Commit 5445cd90 authored by Pauline Pommeret's avatar Pauline Pommeret

Making description human-readable

parent cba47ff7
......@@ -17,12 +17,38 @@ if __name__ == "__main__":
DBCURSOR = database.PGCursor()
# Use argparse to parse arguments. We first create a parser.
TEXT = "This program creates a postgresql database that holds the following data:\n - sequence information (name, accession number, sequence alphabet, description, etc)\n - analysis parameters (Student table's alpha, number of bp considered as center, smooth window, etc)\n - relevant information on the TRX signal FFT\n - relevant information on the MD helicoidal parameters FFT\n - Spearman and Pearson correlations between every helicoidal parameters for every frame of the MD\n\nThe data directory must be organized this way:\n datadir\n \\-dir1\n \\-group (mandatory)\n \\-sequence.fasta (mandatory)\n \\-rise.dat\n \\-roll.dat\n \\-tilt.dat\n \\-twist.dat\n \\-shift.dat\n \\-slide.dat\n \\-...\n\nA .dat file must me organized this way:\n frame C16/C17 C17/G18 G18/A19 ...\n 0 -1.0 9.0 -1.8\n 1 -4.4 -7.6 -0.1\n 2 -6.4 1.0 -6.0\n 3 -3.6 -1.1 -2.5\n\n"
TEXT = """This program creates a postgresql database that holds the following data:
- sequence information (name, accession number, sequence alphabet, description, etc)
- analysis parameters (Student table's alpha, number of bp in center, smooth window, etc)
- relevant information on the TRX signal FFT
- relevant information on the MD helicoidal parameters FFT
- Spearman and Pearson correlations between every helicoidal parameters for every frame of the MD
The data directory must be organized this way:
datadir
\\-dir1
\\-group (mandatory)
\\-sequence.fasta (mandatory)
\\-rise.dat
\\-roll.dat
\\-tilt.dat
\\-twist.dat
\\-shift.dat
\\-slide.dat
\\-...
A .dat file must me organized this way:
frame C16/C17 C17/G18 G18/A19 ...
0 -1.0 9.0 -1.8
1 -4.4 -7.6 -0.1
2 -6.4 1.0 -6.0
3 -3.6 -1.1 -2.5
PARSER = argparse.ArgumentParser(description=TEXT, \
formatter_class=RawDescriptionHelpFormatter)
"""
PARSER = argparse.ArgumentParser(description=TEXT, formatter_class=RawDescriptionHelpFormatter)
# Adding arguments to the parser
PARSER.add_argument("-a", "--alphabet", type=str, default="dna", help="[str] sequences alphabet (dna, rna, prot), currently only dna is implemented (default: 'dna')", action="store")
......
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