Hi Everyone,
I am new in the world of UNIX and Shell scripting.
I am working with a sequence file that looks like this:
>contig00001 length=128 numreads=2
aTGTGCTGGgTGGGTGCCTGTTgCCccATGCTCCAGTtCAGGATTtCAGGCAttCTCATG
TCCAGCATTTCTATTTAATCCTGCTGCTGGACTTGGGTGGtCTCAGTCtGGGAAGTGAGC
tGTCTGTG... (8 Replies)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Hi,
I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 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)
Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below.
Could you please help out to achieve solution through shell script..
File content:
... (2 Replies)
Discussion started by: nani2019
2 Replies
LEARN ABOUT LINUX
bytes
bytes(3pm) Perl Programmers Reference Guide bytes(3pm)NAME
bytes - Perl pragma to force byte semantics rather than character semantics
NOTICE
This pragma reflects early attempts to incorporate Unicode into perl and has since been superseded. It breaks encapsulation (i.e. it
exposes the innards of how the perl executable currently happens to store a string), and use of this module for anything other than
debugging purposes is strongly discouraged. If you feel that the functions here within might be useful for your application, this possibly
indicates a mismatch between your mental model of Perl Unicode and the current reality. In that case, you may wish to read some of the perl
Unicode documentation: perluniintro, perlunitut, perlunifaq and perlunicode.
SYNOPSIS
use bytes;
... chr(...); # or bytes::chr
... index(...); # or bytes::index
... length(...); # or bytes::length
... ord(...); # or bytes::ord
... rindex(...); # or bytes::rindex
... substr(...); # or bytes::substr
no bytes;
DESCRIPTION
The "use bytes" pragma disables character semantics for the rest of the lexical scope in which it appears. "no bytes" can be used to
reverse the effect of "use bytes" within the current lexical scope.
Perl normally assumes character semantics in the presence of character data (i.e. data that has come from a source that has been marked as
being of a particular character encoding). When "use bytes" is in effect, the encoding is temporarily ignored, and each string is treated
as a series of bytes.
As an example, when Perl sees "$x = chr(400)", it encodes the character in UTF-8 and stores it in $x. Then it is marked as character data,
so, for instance, "length $x" returns 1. However, in the scope of the "bytes" pragma, $x is treated as a series of bytes - the bytes that
make up the UTF8 encoding - and "length $x" returns 2:
$x = chr(400);
print "Length is ", length $x, "
"; # "Length is 1"
printf "Contents are %vd
", $x; # "Contents are 400"
{
use bytes; # or "require bytes; bytes::length()"
print "Length is ", length $x, "
"; # "Length is 2"
printf "Contents are %vd
", $x; # "Contents are 198.144"
}
chr(), ord(), substr(), index() and rindex() behave similarly.
For more on the implications and differences between character semantics and byte semantics, see perluniintro and perlunicode.
LIMITATIONS
bytes::substr() does not work as an lvalue().
SEE ALSO
perluniintro, perlunicode, utf8
perl v5.12.1 2010-04-26 bytes(3pm)