Hi all,
I have searched and found various threads about removing spaces from a field within a text file. Unfortunately, I have not found exactly what I'm looking for, nor am I adept enough to modify what I've found into what I need.
I use the following command to remove the first line... (3 Replies)
Hi everybody!
I want to cut the last field from string, can anybody help me??
String input:: /abc1/abc2/abc3
output:: /abc1/abc2
Regards,
Kiran (2 Replies)
Hi
i have file with data:
abc,*xyz,#abc
123,#123,1234
*123,#123,abc
So i want to remove only fields starting with * and # and i want output as:
abc,,
123,,1234
,,abc
Please suggest something
Thanks
Sumit (3 Replies)
I'm trying to use sed to remove the value of one field from another field. For example:
cat inputfile
123|ABC|Generic_Textjoe@yahoo.com|joe@yahoo.com|DEF
456|GHI|Other_recordjohn@msn.com|john@msn.com|JKL
789|MNO|No_Email_On_This_One|smith@gmail.com|PQR
I would like to remove the email... (2 Replies)
Hi
I have a file with fields delimited by |. I need to remove the first field from the file. I tried cut but it just extracts that field.
sample.output
abc|100|name1
cde|200|name2
efg|300|name3
Output should be
sample.output
100|name1
200|name2
300|name3
thanks
Var (6 Replies)
Hi all !
I'm sure it is a basic question but I didn't find any threads that fit my need.
How to remove empty fields with awk?
Or in other words, how to shift all the fields after an empty field on the left?
input:
1|2||3|4|5||6
wanted:
1|2|3|4|5|6
I tried:
awk '{for(i=1; i<=NF;... (7 Replies)
Hi,
I have a '~' delimited file and i want to remove the last field using awk. Please find the sample records below:
1428128~1~0~1100426~003~50220~005~14~0~194801~11~0~3~14~0~50419052335~0~0820652001~2~00653862 ~0~1~0~00126~1~20000110~20110423~R~ ~0~Z~1662.94~ ~002041~0045~Z~... (3 Replies)
Thank you for 4 looking this post.
We have a tab delimited file where we are facing problem in a lot of funny character. I have tried using awk but failed that is not working.
In the 5th field ID which is supposed to be a integer only of that file, we are getting corrupted data as below.
I... (12 Replies)
Hi all,
I want to remove empty field in a text file. I tried to used sed. But it failed.
Input:
LG10_PM_map_19_LEnd 1000560 G AG AG
LG10_PM_map_19_LEnd 1005621 G AG
LG10_PM_map_19_LEnd 1011214 A AG AG
LG10_PM_map_19_LEnd 1011673 T CT CT ... (3 Replies)
I am trying to remove lines in the target.txt file if $5 before the - in that file matches sorted_list. I have tried grep and awk. Thank you :).
grep
grep -v -F -f targets.bed sort_list
grep -vFf sort_list targets
awk
awk -F, '
> FILENAME == ARGV {to_remove=1; next}
> ! ($5 in... (2 Replies)
Discussion started by: cmccabe
2 Replies
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)