Hi perl monks, I would like to combine the information from 3 tab-delimited files. Some of the entries are duplicated, so I would like to select one of these from each file based on specific criteria

eg:

File1:

>3841    29    58.786702607127    GAGTAGTTCATAATAAAGAGGAGGCTGGT    
>3841    28    58.3143841442903    AGTAGTTCATAATAAAGAGGAGGCTGGT    
>486    26    59.8238809443041    CATTTTTCCTGAGCGTTTTCCTGAGC    
>486    25    59.1450485783588    ATTTTTCCTGAGCGTTTTCCTGAGC    
>486    24    58.9556227674582    TTTTTCCTGAGCGTTTTCCTGAGC    
>486    23    58.6081353592492    TTTTCCTGAGCGTTTTCCTGAGC    
>486    22      58.2296488444454    TTTCCTGAGCGTTTTCCTGAGC    
>136    25    Tm=59.8064145079347    CGAACAGAGGTCTCATGGAGAAACG

[download]

File2:

>3841    29    58.5812405420724    GAGTAGTTCATAATAAAGAGGAGGCTGGA    
>3841    28    58.0989000498791    AGTAGTTCATAATAAAGAGGAGGCTGGA    
>486    26    58.9706961902307    CATTTTTCCTGAGCGTTTTCCTGAGT    
>486    25    58.2353328662615    ATTTTTCCTGAGCGTTTTCCTGAGT    
>486    24    58.0079403206259    TTTTTCCTGAGCGTTTTCCTGAGT    
>136    25    59.2231929175504    CGAACAGAGGTCTCATGGAGAAACA    
>253    36    59.6147860412319    CAGAGATGATTTGTGCATTATAATTGTAATTTGGGT

[download]

File3:

>3841    26    58.289789463114    CCAGGTTATTTATTTCAGCGGGAACT    
>486    23    58.6732344878087    GCAAATGGCTCTAAGGATCAGCC    
>294    21    58.8403250231655    GTCGGAGCTCTCTCAGAACCC    
>253    25    58.3051993710611    CACTCGAGTTGCAGTTATGTTCCTC    
>287    21    59.5292339759331    TCCTTAGCCAGACGAACACGC    
>544    21    59.5408471700017    TACAGCAGGTCAACCCGTTCG    
>856    19    58.7421506440351    GGTGAGGATGTCGCCCTCA

[download]

So the script would search through File 3 line by line and compare column1 (the >number with the entries in column1 of files 1 and 2). If there are duplicate >number entries, a single >contig entry from files 1 and 2 would be selected based on the relative value to the number in column 3.

For example the first entry of File 3 is >3841 with a value of 58.289789463114

File 1 has two entries for >3841 and the second has a value in column 3, closest to the File 3 entry (58.3143841442903) so this would be selected.

File 2 also has two entries for >3841 and in this case the second entry would be selected as the value in column 3 (58.0989000498791) is closest to the column 3 value in File3.

The script would then print out a tab de-limited file with the following format:

>3841   AGTAGTTCATAATAAAGAGGAGGCTGGT   AGTAGTTCATAATAAAGAGGAGGCTGGA   
+CCAGGTTATTTATTTCAGCGGGAACT
>486   TTTTCCTGAGCGTTTTCCTGAGC   CATTTTTCCTGAGCGTTTTCCTGAGT   GCAAATGG
+CTCTAAGGATCAGCC

[download]

Any help from the monks on this would be appreciated.

In reply to Combining 3 files by garyboyd

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