Commit fcc6e035 authored by Pauline Pommeret's avatar Pauline Pommeret

Description

parent fb216674
......@@ -16,15 +16,21 @@ if __name__ == "__main__":
DBCURSOR = database.PGCursor()
# Use argparse to parse arguments. We first create a parser.
PARSER = argparse.ArgumentParser(description="ToDo")
PARSER = argparse.ArgumentParser(description="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 considered as 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
")
# 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")
PARSER.add_argument("-A", "--alpha", type=float, default=0.05, help="[float] alpha parameter of the Student table that is to be used in the statistical analysis (default: 0.05)", action="store")
PARSER.add_argument("-c", "--centering", type=int, default=72, help="[int] number of bp that are to be considered as the center of the sequence (default: 72)", action="store")
PARSER.add_argument("-g", "--graph", type=int, default=None, help="[int] number of graphs that are to be plotted, currently not implemented (default: None)", action="store")
PARSER.add_argument("-s", "--sliding", type=int, default=72, help="[int] number of bp that are to be included in the smoothing window (default: 72)", action="store")
PARSER.add_argument("-t", "--trx-scale-file", type=str, default=trx_lib.SCALE_FILE, help="[str] path to trx scale file (default: trx_lib.SCALE_FILE)", action="store")
PARSER.add_argument("-g", "--graph", type=int, default=None, help="[int] number of graphs that are to be plotted, currently not implemented (default: None)", action="store")
PARSER.add_argument("datadir", type=str, help="[str] path to the data directory", action="store")
# Then, parse it
......
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