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Full Discussion: merge multiple tables with perl
Top Forums Shell Programming and Scripting merge multiple tables with perl Post 302564066 by durden_tyler on Wednesday 12th of October 2011 06:22:22 PM
Old 10-12-2011
Maybe something like this?

Code:
$
$
$ perl -F"\t" -lane 'BEGIN {@hdr = qw(chromo pos ref
                                    alleles.SampleA refAllele.SampleA refCount.SampleA refFreq.SampleA
                                    altAllele.SampleA altCount.SampleA altFreq.SampleA
                                    alleles.SampleB refAllele.SampleB refCount.SampleB refFreq.SampleB
                                    altAllele.SampleB altCount.SampleB altFreq.SampleB
                                    alleles.SampleC refAllele.SampleC refCount.SampleC refFreq.SampleC
                                    altAllele.SampleC altCount.SampleC altFreq.SampleC
                                    alleles.SampleD refAllele.SampleD refCount.SampleD refFreq.SampleD
                                    altAllele.SampleD altCount.SampleD altFreq.SampleD)
                           }
                     $x{join"\t",@F[0..2]}.="\t".join"\t",@F[3..9];
                     END
                     {
                       print join " ", @hdr;
                       foreach $k (sort keys %x) {print "$k\t$x{$k}" if $k !~ /chromo/}
                     }' samplea sampleb samplec sampled
chromo pos ref alleles.SampleA refAllele.SampleA refCount.SampleA refFreq.SampleA altAllele.SampleA altCount.SampleA altFreq.SampleA alleles.SampleB refAllele.SampleB refCount.SampleB refFreq.SampleB altAllele.SampleB altCount.SampleB altFreq.SampleB alleles.SampleC refAllele.SampleC refCount.SampleC refFreq.SampleC altAllele.SampleC altCount.SampleC altFreq.SampleC alleles.SampleD refAllele.SampleD refCount.SampleD refFreq.SampleD altAllele.SampleD altCount.SampleD altFreq.SampleD
chr1    30146   A               A       A       31      100     NA      0       NA      A       A       10      100     NA      0       NA      A    NA0
chr1    55217   G               G       G       2       100     NA      0       NA      G       G       2       100     NA      0       NA      A/G  NA0
chr1    55223   C               C       C       2       100     NA      0       NA      T/C     0       0       T       4       57              C    NA0
chr1    55987   C               C       C       19      100     NA      0       NA      C       C       8       100     NA      0       NA      C    NA0
chr1    56065   T               T       T       18      90      NA      2       NA
chr1    62138   T               T       T       114     100     NA      0       NA      C       0       0       C       10      100             T/C  100
chr1    62233   A               A       A       110     100     NA      0       NA      A       A       34      100     NA      0       NA      G/A  NA0
chr1    64310   A               A       A       64      100     NA      0       NA      A       A       37      100     NA      0       NA      A    NA0
chr1    64321   A               A       A       17      100     NA      0       NA      A       A       9       100     NA      0       NA      C    100
chr1    64377   A               A       A       56      98      NA      1       NA      A       A       27      100     NA      0       NA      A    NA0
chr1    65570   A               C       0       0       C       2       100             A       A       3       100     NA      0       NA
chr1    66577   T               T       T       45      100     NA      0       NA
$
$
$
$

tyler_durden
 

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LEARN ABOUT DEBIAN

tm::coverage

TM::Coverage(3pm)					User Contributed Perl Documentation					 TM::Coverage(3pm)

NAME

       TM::Coverage - Topic Maps, Code Coverage

DESCRIPTION

       This auxiliary package keeps track of the code coverage. Probably quite irrelevant for a user.

       Automatically generated for TM (1.44).

