Create a single bash script that does the following:
a. Print out the number of occurrences for each motif that is found in the bacterial genome and output to a file called motif_count.txt
b. Create a fasta file for each motif (so 3 in total) which contains all of the genes and their corresponding sequences that have that motif. Each file should be named after the motif (ie ATG.txt) and outputted to a new directory called motifs
motif file is a txt file with these motifs : ATG, GGGGG, ATTTT
the bacterial genome file is fasta file with the following lines
I have a very basic bash shell script, which has many "while... done; for .... done" loop clauses, like the following
~~
#!/bin/bash
while blablalba; do
....
done < /tmp/file
for line in `cat blablabla`; do grep $line /tmp/raw ; done > /tmp/1;
while blablalba2; do
....
done <... (2 Replies)
SEND_MESSAGE=test
echo $SEND_MESSAGE
if
then
echo `date` > update_dt_ccaps.lst
echo "The file transfer failed" >> update_dt_ccaps.lst
SEND_MESSAGE=false
fi
The above code is showing error in bash shell as :
./test: line 5: [: test: integer expression expected
... (2 Replies)
I'm trying to search all .odt files in a directory for a string in the text of the file.
I've found a bash script that works, except that it can't handle whitespace in the filenames.
#!/bin/bash
if ; then
echo "Usage: searchodt searchterm"
exit 1
fi
for file in $(ls *.odt); do
... (4 Replies)
Hi,
I am working on bash script after a long time. I am getting error near done statement while running a for loop snippet. The error says "Syntax error near unexpcted token 'done'"
please suggest what could be wrong. here is the snippet
elements=${#option_arr} //an array of values... (1 Reply)
Having issues with an expect script. I've been scripting bash, python, etc... for a couple years now, but just started to try and use Expect. Trying to create a script that takes in some arguments, and then for now, just runs a pwd command(for testing, final will be command I pass).
Here is... (0 Replies)
Hi Folks,
I have a loop that goes through an array and the output is funky.
sample:
array=( 19.239.211.30 )
for i in "${array}"
do
echo $i
iperf -c $i -P 10 -x CSV -f b -t 50 | awk 'END{print '$i',$6}' >> $file
done
Output:
19.239.211.30
19.2390.2110.3 8746886
seems that when... (2 Replies)
I have the following while loop that I put in a script, demo.sh:
while read rna; do
aawork=$(echo "${rna}" | sed -n -e 's/\(...\)\1 /gp' | sed -f rna.sed)
echo "$aawork" | sed 's/ //g'
echo "$aawork" | tr ' ' '\012' | sort | sed '/^$/d' | uniq -c | sed 's/*\(*\) \(.*\)/\2: \... (3 Replies)
Hi Everybody,
I'm a newbie to shell scripting, and I'd appreciate some help. I have a bunch of .txt files that have some unwanted content. I want to remove lines 1-3 and 1028-1098.
#!/bin/bash
for '*.txt' in <path to folder>
do
sed '1,3 d' "$f";
sed '1028,1098 d' "$f";
done
I... (2 Replies)
Dear all,
Please help with the following.
I have a file, let's call it data.txt, that has 3 columns and approx 700,000 lines, and looks like this:
rs1234 A C
rs1236 T G
rs2345 G T
Please use code tags as required by forum rules!
I have a second file, called reference.txt,... (1 Reply)
Hi everyone
I need some help
I want to create an script which does some processing
it takes the two arguments 201901010000 and 201901020200 - so YYYMMDDHHMM
I want to split processing into hours from start until end,
I dont get why this works but when I add to a future variable... (1 Reply)
Discussion started by: kl1ngac1k
1 Replies
LEARN ABOUT DEBIAN
glam2format
GLAM2FORMAT(1) glam2 Manual GLAM2FORMAT(1)NAME
glam2format - converts GLAM2 motifs to FASTA or MSF format
SYNOPSIS
glam2format [options] my_format my_motif.glam2
Formats: fasta, msf.
DESCRIPTION
glam2format reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the
alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the
other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in glam2 output is
converted.
OPTIONS (DEFAULT SETTINGS)-o
Output file (stdout).
-c
Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This
best reflects glam2's intention, but it can make the alignment large and full of gaps. With -c, inserted residues are written as
arbitrarily aligned with each other, just as they appear in the glam2 output.
-f
Sequence file to make a "global" alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking
sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the -c option. The sequences should
have unique names and their order should be unchanged.
SEE ALSO boxshade(1), glam2(1), glam2mask(1), glam2-purge(1), glam2scan(1)
The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in
/usr/share/doc/glam2/.
REFERENCE
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and
deletions, PLoS Computational Biology (in press).
AUTHORS
Martin Frith
Author of GLAM2.
Timothy Bailey
Author of GLAM2.
Charles Plessy <plessy@debian.org>
Formatted this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
The source code and the documentation of GLAM2 are released in the public domain.
GLAM2 1056 05/19/2008 GLAM2FORMAT(1)
07-30-2019
