Wednesday, March 23, 2016

Remove multiple consecutive characters in a file - example of removing multiple space separators

This may come handy to all of those who like to paste tab separated files into nano, and then tabs get converted into series of spaces. To convert back to a single space delimiter use tr with a squeeze -s option:

mpjanic@valkyr:~/REBUTTAL_F1000RESEARCH$ cat tmp
rs1951351       14      91832947        G       A       7.1E-02 1.04    1.00    1.08    9580    53810
rs4900109       14      91833144        T       G       1.6E-01 1.03    0.99    1.07    9580    53810
rs4904864       14      91834272        G       A       6.6E-02 1.04    1.00    1.08    9580    53810
rs1885193       14      91835107        G       A       3.3E-01 1.02    0.98    1.05    12171   56862
rs12892379      14      91836910        T       C       6.6E-02 1.04    1.00    1.08    9580    53810
rs1957283       14      91837433        A       G       5.9E-01 1.02    0.95    1.09    9580    53810
rs4904866       14      91838256        T       C       1.5E-01 1.03    0.99    1.07    9580    53810
rs7145248       14      91839145        T       C       5.5E-01 1.02    0.96    1.09    9580    53810
rs12434570      14      91840166        T       C       5.6E-01 1.02    0.96    1.09    9580    53810
rs8021744       14      91843048        T       C       5.6E-01 1.02    0.96    1.09    9580    53810
rs12896399      14      91843416        T       G       1.3E-01 1.03    0.99    1.07    9580    53810
rs746588        14      91845133        T       C       5.7E-01 1.02    0.95    1.09    9580    53810
rs11622569      14      91845155        A       T       5.7E-02 1.04    1.00    1.08    9580    53810
rs746586        14      91845720        T       C       1.2E-01 1.03    0.99    1.07    9580    53810
rs1075830       14      91845915        C       A       5.1E-01 1.01    0.98    1.05    12171   56862
rs8018017       14      91846171        C       G       7.2E-01 1.01    0.95    1.07    11223   52455
rs941799        14      91846578        T       C       1.2E-01 1.03    0.99    1.07    9580    53810
rs1885194       14      91847215        C       T       1.2E-01 1.03    0.99    1.07    9580    53810
rs10484035      14      91848310        C       T       2.6E-01 1.02    0.99    1.06    12171   56862
rs17128162      14      91850110        A       G       3.0E-01 1.06    0.95    1.19    3788    20758
rs17184180      14      91850140        A       T       1.2E-01 1.03    0.99    1.07    9580    53810
mpjanic@valkyr:~/REBUTTAL_F1000RESEARCH$ tr -s " " <tmp >tmp2
mpjanic@valkyr:~/REBUTTAL_F1000RESEARCH$ cat tmp2
rs1951351 14 91832947 G A 7.1E-02 1.04 1.00 1.08 9580 53810
rs4900109 14 91833144 T G 1.6E-01 1.03 0.99 1.07 9580 53810
rs4904864 14 91834272 G A 6.6E-02 1.04 1.00 1.08 9580 53810
rs1885193 14 91835107 G A 3.3E-01 1.02 0.98 1.05 12171 56862
rs12892379 14 91836910 T C 6.6E-02 1.04 1.00 1.08 9580 53810
rs1957283 14 91837433 A G 5.9E-01 1.02 0.95 1.09 9580 53810
rs4904866 14 91838256 T C 1.5E-01 1.03 0.99 1.07 9580 53810
rs7145248 14 91839145 T C 5.5E-01 1.02 0.96 1.09 9580 53810
rs12434570 14 91840166 T C 5.6E-01 1.02 0.96 1.09 9580 53810
rs8021744 14 91843048 T C 5.6E-01 1.02 0.96 1.09 9580 53810
rs12896399 14 91843416 T G 1.3E-01 1.03 0.99 1.07 9580 53810
rs746588 14 91845133 T C 5.7E-01 1.02 0.95 1.09 9580 53810
rs11622569 14 91845155 A T 5.7E-02 1.04 1.00 1.08 9580 53810
rs746586 14 91845720 T C 1.2E-01 1.03 0.99 1.07 9580 53810
rs1075830 14 91845915 C A 5.1E-01 1.01 0.98 1.05 12171 56862
rs8018017 14 91846171 C G 7.2E-01 1.01 0.95 1.07 11223 52455
rs941799 14 91846578 T C 1.2E-01 1.03 0.99 1.07 9580 53810
rs1885194 14 91847215 C T 1.2E-01 1.03 0.99 1.07 9580 53810
rs10484035 14 91848310 C T 2.6E-01 1.02 0.99 1.06 12171 56862
rs17128162 14 91850110 A G 3.0E-01 1.06 0.95 1.19 3788 20758
rs17184180 14 91850140 A T 1.2E-01 1.03 0.99 1.07 9580 53810

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