in reply to How to make a hash to evaluate columns between large datasets

Hello Friend,

Just like you, I'm a beginner in this language,

apparently this is a computationally difficult task and can be optimized with the use of threads, I will try to do an implementation like this but, please, answer me a long input file

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Re^2: How to make a hash to evaluate columns between large datasets
by Laurent_R (Canon) on Aug 23, 2018 at 16:46 UTC
    Hi rozcovo,

    IMHO, this is not a computationally difficult task. It really boils down to first loading the reference data into a hash and, then, read a single input file and lookup into the hash. Quite simple. And since there is apparently only one data input file, I doubt that using threads will bring any performance benefit.

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Re^2: How to make a hash to evaluate columns between large datasets
by rambosauce (Novice) on Aug 23, 2018 at 20:22 UTC

    Here is a head from my input file, and the columns are the following information: ID, strand, chromosome, start, sequence, quality score, and positions in the genome. The last two are unnecessary for what I need, so the script is only defining strand, chromosome, start, and length of sequence to find the end. I use these to then parse through the reference file to grab the info in the last column of the reference, and append most of the info from the original input.

    I chose this header as it has some of info I hope to overlook, such as chromosome missing in the reference (line 1) and different sites on the same chromosome (lines 3 and 4).

    3-51568    +    HSV1_17    9285    TGGGCAAACACTTGGGGACTG    IIIIIIIIII
+IIIIIIIIIII    0
2-70337    +    KI270733.1    135235    TCGCTGCGATCTATTGAAAGTCAGCCCTCG
+ACACAAGGGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4  
+  
2-70337    +    21    8446166    TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAG
+GGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4    
2-70337    +    21    8218896    TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAG
+GGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4    
2-70337    +    GL000220.1    118372    TCGCTGCGATCTATTGAAAGTCAGCCCTCG
+ACACAAGGGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4  
+  
2-70337    +    21    8401935    TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAG
+GGTTTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    4    
1-130983    +    2    32916254    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5    
1-130983    +    2    32916255    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5    
1-130983    +    2    32916256    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5    
1-130983    +    2    32916257    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    IIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    5

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