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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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Bio::SeqFeature::Tools::FeatureNamer(3pm)		User Contributed Perl Documentation		 Bio::SeqFeature::Tools::FeatureNamer(3pm)

NAME
Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features SYNOPSIS
use Bio::SeqIO; use Bio::SeqFeature::Tools::FeatureNamer; # first fetch a genbank SeqI object $seqio = Bio::SeqIO->new(-file=>'AE003644.gbk', -format=>'GenBank'); $seq = $seqio->next_seq(); $namer = Bio::SeqFeature::Tools::FeatureNamer->new; my @features = $seq->get_SeqFeatures; foreach my $feature (@features) { $namer->name_feature($feature) unless $feature->display_name; } DESCRIPTION
This is a helper class for providing names for SeqFeatures The Bio::SeqFeatureI class provides a display_name method. Typically the display_name is not set when parsing formats such as genbank - instead properties such as label, product or gene are set in a somewhat inconsistent manner. In addition, when generating subfeatures (for example, exons that are subfeatures of a transcript feature), it is often desirable to name these subfeatures before either exporting to another format or reporting to the user. This module is intended to help given uniform display_names to features and their subfeatures. TODO
Currently the naming policy is hardcoded. It may be desirable to allow plugging in variations on naming policies; this could be done either by subclassing, anonymous subroutines (closures) or parameterization. Contact the author if you feel you have need for a different naming policy FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Chris Mungall Email: cjm AT fruitfly DOT org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new(); Function: constructor Example : Returns : a new Bio::SeqFeature::Tools::FeatureNamer Args : see below name_feature Title : name_feature Usage : $namer->name_feature($sf); Function: sets display_name Example : Returns : Args : L<Bio::SeqFeatureI> This method calls generate_feature_name() and uses the returned value to set the display_name of the feature name_contained_features Title : name_contained_features Usage : $namer->name_contained_features($sf); Function: sets display_name for all features contained by sf Example : Returns : Args : L<Bio::SeqFeatureI> iterates through all subfeatures of a certain feature (using get_all_SeqFeatures) and names each subfeatures, based on the generated name for the holder feature A subfeature is named by concatenating the generated name of the container feature with the type and a number. For example, if the containing feature is a gene with display name dpp, subfeatures will be named dpp-mRNA-1 dpp-mRNA2 dpp-exon1 dpp-exon2 etc generate_feature_name Title : generate_feature_name Usage : $name = $namer->generate_feature_name($sf); Function: derives a sensible human readable name for a $sf Example : Returns : str Args : L<Bio::SeqFeatureI> returns a generated name (but does not actually set display_name). If display_name is already set, the method will return this Otherwise, the name will depend on the property: label product gene locus_tag (in order of priority) perl v5.14.2 2012-03-02 Bio::SeqFeature::Tools::FeatureNamer(3pm)
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