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
bp_process_gadfly
BP_PROCESS_GADFLY(1p) User Contributed Perl Documentation BP_PROCESS_GADFLY(1p)NAME
process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
SYNOPSIS
% process_gadfly.pl ./RELEASE2 > gadfly.gff
DESCRIPTION
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the
"correct" version of the GFF format.
To use this script, download the whole genome FASTA file and save it to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give the filename.) Do the same for the whole genome
GFF annotation file (the saved file will be called something like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If you wish
you can download the ZIP compressed versions of these files.
Next run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file:
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
(Where "fly" is the name of the database. Change it as appropriate. The database must already exist and be writable by you!)
The resulting database will have the following feature types (represented as "method:source"):
Component:arm A chromosome arm
Component:scaffold A chromosome scaffold (accession #)
Component:gap A gap in the assembly
clone:clonelocator A BAC clone
gene:gadfly A gene accession number
transcript:gadfly A transcript accession number
translation:gadfly A translation
codon:gadfly Significance unknown
exon:gadfly An exon
symbol:gadfly A classical gene symbol
similarity:blastn A BLASTN hit
similarity:blastx A BLASTX hit
similarity:sim4 EST->genome using SIM4
similarity:groupest EST->genome using GROUPEST
similarity:repeatmasker A repeat
IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not work with earlier releases.
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_PROCESS_GADFLY(1p)
07-30-2019
