Hello, I want to rename multiple files and catch some points about backreference within sed and regex.
Here is a part of my file list. Input:
Note: The file names are not necessarily continuous from A~Z or 921 ~ 997, as some of the files may be missing and there are other types of the file with different pattern in the same folder.
I want to put the prefix "CGW-" to each file name and change the extension to fasta. Output:
I have used two steps do the job, one at a time:
then
It seems using the backreference will do the same job better and easier. But I could not find clues in this forum or Google. Any expertise is greatly appreciated. Thanks a lot!
Hi
I have the following file that i need to run a sed command on
1<tab>running
2<tab>running
3<tab>running
4<tab>running
I want to be able to replace a line i.e the second one with '2<tab>failed'. As the first number is unique that can be used to search for the relevant line (using ^2 i... (5 Replies)
My egrep outputs this:
$ cat html.out|sed -n '/bluetext/s/ / /gp'|egrep '{5}'
<span class="bluetext"><b> Lexington Park, MD 20653</b></span>
But my backreference \1 is empty. I dont understand why. Can someone clarify?
$ cat html.out|sed -n '/bluetext/s/ / /gp'|sed -n... (1 Reply)
Hello
I have a bash script where I need to do a substring replacement like this:
variable2=${variable1/foo/bar}
However, I only want "foo" replaced if it is at the end of the line.
However, this does not work:
variable2=${variable1/foo$/bar}
as you can see I'm using the $ regex for... (2 Replies)
This seems like it should be an easy problem, but I'm a noob and I can't figure it out. I'm trying to use sed, but would be happy to use anything that does the job.
I am trying to trim off a fixed number of unknown characters from 2 different : delimited fields while keeping the intervening... (4 Replies)
I am trying to replace the line which has string "tablespace" not case senstive....
with below simple script: mysrcipt.sh
sed "s/.*/TABLESPACE USERS/g" create_table > tmp
mv tmp create_table
Is there any better way to do it? If Search string tooooooo long it will be tough to code in... (4 Replies)
I am having trouble parsing rpm filenames in a shell script.. I found a snippet of perl code that will perform the task but I really don't have time to rewrite the entire script in perl. I cannot for the life of me convert this code into something sed-friendly:
if ($rpm =~ /(*)-(*)-(*)\.(.*)/)... (1 Reply)
Hi,
I need to use the regex in the replacement string in SED command.
something like
sed -e ' s/\(^\{5\}\).\{150\}\(.*\)$/\10\{30\}1\{30\}A\{60\}B\{30\}\2/' abc
which means for all the lines in file abc that starts with 5 characters, I need to replace character 6-151... (6 Replies)
Hello to all,
I have this sed script that replaces hex strins within a binary file.
As you can see, I want to replace all bytes 4X with 2X (where X could take values 0 to F).
sed -e 's/\x40/\x20/g' -e 's/\x41/\x21/g' -e 's/\x42/\x22/g' -e 's/\x43/\x23/g' -e 's/\x44/\x24/g' -e... (7 Replies)
Hi,
I'm using /bin/sh
I would appreciate if someone could help me with SED syntax for a "simple" line.
Here is where I Got to:
I have these strings that are returned by my(Examples) (naturally "FullPath" is always changing don't hardcode this lol)
FullPath/AAA.framework... (3 Replies)
I have some text like
EU1BTDAT:ASSGNDD filename='$SEQFILES/SUNIA.PJ008202.CARDLIB/DATECARD'
EU1BTDATEST:ASSGNDD filename='$SEQFILES/SUNIA.PJ008202.CARDLIB/DATECARD'
EU1CLOSEDATES:ASSGNDD filename='$SEQFILES/SUNIA.PJ008202.CARDLIB/DATECARD'
EU1DATED:ASSGNDD... (8 Replies)
Discussion started by: gotamp
8 Replies
LEARN ABOUT DEBIAN
bio::seqio::fasta
Bio::SeqIO::fasta(3pm) User Contributed Perl Documentation Bio::SeqIO::fasta(3pm)NAME
Bio::SeqIO::fasta - fasta sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from fasta flat file databases.
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 one
of 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/
AUTHORS - Ewan Birney & Lincoln Stein
Email: birney@ebi.ac.uk
lstein@cshl.org
CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object, or nothing if no more available
Args : NONE
write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: Writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of 1 or more Bio::PrimarySeqI objects
width
Title : width
Usage : $obj->width($newval)
Function: Get/Set the line width for FASTA output
Returns : value of width
Args : newvalue (optional)
preferred_id_type
Title : preferred_id_type
Usage : $obj->preferred_id_type('accession')
Function: Get/Set the preferred type of identifier to use in the ">ID" position
for FASTA output.
Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
Args : string when setting. This must be one of values defined in
@Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
accession, accession.version, display, primary
Throws : fatal exception if the supplied id type is not in @SEQ_ID_TYPES.
perl v5.14.2 2012-03-02 Bio::SeqIO::fasta(3pm)