The codes are compiled together various sources to make it useful for the data I am analyzing. Used exclusively for bacterial
genome sequences and generate inputs for different software. 

file_conversion.py
converts file from fasta ('.fas') to nexus ('.nex') or vice-versa
usage: python file_conversion.py {filename_with_extension} #(testing changes)

convert_to_single_line_sequences.sh
bash script that converts a multiline fasta file to single line. For example
>Contig_1
AAAATTCCACTTCTGGCGTCTGCTAATGGGCGGGGGGATTACCACCTCGCCTATGCGTGTGCTGTTGCGG
ACTGCGACGCAGGCCGCGTGACCTGGTGGCCGTCCACGCATGCTCCACGGCAAGCGCGTAGCGCTGCCCG
TCGCCGTGGGGGATGGGTGTATCCATCCCCAGGCGTCGGGGAAGCGGTGGGGCATGGGTGGGCGGGCCTG
ACGGTTGCAGCTCGTCCCCGGCTTGTCCACGGGGGCGGCCAACGGCCGACGCTGACCAGGTGGTGCCGTC
>Contig_2
TCGCCGTGGGGGATGGGTGTATCCATCCCCAGGCGTCGGGGAAGCGGTGGGGCATGGGTGGGCGGGCCTG
ACGGTTGCAGCTCGTCCCCGGCTTGTCCACGGGGGCGGCCAACGGCCGACGCTGACCAGGTGGTGCCGTC

is converted to:

>Contig_1
AAAATTCCACTTCTGGCGTCTGCTAATGGGCGGGGGGATTACCACCTCGCCTATGCGTGTGCTGTTGCGGACTGCGACGCAGGCCGCGTGACCTGGTGGCCGTCCACGCATGCTCCACGGCAAGCGCGTAGCGCTGCCCGTCGCCGTGGGGGATGGGTGTATCCATCCCCAGGCGTCGGGGAAGCGGTGGGGCATGGGTGGGCGGGCCTGACGGTTGCAGCTCGTCCCCGGCTTGTCCACGGGGGCGGCCAACGGCCGACGCTGACCAGGTGGTGCCGTC
>Contig_2
TCGCCGTGGGGGATGGGTGTATCCATCCCCAGGCGTCGGGGAAGCGGTGGGGCATGGGTGGGCGGGCCTGACGGTTGCAGCTCGTCCCCGGCTTGTCCACGGGGGCGGCCAACGGCCGACGCTGACCAGGTGGTGCCGTC

usage:
if there are multiple fasta files that you want to change to single line fasta file
genome1.fasta, genome2.fasta, genome3.fasta
put them all in a single folder along with this script and run following on your terminal:
=> bash convert_to_single_line_sequences.sh
The folder will now have:
genome1.fasta, genome2.fasta, genome3.fasta, genome1_single_line.fas, genome2_single_line.fas, genome3_single_line.fas

Converting to single line sequences of contigs can be useful to calculate the genome quality like N50, total contig length etc. 

Use genome_qualiity.py script to calculate some basic genome qualities as:

usage: python genome_quality.py {file_converted_to_single_lines}