in reply to Re^5: First foray into Perl
in thread First foray into Perl

Another Note: I just noticed that the latest example data here end with the following three lines: 

TF      Unknown
TF Name Unknown
Gene    ENSG00000113916

[download]
These look like the start of another record and screw up parsing. Is this the intended and necessary ending of a full set of data records? It's a problem if so. (The absence of an unambiguous multi-line record delimiter is another problem, but can be finessed if necessary.)

Also: Any word yet on the tab-versus-spaces field delimiter question posted above?

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Re^7: First foray into Perl
by LostWeekender (Novice) on Mar 25, 2014 at 21:48 UTC

    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

    [download]

    Thanks again!

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[d/l]

      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)
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[d/l]
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        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!

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