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help.txt
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31 lines (31 loc) · 2.42 KB
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############## HELP ############################################################
# #
# RunFastaReader is a tool to read fasta-files, and print them in a formatted #
# manner. The following flags define the command line input: #
# #
# -h (--h, -help, --help): #
# Prints this help to the console (you might have got it before you read this#
# -i <inputFile> (--i, -input, --input): #
# after the flag -i follows the file name of the fasta-file to be read. #
# -o <outputFile> (--o, -output, --output): #
# outputFile specifies where to write the formatted fasta file #
# (not yet implemented) #
# -l <expression> (--l, -lines, --lines): #
# The expression defines which entries in the fasta-file are to be printed. #
# expression contains numbers and/or number ranges. If it contains more than #
# one number/ranges they are seperated by a comma. Ranges consist of two #
# numbers denoting the start and end point of the range, seperated by a #
# dash. Example: #
# 1,2,4-10,500 #
# The lines 1,2,4,5,6,7,8,9,10,500 are printed. #
# Duplicates are removed, lines are printed in an ordered fashion. #
# -r <int> (--r, -header, --header): #
# int sets the maximum number of characters of the header that shall be #
# displayed. #
# -s <int> (--s, -sequence, --sequences): #
# int sets the maximum number of characters of the sequence, that shall #
# be displayed until a new line. #
# #
# Note: the fasta-file must have the extension .fasta or .fa and must only #
# consist of chars element {AGCTU-} as this reader is for RNA. #
################################################################################