Python script that converts FASTA files with multiline sequences (wrapped) to FASTAs files with single line sequences (unwrapped).

FastaMLtoSL.py

#!/usr/bin/env python 
# Created by: Lee Bergstrand 
# Descript: Converts multiline FASTAs to single line FASTAs
#  
# Usage: FastaMLtoSL.py <sequences.faa> 
# Example: FastaMLtoSL.py mySeqs.faa 
#----------------------------------------------------------------------------------------
#===========================================================================================================
#Imports:
	
import sys
import re
#===========================================================================================================
# Functions:

# 1: Checks if in proper number of arguments are passed gives instructions on proper use.
def argsCheck(numArgs):
	if len(sys.argv) < numArgs or len(sys.argv) > numArgs:
		print("Converts multiline FASTAs to single line FASTAs")
		print("By Lee Bergstrand\n")
		print("Usage: " + sys.argv[0] + " <sequences.fasta>")
		print("Examples: " + sys.argv[0] + " mySeqs.fasta")
		exit(1) # Aborts program. (exit(1) indicates that an error occurred)
#===========================================================================================================
# Main program code:
	
# House keeping...
argsCheck(2) # Checks if the number of arguments are correct.

# Stores file one for input checking.
inFile  = sys.argv[1]
outFile = inFile + ".out" 

print(">> Opening FASTA file...")
# Reads sequence file list and stores it as a string object. Safely closes file:
try:	
	with open(inFile,"r") as newFile:
		sequences = newFile.read()
		sequences = re.split("^>", sequences, flags=re.MULTILINE) # Only splits string at the start of a line.
		del sequences[0] # The first fasta in the file is split into an empty empty element and and the first fasta
						 # Del removes this empty element.
		newFile.close()
except IOError:
	print("Failed to open " + inFile)
	exit(1)

print(">> Converting FASTA file from multiline to single line and writing to file.")
# Conversts multiline fasta to single line. Writes new fasta to file.
try:	
	with open(outFile,"w") as newFasta:
		for fasta in sequences:
			try:
				header, sequence = fasta.split("\n", 1) # Split each fasta into header and sequence.
			except ValueError:
				print(fasta)
			header = ">" + header + "\n" # Replace ">" lost in ">" split, Replace "\n" lost in split directly above.
			sequence = sequence.replace("\n","") + "\n" # Replace newlines in sequence, remember to add one to the end.
			newFasta.write(header + sequence)
		newFasta.close()
except IOError:
	print("Failed to open " + inFile)
	exit(1)

print(">> Done!")

My "coverage-threshold" modified version can be found here:
https://gist.github.com/Krailon/3ae4f43460292910b3aa

Love it BRILLIANT LeeBergstrand

Very helpful, thanks.