I am new to the world of UNIX scripting - and would like to make the following script:
I have 100 files numbered 1-100. However - i would like to continue the file list - so that I add another 100 files following on, so that file 101 = 99; file 102 = 98 ; 103 = 97 and so on....
(basically ...... (6 Replies)
Hi,
I am a beginner in awk scripting! I need your help; I want to replace the fifth column number (which is 15 here) here in this file for example :
ATOM 142 N PRO A 15
ATOM 143 CD PRO A 15
ATOM 144 HD1 PRO A 15
ATOM ... (5 Replies)
I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATACGAT
I know I can extract the IDs alone with the following code
grep... (3 Replies)
Hi All
I have a folder that contains hundreds of file with a names
3.msa
4.msa
21.msa
6.msa
345.msa
456.msa
98.msa
...
...
...
I need rename each of this file by adding "core_" in the begiining of each file such as
core_3.msa
core_4.msa
core_21.msa (4 Replies)
Hi All,
I have 100 files named - rep-0.txt, rep-2.txt...rep-99.txt.
They each contain information in the following format:
abc 1 qwe
asd 2 zxc
poi 3 lkj
pdh 4 ldf
hgf 5 tyu
i would like to re-number , so that all the new files (rep0.dat, rep1,dat....) have... (1 Reply)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
I am new to the world of Linux scripting, and would like to make the following 2 scripts:
I have 67 files named Alk-0001.txt to Alk-0067.txt
I would like them to be numbered Alk-002.txt to Alk-0134.txt
eg
Alk-0001.txt > Alk-0002.txt
Alk-0002.txt > Alk-0004.txt
Alk-0003.txt > Alk-0006.txt
... (3 Replies)
Hi,
In sftp script to get files, I have to rename all the files which I am picking. Rename command does not work here. Is there any way to do this?
I am using #!/bin/ksh
For eg: sftp user@host <<EOF
cd /path
get *.txt
rename *.txt *.txt.done
... (7 Replies)
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
11 Replies
LEARN ABOUT DEBIAN
tfbs::patterngen::simplepfm
TFBS::PatternGen::SimplePFM(3pm) User Contributed Perl Documentation TFBS::PatternGen::SimplePFM(3pm)NAME
TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory
SYNOPSIS
my @sequences = qw( AAGCCT AGGCAT AAGCCT
AAGCCT AGGCAT AGGCCT
AGGCAT AGGTTT AGGCAT
AGGCCT AGGCCT );
my $patterngen =
TFBS::PatternGen::SimplePFM->new(-seq_list=>@sequences);
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be
passed either as strings, as Bio::Seq objects or as a fasta file.
This pattern generator always creates only one pattern from a given set of sequences.
new
Title : new
Usage : my $db = TFBS::PatternGen::SimplePFM->new(%args);
Function: the constructor for the TFBS::PatternGen::SimplePFM
object
Returns : a TFBS::PatternGen::SimplePFM obkect
Args : This method takes named arguments;
you must specify one of the following
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
pattern
all_patterns
patternSet
The three above methods are used fro the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::SimplePFM(3pm)