06-21-2009
Edited: compare two files and print mismatch
Using unix shell script, how to compare two files and print lines with mismatch? Below are the requirements:
1. The number of lines on the two files is not the same.
2. The difference/mismatch can be found on the second or third column.
3. The comparison is not between line 1 of file 1 and line 1 of file 2. Rather, the comparison is on line 1 of file 1 and the line on file 2 that has the same first word on the line 1 of file 1.
To demonstrate:
FILE 1:
abc 123 678
def 456 901
ghi 789 234
jkl 012 567
mno 345 890
FILE 2:
def 456 901
abc 124 678
mno 345 890
ghi 789 244
OUTPUT FILE:
"from file 1"
abc 123 678
ghi 789 234
"from file 2"
abc 124 678
ghi 789 244
i hope someone can help me with this. Thanks!
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LEARN ABOUT DEBIAN
bio::updateableseqi
Bio::UpdateableSeqI(3pm) User Contributed Perl Documentation Bio::UpdateableSeqI(3pm)
NAME
Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
SYNOPSIS
See Bio::SeqI for most of the documentation. See the documentation of the methods for further details.
DESCRIPTION
Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users to perform basic editing functions
(update/delete) on their component SeqFeatures.
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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - David Block
Email dblock@gene.pbi.nrc.ca
CONTRIBUTORS
Ewan Birney forced me to this...
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
delete_feature
Title : delete_feature
Usage : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent. Keeps track of the features
of the $gene object that may be left as orphans and returns them as a listref.
Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
$orphanlist is a reference to a list containing $exon{'2'};
Returns : a listref of orphaned features after the deletion of $feature (optional)
Args : $feature - the feature to be deleted
$transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
transcripts in a gene.
$gene - the gene containing the $transcript and/or the $feature
perl v5.14.2 2012-03-02 Bio::UpdateableSeqI(3pm)