Source code for conkit.command_line.conkit_msatool
#!/usr/bin/env python
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"""This script analyses a Multiple Sequence Alignment.
It provides you estimates about the quality, which will allow
you to determine its usefulness for covariance-based contact
prediction.
"""
__author__ = "Felix Simkovic"
__date__ = "21 Nov 2016"
__version__ = "0.13.3"
import argparse
import conkit.command_line
import conkit.io
import conkit.plot
import conkit.plot.tools
logger = None
[docs]def main():
parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("msafile", help="Multiple Sequence Alignment file")
parser.add_argument("msaformat", help="Multiple Sequence Alignment format")
args = parser.parse_args()
global logger
logger = conkit.command_line.setup_logging(level="info")
msa = conkit.io.read(args.msafile, args.msaformat)
plot = args.msafile.rsplit(".", 1)[0] + ".png"
figure = conkit.plot.SequenceCoverageFigure(msa, legend=True)
figure.ax.set_aspect(conkit.plot.tools.get_adjusted_aspect(figure.ax, 0.3))
figure.savefig(plot)
logger.info("Input MSA File: %s", args.msafile)
logger.info("Input MSA Format: %s", args.msaformat)
logger.info("Length of the Target Sequence: %d", msa.top_sequence.seq_len)
logger.info("Total Number of Sequences: %d", msa.nseq)
logger.info("Number of Effective Sequences: %d", msa.meff)
logger.info("Sequence Coverage Plot: %s", plot)
if __name__ == "__main__":
import sys
import traceback
try:
main()
sys.exit(0)
except Exception as e:
if not isinstance(e, SystemExit):
msg = "".join(traceback.format_exception(*sys.exc_info()))
logger.critical(msg)
sys.exit(1)