in reply to Re^6: First foray into Perl
in thread First foray into Perl

Hi, thank you very much for looking at this.

The spacing change was inadvertent, not quite sure what happened there.

The last three lines are the start of another record and can be ignored/removed. I do have another version of the record file with records delimited by a double space, thusly: 


TF      Unknown
TF Name Unknown
Gene    ENSG00000113916
Motif   ENSG00000113916___1|4x3
Family  C2H2 ZF
Species Homo_sapiens
Pos     A       C       G       T
1       0.427379        0.0647991       0.288826        0.218996
2       0.201974        0.139791        0.35254 0.305695
3       0.11714 0.118042        0.143884        0.620934
4       0.637331        0.0996546       0.228428        0.0345867
5       0.0971289       0.591289        0.134781        0.176801
6       0.0715039       0.0237142       0.0432674       0.861514
7       0.73769 0.117011        0.059703        0.0855963
8       0.0728444       0.00877167      0.877166        0.0412175
9       0.959269        0.0131077       0.0159611       0.0116621
10      0.612865        0.057845        0.0583267       0.270963


TF      Unknown
TF Name Unknown
Gene    ENSG00000161940
Motif   ENSG00000161940___1|1x3
Family  C2H2 ZF
Species Homo_sapiens
Pos     A       C       G       T
1       0.614704        0.122914        0.125116        0.137266
2       0.0954267       0.010422        0.851317        0.0428343
3       0.959146        0.00959146      0.0112618       0.0200008
4       0.91149 0.0146678       0.0135794       0.0602625
5       0.67464 0.0388388       0.13716 0.149361
6       0.104655        0.0579394       0.804166        0.0332392
7       0.789171        0.102902        0.0490883       0.0588389
8       0.776513        0.0273768       0.144501        0.0516094
9       0.130657        0.06051 0.0793659       0.729467
10      0.626753        0.0648533       0.143976        0.164418

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Thanks again!

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Re^8: First foray into Perl
by AnomalousMonk (Archbishop) on Mar 26, 2014 at 00:38 UTC

    Here's a version for double-newline record separators, still no tabs, only 1+ spaces separate fields. Included new  ENSG00000113916___1|4x3 motif in test data. Most of notes and caveats of Re: First foray into Perl still apply.

    Read more... (6 kB)
[reply]
[d/l]
[select]

      Wow - Thanks so much for your efforts on this. Really appreciated! I'm still working on using it to extract sequences from my 15,000 record file so can't state success quite yet but I'll let you know.

      Cheers!

[reply]

        A minor update: This version of the loop may be a bit nicer (tested): 

        # works -- a while loop might be more efficient/elegant
MAX_BASES:
while (@base_values) {  # @base_values is consumed
    $max_bases .= $_->[1] for  # append base of each max
        reduce { $a->[0] > $b->[0] ? $a : $b }      # max in group
        map [ shift(@base_values), $_ ], @base_ord  # groups of n
        ;
    }

        [download]
[reply]
[d/l]
        Perl may seem foreign if you are new to it - Learning Perl as an introduction, and Perl Cookbook are 2 good sources on Perl.

        Don't get discouraged as I am now trying to learn a new GUI, Xojo which uses a form of the Visual Basic language and to learn all the new ways of string matching, working with arrays and converting numbers to printable strings is challenging. I will probably need to get a book that explains it all. Just doing the beginners' tutorial is difficult.

[reply]

In Section Seekers of Perl Wisdom