ascatanach

for i in {0..9000000..1000000}
do
    echo -e "$i" | awk -v OFS="\t" 'BEGIN { FS = "," } ;{print "chr25",$1,$1+1000000}'
done > 00.data/windows.bed

ascatanach

Use of uninitialized value $total in concatenation (.) or string at misa.pl line 224, chunk 99., means the conditions in the ini file are too stringent

Problem: MISA and the associated scripts from Thomas Thiel and available at http://pgrc.ipk-gatersleben.de/misa/ were written for use with early versions of primer3. These work with primer3 version 1.1.1 (and likely others), however, later versions (2.2.3 and 2.3.5 anyway) throw an error such as
Use of uninitialized value $count in concatenation (.) or string at ./p3_out.pl line 76, <SRC> chunk 11.
These come from later versions of primer3 using different input tags.

Solutions: 2.2.3 accepts the switch -io_version=3 which invokes the use of an old set of input tags and should fix the problem. 2.3.5 does not accept -io_version=3 so a more involved workaround is required. A primer3 settings file is required, called using the switch -p3_settings_file=<file>, which contains the following:

ascatanach

Compiled 21/5/2015 from:
https://github.com/IRkernel/IRkernel
quinnj/Sublime-IJulia#45

Upgrade R base (need to repeat this after upgrade so might as well start with the latest)
$ sudo apt-get update

$ sudo apt-get install r-base

Need another repository to get the dependencies:

ascatanach

#!/usr/bin/perl -w

#adapted from Neilfws at https://www.biostars.org/p/2822/
#perl script to extract a subset of a fasta file of sequences listed in an id file
#NB The output needs a little edting, place the first ">" and remove the last.
#ids only up to first white space


use strict;

ascatanach

%%bash
cat infile | sed 's/\r$//' > temp
mv temp infile

ascatanach

tr '\n' ' ' < input_filename

ascatanach

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console