I get a text file with 70+ columns (seperated by Tab) and about 10000 rows. The 58th Column is all numbers. But sometimes 58th columns has "/xxx=##" after the numeric data. I want to truncate this string using the script. Any Ideas...:confused: (3 Replies)
how to use sed command to find and replace a directory
i have a file.. which contains lot of paths ...
for eg.. file contains..
/usr/kk/rr/12345/1
/usr/kk/rr/12345/2
/usr/kk/rr/12345/3
/usr/kk/rr/12345/4
/usr/kk/rr/12345/5
/usr/kk/rr/12345/6
/usr/kk/rr/12345/7... (1 Reply)
find . -type f -name "*.sql" -print|xargs perl -i -pe 's/pattern/replaced/g'
this is simple logic to find and replace in multiple files & folders
Hope this helps.
Thanks
Zaheer (0 Replies)
HI,
Please find the text below. I receive a .csv file on server. I need the comma(,) in the second column to be replaced by a semi-colon( ; ).
How to do it. Please help.
Sample text:
"1","lastname1,firstname1","xxxxxx","19/10/2009","23/10/2009","0","N","Leave"... (2 Replies)
Hi all ,
I'm new to unix
I have a checked project , there exists a file called xxx.config .
now my task is to find all the files in the checked out project which references to this xxx.config file.
how do i use grep or find command . (2 Replies)
Hi All,
I have a unix shell script file as below.
My task is
a)to replace 248 to 350 and need to create a new file as BW3_350.sh
b)to replace 248 to 380 and need to create a new file as BW3_380.sh
c)to replace 248 to 320 and need to create a new file as BW3_320.sh
there is no... (6 Replies)
hi,
I would like to monitor a log file, which rolls over, everytime a server is restarted.
I would like to grep for a string, and to be more efficient i'd like to grep only newly appended data. so something like a 'tail -f' would do, however, as the log rolls over i think a 'tail -F' is... (2 Replies)
Hi
I am looking to rename the contents of this dir, each one with a new timestamp, interval of a second for each so it the existing format is on lhs and what I want is to rename each of these to what is on rhs..hopefully it nake sense
CDR.20060505.150006.gb CDR.20121211.191500.gb... (3 Replies)
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
LEARN ABOUT DEBIAN
bio::alignio::fasta
Bio::AlignIO::fasta(3pm) User Contributed Perl Documentation Bio::AlignIO::fasta(3pm)NAME
Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for
the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.
FEEDBACK
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
Peter Schattner
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
See Bio::Align::AlignI
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
See Bio::Align::AlignI
_get_len
Title : _get_len
Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
width
Title : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::AlignIO::fasta(3pm)