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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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Regexp::Common::delimited(3)				User Contributed Perl Documentation			      Regexp::Common::delimited(3)

NAME
Regexp::Common::delimited -- provides a regex for delimited strings SYNOPSIS
use Regexp::Common qw /delimited/; while (<>) { /$RE{delimited}{-delim=>'"'}/ and print 'a " delimited string'; /$RE{delimited}{-delim=>'/'}/ and print 'a / delimited string'; } DESCRIPTION
Please consult the manual of Regexp::Common for a general description of the works of this interface. Do not use this module directly, but load it via Regexp::Common. $RE{delimited}{-delim}{-esc} Returns a pattern that matches a single-character-delimited substring, with optional internal escaping of the delimiter. When "-delim=S" is specified, each character in the sequence S is a possible delimiter. There is no default delimiter, so this flag must always be specified. If "-esc=S" is specified, each character in the sequence S is the delimiter for the corresponding character in the "-delim=S" list. The default escape is backslash. For example: $RE{delimited}{-delim=>'"'} # match "a " delimited string" $RE{delimited}{-delim=>'"'}{-esc=>'"'} # match "a "" delimited string" $RE{delimited}{-delim=>'/'} # match /a / delimited string/ $RE{delimited}{-delim=>q{'"}} # match "string" or 'string' Under "-keep" (See Regexp::Common): $1 captures the entire match $2 captures the opening delimiter (provided only one delimiter was specified) $3 captures delimited portion of the string (provided only one delimiter was specified) $4 captures the closing delimiter (provided only one delimiter was specified) $RE{quoted}{-esc} A synonym for $RE{delimited}{q{-delim='"`}{...}} SEE ALSO
Regexp::Common for a general description of how to use this interface. AUTHOR
Damian Conway (damian@conway.org) MAINTAINANCE
This package is maintained by Abigail (regexp-common@abigail.be). BUGS AND IRRITATIONS
Bound to be plenty. For a start, there are many common regexes missing. Send them in to regexp-common@abigail.be. LICENSE and COPYRIGHT This software is Copyright (c) 2001 - 2009, Damian Conway and Abigail. This module is free software, and maybe used under any of the following licenses: 1) The Perl Artistic License. See the file COPYRIGHT.AL. 2) The Perl Artistic License 2.0. See the file COPYRIGHT.AL2. 3) The BSD Licence. See the file COPYRIGHT.BSD. 4) The MIT Licence. See the file COPYRIGHT.MIT. perl v5.18.2 2013-03-08 Regexp::Common::delimited(3)
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