diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/filter_melting_temperature.py | 28 |
1 files changed, 19 insertions, 9 deletions
diff --git a/src/filter_melting_temperature.py b/src/filter_melting_temperature.py index 26f6b54..b452b92 100644 --- a/src/filter_melting_temperature.py +++ b/src/filter_melting_temperature.py @@ -1,10 +1,11 @@ #!/usr/bin/env python +import argparse import sys +import math """Calculate the thermodynamic melting temperatures of nucleotide sequences.""" -import math -def Tm_staluc(s, dnac=5000, na=10, mg=20, dNTPs=10): +def Tm_staluc(s, dna=5000, na=10, mg=20, dntps=10): """Returns DNA/DNA tm using nearest neighbor thermodynamics. dnac is DNA concentration [nM] @@ -73,7 +74,7 @@ def Tm_staluc(s, dnac=5000, na=10, mg=20, dNTPs=10): vsTC,vh = tercorr(sup) vs = vsTC - k = (dnac/4.0)*1e-9 + k = (dna/4.0)*1e-9 #With complementary check on, the 4.0 should be changed to a variable. #DNA/DNA @@ -102,10 +103,10 @@ def Tm_staluc(s, dnac=5000, na=10, mg=20, dNTPs=10): tm = ((1000* (-dh))/(-ds+(R * (math.log(k)))))-273.15 Mmg = mg * 1E-3 Mna = na * 1E-3 - Mdntp = dNTPs * 1E-3 + Mdntp = dntps * 1E-3 - Fmg = ((3E4 * Mdntp - 3E4 * Mmg + 1) + ((3E4 * Mdntp - 3E4 * Mmg + 1)**2 + 4 * 3E4 * Mmg)**0.5 )/ (2 * 3E4) - cationratio = - Fmg**0.5 / Mna + Fmg = (-(3E4 * Mdntp - 3E4 * Mmg + 1) + ((3E4 * Mdntp - 3E4 * Mmg + 1)**2 + 4 * 3E4 * Mmg )**0.5 )/ (2 * 3E4) + cationratio = Fmg**0.5 / Mna if cationratio < 0.22: SaltCorrectedTm = 1 / ( (1 / tm) + ((4.29 * fgc(s) - 3.95) * math.log(Mna) + 0.940 * (math.log(Mna))**2) * 1E-5 ) @@ -141,11 +142,20 @@ def in_temp_range(kmer): return min_melting_temp < melt_temp < max_melting_temp -min_melting_temp = float(sys.argv[1]) -max_melting_temp = float(sys.argv[2]) if __name__ == "__main__": + + parser = argparse.ArgumentParser(description="Filter mers, input is stdin, output is stdout") + parser.add_argument("-m", "--min", help="min melting temp [c]", required=True, type=float) + parser.add_argument("-x", "--max", help="max melting temp [c]", required=True, type=float) + parser.add_argument("-d", "--dna", help="DNA concentation [nM]", required=False, type=int, default=5000) + parser.add_argument("-n", "--na", help="sodium concentation [mM]", required=False, type=int, default=10) + parser.add_argument("-g", "--mg", help="magnesium concentation [mM]", required=False, type=int, default=20) + parser.add_argument("-p", "--dntp", help="dNTPs concentation [mM]", required=False, type=int, default=10) + + ar = parser.parse_args() + for line in sys.stdin: - if min_melting_temp < Tm_staluc(line.split("\t")[0]) < max_melting_temp: + if ar.min < Tm_staluc(line.split("\t")[0], dna=ar.dna, na=ar.na, mg=ar.mg, dntps=ar.dntp) < ar.max: sys.stdout.write(line) |