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Top Forums UNIX for Dummies Questions & Answers Replace period in a tab delimited file to a number Post 302949772 by genehunter on Thursday 16th of July 2015 01:00:08 AM
Old 07-16-2015
Linux Replace period in a tab delimited file to a number

I have a file like this.
It is tab delimited.
Unfortunately, the missing data was filled in with a period "." (see the leading lines 1-5 columns)
I want to substitute the periods for misisng data with an integer "-999".
however, I do not want the global replace to change the other periods seen in the file.
for e.g, c.17_18del or p.P6fs should stay without change.
awk or sed preferred, but also willing to try other simple solutions.
Have only rudimentary bash programming skills.
Attached an example file.
Thanks
~ GH
Code:
1kgp_all    1kgp_amr    1kgp_eur    esp6500siv2_aa    esp6500siv2_all    esp6500siv2_ea    cosmic70    AAChange.ensGene    AAChange.refGene    FS
.    .    .    .    .    .    ID    EN134250:ENST00000256646:exon1:c.17_18del:p.P6fs    NOTCH2:NM_001200001:exon1:c.17_18del:p.P6fs,NOTCH2:NM_024408:exon1:c.17_18del:p.P6fs    22.816
.    .    .    .    .    .    .    EN168614:ENST00000281815:exon13:c.G604T:p.E202X,EN168614:ENST00000338347:exon14:c.G1810T:p.E604X    UNKNOWN    1.684
.    .    .    .    .    .    .    EN211725:ENST00000390372:exon2:c.T302A:p.L101X    .    5.782
.    .    .    .    .    .    .    EN211721:ENST00000390368:exon2:c.273_274del:p.E91fs    .    85.008
.    .    .    .    .    .    .    EN211721:ENST00000390368:exon2:c.266_267del:p.T89fs    .    93.895
0.0103834    0.0173    0.0249    0.0057    0.0226    0.0312    ID    .    .    0.867
.    .    .    .    .    .    .    .    .    6.763
0.0181709    0.0231    0.0308    0.0098    0.0229    0.0297    .    EN140798:ENST00000311303:exon22:c.G3071A:p.W1024X    ABCC12:NM_033226:exon22:c.G3071A:p.W1024X    1.154
0.0171725    0.0115    0.0398    0.0093    0.0225    0.0293    .    EN177558:ENST00000324675:exon1:c.G693A:p.W231X    FAM187B:NM_152481:exon1:c.G693A:p.W231X    3.217
0.0173722    0.0303    0.0467    0.008    0.0354    0.0494    .    EN141959:ENST00000403390:exon2:c.C154T:p.R52X    PFKL:NM_001002021:exon4:c.C163T:p.R55X    0


Last edited by Don Cragun; 07-16-2015 at 02:29 AM.. Reason: Change ICODE tags to CODE tags.
 

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annuity(3M)															       annuity(3M)

NAME
annuity(), annuityf(), annuityl(), annuityw(), annuityq() - present value factor for annuity SYNOPSIS
DESCRIPTION
The function computes the present value factor for an annuity: (1 - (1 + rate) ** (-periods)) / rate is a version of it takes arguments and returns a result. is a version of it takes arguments and returns a result. is an version of it takes arguments and returns an result. is equivalent to on HP-UX systems. USAGE
To use these functions, compile either with the default option or with the and options. To use compile with the option. Make sure your program includes Link in the math library by specifying on the compiler or linker command line. RETURN VALUE
If periods equals zero, returns 0.0. Else, if rate equals zero, returns periods. Else, if either argument is a NaN, returns a NaN. Else, if rate < -1, returns a NaN and raises the invalid exception. Else, if rate = -1 and periods = +INFINITY, returns +INFINITY. Else, if rate equals -1 and periods > 0, is equivalent to Else, if rate equals -1, returns -1. Else, if rate equals +INFINITY and periods >= 0, returns +0.0. Else, if rate equals +INFINITY and -1 < periods < 0, returns -0.0. Else, if rate equals +INFINITY and periods = -1, returns -1. Else, if rate equals +INFINITY, returns -INFINITY. Else, if periods is infinite and (rate * periods) > 0, is equivalent to Else, if periods is infinite, returns periods. returns a properly signed infinity in lieu of a value whose magnitude is too large, and raises the overflow and inexact exceptions. raises the underflow and inexact exceptions whenever a result is tiny (essentially denormal or zero) and thereby suffers loss of accuracy, and may raise those exceptions if the result is merely tiny. ERRORS
No errors are defined. SEE ALSO
compound(3M), exp(3M), expm1(3M), pow(3M), math(5). STANDARDS CONFORMANCE
These functions are not specified by any standard. HP Integrity Server Only annuity(3M)
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