def main():
parser = argparse.ArgumentParser()
parser.add_argument("--min-length", dest="min_prot_length", default=0, help="Minimum protein length", type=int)
parser.add_argument("--max-length", dest="max_prot_length", default=10000, help="Maximum protein length", type=int)
parser.add_argument("--min-bits", dest="min_bits_saved", default=-10000, help="Minimum bits saved", type=float)
parser.add_argument("--max-bits", dest="max_bits_saved", default=10000, help="Maximum bits saved", type=float)
parser.add_argument("--min-bits-ratio", dest="min_bits_ratio", default=0, help="Minimum bits saved per position", type=float)
parser.add_argument("--max-bits-ratio", dest="max_bits_ratio", default=10000, help="Maximum bits saved per position", type=float)
parser.add_argument("--stem", dest="stem", default="filtered", help="Output file stem")
parser.add_argument("--direction", dest="direction", help="Search direction", default=set(["left", "right"]), type=float, choices=["left", "right"])
parser.add_argument("hmmgs_file")
parser.add_argument("hmmgs_nucl_seqs")
parser.add_argument("hmmgs_prot_seqs")
#min_prot_length=0, max_prot_length=10000, min_bits_saved=-1000, max_bits_saved=10000, min_bits_ratio=0, max_bits_ratio=10000, direction=set(["left", "right"]), state_after=0, state_before=10000
args = parser.parse_args()
nucl_seqs = SeqIO.to_dict(SeqIO.parse(open(args.hmmgs_nucl_seqs), "fasta"))
prot_seqs = SeqIO.to_dict(SeqIO.parse(open(args.hmmgs_prot_seqs), "fasta"))
hmmgs_lines = [x for x in hmmgs_utils.read_hmmgs_file(args.hmmgs_file)]
hmmgs_utils.plot_bits_ratio(hmmgs_lines, "prefilter.eps")
filter_params = copy.copy(vars(args))
del filter_params["hmmgs_file"]
del filter_params["stem"]
del filter_params["hmmgs_nucl_seqs"]
del filter_params["hmmgs_prot_seqs"]
filtered_lines = [x for x in hmmgs_utils.filter(hmmgs_lines, **filter_params)]
hmmgs_utils.plot_bits_ratio(filtered_lines, "postfilter.eps")
filtered_hmmgs = open("{0}_hmmgs.txt".format(args.stem), "w")
filtered_nucl = open("{0}_nucl.fasta".format(args.stem), "w")
filtered_prot = open("{0}_prot.fasta".format(args.stem), "w")
hmmgs_header = hmmgs_utils.read_hmmgs_header(args.hmmgs_file)
hmmgs_utils.write_hmmgs_header(filtered_hmmgs, hmmgs_header)
for line in filtered_lines:
hmmgs_utils.write_hmmgs_line(filtered_hmmgs, hmmgs_header, line)
filtered_nucl.write(">{0}\n{1}\n".format(line["contig_id"], nucl_seqs[line["contig_id"]].seq))
filtered_prot.write(">{0}\n{1}\n".format(line["contig_id"], prot_seqs[line["contig_id"]].seq))
#!/usr/bin/env python
import sys
import hmmgs_utils
from Bio import SeqIO
if len(sys.argv) != 3:
print >>sys.stderr, "USAGE: attach_starting_mer.py <hmmgs_file"
sys.exit(1)
hmmgs_results = {}
for line in hmmgs_utils.read_hmmgs_file(sys.argv[1]):
hmmgs_results[line[0]] = line
for seq in SeqIO.parse(open(sys.argv[2]), "fasta"):
pass
#!/usr/bin/env python
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import hmmgs_utils
import sys
if len(sys.argv) != 3:
print "USAGE: scatter_length_to_bits.py <hmmgs_file> <chart_file>"
sys.exit(1)
lengths = []
bits = []
for line in hmmgs_utils.read_hmmgs_file(sys.argv[1]):
prot_length = int(line.prot_length)
bits_saved = float(line.bits)
lengths.append(prot_length)
bits.append(bits)
plt.scatter(lengths, bits)
plt.savefig(sys.argv[2])