	  ---------------------------- ------ ------ ------ ------ ------ ------ ------
	  File				 stmt	bran   cond    sub    pod   time  total
	  ---------------------------- ------ ------ ------ ------ ------ ------ ------
	  blib/lib/TM.pm		 96.4	84.5   58.0   93.7   90.6   27.5   89.6
	  blib/lib/TM/Analysis.pm	100.0	90.9	n/a  100.0  100.0    0.0   97.5
	  blib/lib/TM/AsTMa/Fact.pm	100.0	 n/a	n/a  100.0    n/a    0.0  100.0
	  blib/lib/TM/AsTMa/Fact2.pm	100.0	 n/a	n/a  100.0    n/a    0.0  100.0
	  blib/lib/TM/Bulk.pm		 76.8	71.4   62.5   85.7  100.0    0.0   75.3
	  blib/lib/TM/CTM/CParser.pm	 65.6	34.3   31.0   84.6    0.0    1.6   52.5
	  blib/lib/TM/CTM/Parser.pm	 90.9	50.0	n/a  100.0    0.0    0.0   79.4
	  blib/lib/TM/DM.pm		100.0	65.0   66.7  100.0    n/a    0.0   96.5
	  blib/lib/TM/Graph.pm		 99.1	88.5	n/a  100.0  100.0    0.0   97.4
	  blib/lib/TM/Index.pm		100.0	80.0   60.0  100.0   83.3    0.3   87.8
	  .../Index/Characteristics.pm	100.0  100.0	n/a  100.0    0.0    0.0   97.0
	  blib/lib/TM/Index/Match.pm	 98.5	87.5	n/a  100.0  100.0    0.5   97.6
	  blib/lib/TM/LTM/CParser.pm	 84.9	45.3   42.7   98.2    0.0    0.2   67.8
	  blib/lib/TM/LTM/Parser.pm	 95.7	62.5   50.0  100.0    0.0    0.0   87.1
	  blib/lib/TM/Literal.pm	 45.8	 0.0   11.8   30.0    0.0    0.4   24.2
	  blib/lib/TM/MapSphere.pm	 96.5	84.6   68.8  100.0  100.0    0.0   91.7
	  .../TM/Materialized/AsTMa.pm	100.0	 n/a	n/a  100.0    0.0    0.0   95.5
	  ...ib/TM/Materialized/LTM.pm	100.0	 n/a	n/a  100.0    0.0    0.0   95.5
	  .../TM/Materialized/MLDBM.pm	100.0	83.3	n/a  100.0    0.0    0.0   92.6
	  ...b/TM/Materialized/Null.pm	100.0	 n/a	n/a  100.0    n/a    0.0  100.0
	  ...TM/Materialized/Stream.pm	100.0  100.0  100.0  100.0    0.0    0.0   96.0
	  ...ib/TM/Materialized/XTM.pm	100.0	 n/a	n/a  100.0    0.0    0.0   96.7
	  blib/lib/TM/PSI.pm		100.0	 n/a	n/a  100.0    n/a    0.0  100.0
	  blib/lib/TM/QL.pm		 91.4	61.5   66.7  100.0   50.0    0.1   83.9
	  blib/lib/TM/QL/CParser.pm	 76.2	42.4   41.9   90.3    0.0    9.1   62.0
	  blib/lib/TM/QL/PE.pm		 83.8	77.3   80.0   91.7    0.0   52.5   80.5
	  blib/lib/TM/QL/TS.pm		 65.2	35.4   27.8   70.8   53.3    2.4   56.9
	  blib/lib/TM/ResourceAble.pm	 88.1	87.5	n/a  100.0  100.0    0.0   90.0
	  .../TM/ResourceAble/MLDBM.pm	100.0	75.0	n/a  100.0    0.0    0.0   94.2
	  blib/lib/TM/Serializable.pm	 94.9	65.6  100.0  100.0  100.0    0.0   84.1
	  .../TM/Serializable/AsTMa.pm	 99.1	87.9   66.7  100.0  100.0    0.0   94.2
	  ...TM/Serializable/Dumper.pm	100.0	 n/a	n/a  100.0    0.0    0.0   93.5
	  ...ib/TM/Serializable/LTM.pm	 94.1	 n/a	n/a   83.3  100.0    0.0   92.0
	  ...ib/TM/Serializable/XTM.pm	 96.3	85.2   72.9  100.0  100.0    0.2   91.5
	  .../lib/TM/Synchronizable.pm	100.0	75.0  100.0  100.0  100.0    0.0   97.2
	  ...M/Synchronizable/MLDBM.pm	100.0	50.0	n/a  100.0    0.0    0.0   89.3
	  ...nchronizable/MapSphere.pm	100.0	63.6   64.3  100.0  100.0    0.0   88.6
	  ...TM/Synchronizable/Null.pm	100.0	 n/a	n/a  100.0    0.0    0.0   87.5
	  blib/lib/TM/Tau.pm		100.0	91.7   80.0  100.0    0.0    0.0   95.6
	  blib/lib/TM/Tau/Federate.pm	 63.2	39.3	n/a   62.5   27.3    0.0   54.5
	  blib/lib/TM/Tau/Filter.pm	100.0	91.7   66.7  100.0   50.0    0.0   90.0
	  .../TM/Tau/Filter/Analyze.pm	100.0	 n/a	n/a  100.0  100.0    0.0  100.0
	  blib/lib/TM/Tree.pm		100.0	57.1   44.4  100.0   66.7    0.0   88.0
	  blib/lib/TM/Utils.pm		100.0	50.0	n/a  100.0    0.0    0.0   89.3
	  ...ib/TM/Utils/TreeWalker.pm	100.0  100.0	n/a  100.0    0.0    0.0   96.0
	  ...ib/TM/Workbench/Plugin.pm	100.0	 n/a	n/a  100.0    0.0    0.0   75.0
	  ...M/Workbench/Plugin/Tau.pm	 87.5	50.0	n/a   80.0    0.0    0.0   73.1
	  yapp/astma-fact.yp		 96.9	91.5   73.3   97.8    0.0    4.8   92.7
	  yapp/astma2-fact.yp		 97.4	91.6   58.3  100.0    0.0    0.2   91.6
	  Total 			 76.8	45.2   40.2   91.2   57.0  100.0   63.8
	  ---------------------------- ------ ------ ------ ------ ------ ------ ------

SEE ALSO

       TM

COPYRIGHT AND LICENSE

       Copyright 200[8] by Robert Barta, <drrho@cpan.org>

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.10.1							    2008-10-05							 TM::Coverage(3pm)
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