1 gnl|ti|10014
ACAGTGCTAGCTGATCGTAGCTGAGCGGAG

>007.b1 gnl|ti|10015
AGCTAGCTGATGTCGATGCTGATCGTGATG

>008.b1 gnl|ti|10016
CGATGCTGATGCTGATGCTGTAGCTATACG

>008.g1 gnl|ti|10017
GCTAGCTAGTCGTAGTCGTAGTGTCGTAGG

>009.b1 gnl|ti|10018
CGATGCTAGTCGTAGTCGTAGCTGATGCGT

>010.b1 gnl|ti|10019
CGATCGTAGTCGTAGCTGATGCTGTAGCTG

>010.g1 gnl|ti|10020
CGTAGCTGATCGTAGCGTGACTGTAGCTGG

>011.b1 gnl|ti|10021
CGTAGCTGATGCTGATCGTAGCTAGTCGAT

>011.g1 gnl|ti|10022
CAGCTGATCGTAGCTGATGCTGATGTGTGT
[download]

My script for the same is:

       ......
        s/^>//mg;
    my ($name) = /^([^\n]+)/;

        if($hash{$name} == 10){
        select FILE1;
        }
        if($hash{$name} == 20){
        select FILE2;
        }
        if($hash{$name} == 30){
        select FILE3;
        }
        }
    #print ">$_";
    my $output = $_;
    print ">$output\n";
[download]

Thanks again!

Comment on Re^8: Compare hash with arrays and print Select or Download Code

Replies are listed 'Best First'.
Re^9: Compare hash with arrays and print by almut (Canon) on Jul 13, 2010 at 19:25 UTC
When I try running my script with the following test set , it does not print anything in the output files, instead prints the data onto the screen! This is most likely because with `my ($name) = /^([^\n]+)/;` [download] you're extracting the entire header line as `$name` to be used as the hash key, but you have not set up your hash accordingly with keys such as `"001.b1 gnl\|ti\|10009"`. In this case, none of the `select FILE1` statements would execute, so STDOUT (connected to the screen) remains the default output handle for `print`. Note that `^([^\n]+)` would match everything from the beginning of the record up to the first newline, because the character class `[^\n]` says "match any character but a newline" (the `^` within the class negates). Try one of the other suggestions, or adjust the regex as needed.	[reply] [d/l] [select]
Re^10: Compare hash with arrays and print by ad23 (Acolyte) on Jul 13, 2010 at 21:19 UTC
Gosh! I didn't notice that at all. But now I understand! This seem to run perfectly fine with my test data. However my actual data files are huge. Thanks a tonne again almut. I really appreciate your help!	[reply]
Re^10: Compare hash with arrays and print by ad23 (Acolyte) on Jul 14, 2010 at 13:32 UTC
Hi... Since I am comparing my keys from hash, shouldn't it print out the results in a sorted manner? Do I need to use an array to sort these separately? Thanks!!	[reply]


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