nylander

#!/usr/bin/perl 
#===============================================================================
=pod

=head1
         FILE:  cgt.pl

        USAGE:  ./cgt.pl

  DESCRIPTION:  The intention of the original code was to search genbank

nylander

#!/usr/bin/env perl

use strict;
use warnings;

=pod

=head1

         FILE: extract_masked.pl

nylander

#!/bin/bash

## Fetch scientific name for Genbank accession number
## Version: Mon 20 nov 2017 13:35:49
## By:      {Andreas.Kahari,Johan.Nylander}@nbis.se
## Usage:   ./acc2sci.sh infile-with-accessions
## Notes:   Reads from file or STDIN, prints to STDOUT.
##          No detailed error checking! If any of the Accessions
##          provided as queries are incorrect, the script will
##          exit with msg: "Failure of post to find data to load.."

nylander

>PIS68081.1 anaerobic sulfatase maturase [Vibrio parahaemolyticus 1911C]
MQITQSPQFNGKASKRLHVMAKPIGAACNIDCTYCYYLSKQDLLEYKKGCSPMMDEATLEAYIKQYIEGQ
NTPEIVFSWQGGEPTMLGLDYFKKIVEFQAKYQPEGVKISNDLQTNGTLLNDEWCEFLSENHFLVGLSID
GPEMLHNAYRTNRAGRGTFKQVMNAVELLHKHQVNFATLTCVNNLTSRNPLEVYRFLRDEVRSPQMQFIP
IVEQKTFRTTAPQKWQPQEQLKQGDKRLIPGHKDSVMEPWCVADEAWGNFLIAVFDEWIKNDIGKVFVQY
FEASVEAWMGRANPLCTLGEVCGKGLAMEPNGDVFACDHYVYPEYKIGNIHHDKLDELAYSKEQQKFGFA
KSRLLTQQCRDCEYQFACYGECPKNRFIRTRDGEPGLNYLCAGWKKFFAHADKAMAYILRATGNVVAHGK
YSDSVVRQESEQRPVFETKF
>PIS68069.1 anaerobic sulfatase maturase [Vibrio parahaemolyticus 1911C]
MKDAYVRRFHVMAKPGGAKCNIDCQYCFYLHKENLLHQEKQPKMDDATLEAFVKSYIESQDGEEIVFSWQ

nylander

# gh-93: Repository surgery: Remove large files accidentally added in the past.

- Last modified: fre aug 09, 2019  12:34
- Sign: JN

## Description

Find large, unnecessary files in the MrBayes GitHub repository and delete them.
Saves approx. 132 MB of space (from 212 to 80 MB).

nylander

#NEXUS
[Data from Table 1, Felsenstein, 1992, Evolution, 46(1),1992, pp. 159-173.]
Begin data;
  Dimensions ntax=5 nchar=122;
  Format datatype=restriction missing=?;
  Matrix
    Gibbon  11100000110001000010100111100000011100100100111110000001010001100100000000010000011010100111100011011010111111101101011001
    Orang   11010110100111000000011000101010010000010101010010001000101000000011000000000010000111001110001000110011101001000111001110
    Gorilla 11000101101001010111000001100001110011000000000010100000110100110001011000101011000010000101110000110000101101010110101000
    Chimp   10000110100011111010000001000100110010101000000011000111100010110000100110000011100010001101100000110100001001010110111000

nylander

# Bash alias for better jobinfo output on UPPMAX.
# Last modified: 2020-05-27
# Sign: Johan Nylander
# Include in your ~/.bash_aliases, and
# check that your ~/.bashrc reads your ~/.bash_aliases by, e.g.,
# including this in your ~/.bashrc:
#    if [ -f ~/.bash_aliases ]; then
#      . ~/.bash_aliases
#    fi
#

nylander

8 484
Barbotinia_oraniensis         TCTTGGTCCATTTATATGTGAGATATATGCAATGCTTGGCTCCCTATTTGGATGTGGCTCCATTTGGACAATGTGTATGATTGCTTTCGACCGATACAATGTTATCGTAAAAGGTTTAGCTGGCAAGCCATTAACTATCAGTGGTGCAATTCTGCGTATTGTTTTTCTCTGGGTCTGGGCGGTAGTTTGGACCATTGCACCAATGATAGGATGGAATCGG---TACGTTCCCGAGGGCAACATGACAGCTTGTGGAACTGACTATCTAACTAAGGATTGGTTCTCGAGGTCTTACATTCTTGTATACAGCGTCTTCGTATACTTCATGCCACTTTTCCTCATCATCTACAGTTACTATTTCATCATTGCTGCTGTATCTGCTCATGAAAAAGCTATGCGTGAACAGGCCAAAAAGAWGAATGTAGCTTCTCTACGATCATCCGACAATCAAAATACGAGTGCTGAACATAAACTCGCCAAGGCA
Synergus_gallaepomiformis     ACTAGGTCCATTTATATGTGAGATGTACGGAATGTTTGGCTCTCTATTCGGATGTGGTTCTATTTGGACAATGTGTATGATTGCTTTCGACCGATACAACGTTATCGTAAAAGGTTTAGTTGGCAAGCCCTTAACTATCAGTGGTGCAATCCTGCGCATTGCTTTTCTCTGGATCTGGGCAGTAATTTGGACAATCGCACCAATGATAGGATGGAATCGG---TACGTTCCGGAGGGTAACATGACAGCTTGCGGAACTGACTACCTGAGTAAGGATTGGTTCTCCAGGTCTTACATCATTGTATACAGCGTCTTTGTATACTTCATGCCACTTTTCCTCATCATATACAGTTACTACTTCATCATTGCTGCTGTATCTGCCCACGAGAAGGCTATGCGTGAACAGGCCAAAAAGATGAATGTAGCTTCTCTACGATCATCCGACAATCAAAATACGAGTGCTGAACATAAAC

nylander

#!/bin/bash

# ptemplate - Create a project structure
# Usage: ptemplate myproject
# Last modified: Mon mar 29, 2021  07:55
# Sign: Johan Nylander
# Description: Create a folder structure
# and, if git is available, initilize git-
# version control. No files in folder private
# is under git control, and only the README file

nylander

#! /usr/bin/env perl
#
# Short description for fasta2nexus.pl
#
# Author nylander <johan.nylander@nrm.se>
# Version 0.1
# Copyright (C) 2021 nylander <johan.nylander@nrm.se>
# Modified On 2021-05-21 10:54
# Created  2021-05-21 10:54
#