#!/usr/bin/env python
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if len(sys.argv) != 3:
print ('Usage: SCRIPT [input ninfo] [output ninfo]')
sys.exit(2)
ninfo = NinfoFile(sys.argv[1])
ninfo.open_to_read()
ns = NinfoSet()
ninfo.read_all(ns)
ninfo.close()
ns.update_info()
ns.sort_by_mp()
ns.reassign_id()
ninfo = NinfoFile(sys.argv[-1])
ninfo.open_to_write()
ninfo.write_all(ns)
ninfo.close()
#linesp[4] # dist
#if first:
# delta1 = mp1 - 1
# delta2 = mp2 - 1
# first = False
if side == 1:
#aln[mp1 - delta1] = mp2 - delta2
aln[mp1] = mp2
elif side == 2:
#aln[mp2 - delta2] = mp1 - delta1
aln[mp2] = mp1
else:
print('"side" is not acceptable. See usage')
sys.exit(2)
ns = NinfoSet()
file_ninfo = NinfoFile(sys.argv[1])
file_ninfo.open_to_read()
file_ninfo.read_all(ns)
file_ninfo.close()
ns_new = NinfoSet()
# 両方のユニットともターゲットのときは、
# 両方のIDがalnに含まれていないとaddしない
# BondLengths
add1 = False
add2 = False
for ni in ns.bondlengths:
if ni.iunit1 == target:
#!/usr/bin/env python
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if len(sys.argv) != 3:
print("Usage: SCRIPT [input ninfo 1] [input ninfo 2]")
sys.exit(2)
nf = NinfoFile(sys.argv[1])
nf.open_to_read()
ns1 = NinfoSet()
nf.read_all(ns1)
nf.close()
nf = NinfoFile(sys.argv[2])
nf.open_to_read()
ns2 = NinfoSet()
nf.read_all(ns2)
nf.close()
nhb1 = len(ns1.hbondDTs)
nhb2 = len(ns2.hbondDTs)
# Do not use index 0
flag1 = [False] * (nhb1 + 1)
flag2 = [False] * (nhb2 + 1)
else: # end5 = 'S'
if args.end3 == 'P':
nmp = 3 * len(seq[iseq]) - 3
elif args.end3 == 'S':
nmp = 3 * len(seq[iseq]) - 2
elif args.end3 == 'B':
nmp = 3 * len(seq[iseq]) - 1
nmp_chains.append(nmp)
nmp_offset.append(sum(nmp_offset) + nmp)
################################################
## This is the main object to be constructed ##
################################################
ns = NinfoSet()
##############
## Bond ##
##############
nmp_pre = 0
for iseq in range(n_seq):
iunit = iseq + 1
n_nt = len(seq[iseq])
# for the first nt
if args.end5 == 'P':
# P - S
bl = BondLength(iunit1=iunit,
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if __name__ == '__main__':
if len(sys.argv) != 10:
print(
'Usage: SCRIPT [ninfo (one-by-one)] [unit] [dist] [side] [unit] [dist] [side] [edc (post_edc.out)] [out]'
)
print('')
sys.exit(2)
fninfo_in = NinfoFile(sys.argv[1])
fninfo_in.open_to_read()
ns = NinfoSet()
fninfo_in.read_all(ns)
ns.update_info()
fninfo_in.close()
fninfo_out = NinfoFile(sys.argv[-1])
fninfo_out.open_to_write()
unit_aln1 = int(sys.argv[2])
aln1 = {}
side = int(sys.argv[4])
for line in open(sys.argv[3]):
linesp = line.split()
res1 = int(linesp[0]) # Dunkle res
mp1 = int(linesp[1]) # Dunkle mp
res2 = int(linesp[2]) # Jenner res
from cafysis.elements.ninfo import NinfoSet
if len(sys.argv) != 6:
print(
'Usage: SCRIPT [ninfo file] [edc file] [dist(aln) file] [factor] [output ninfo file]'
)
sys.exit(2)
f_ninfo = NinfoFile(sys.argv[1])
f_edc = open(sys.argv[2], 'r')
f_dist = open(sys.argv[3], 'r')
factor = float(sys.argv[4])
f_out_ninfo = NinfoFile(sys.argv[-1])
f_ninfo.open_to_read()
ninfo = NinfoSet()
f_ninfo.read_all(ninfo)
f_ninfo.close()
f_out_ninfo.open_to_write()
f_out_ninfo._file.write('#0: ' + sys.argv[0] + '\n')
f_out_ninfo._file.write('#1: ' + sys.argv[1] + '\n')
f_out_ninfo._file.write('#2: ' + sys.argv[2] + '\n')
f_out_ninfo._file.write('#3: ' + sys.argv[3] + '\n')
f_out_ninfo._file.write('#4: ' + sys.argv[4] + '\n')
f_out_ninfo._file.write('#5: ' + sys.argv[5] + '\n')
aln = {}
# Read from dist file
'''
# Jenner Dunkle
Created on 2012/01/19
@author: Naoto Hori
'''
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if __name__ == '__main__':
if len(sys.argv) != 3:
print('Usage: %SCRIPT [input ninfo file] [output prefix]')
sys.exit(2)
file_ninfo = NinfoFile(sys.argv[1])
file_ninfo.open_to_read()
ns = NinfoSet()
file_ninfo.read_all(ns)
ns.update_info()
file_ninfo.close()
prefix = sys.argv[2]
ndi = ns.dict_of_ninfoset_by_unit()
for i in range(1, ns.max_unit + 1):
for j in range(i, ns.max_unit + 1):
if ndi[(i, j)].max_unit != 0:
file_out = NinfoFile(prefix + '%03i_%03i.ninfo' % (i, j))
file_out.open_to_write()
file_out.write_all(ndi[(i, j)])
#file_out.write_unit(ns, i, j)
file_out.close()
if not len(sys.argv) in (3, 4):
print('\nUsage 1: % SCRIPT [ninfo file] [output file (csv)]')
print(
' 2: % SCRIPT [ninfo file] [output file (csv)] [output list file]\n'
)
sys.exit(2)
# input
f_ninfo = NinfoFile(sys.argv[1])
f_out = open(sys.argv[2], 'w')
flg_out_list = False
if len(sys.argv) == 4:
flg_out_list = True
f_out_list = open(sys.argv[3], 'w')
ninfo = NinfoSet()
f_ninfo.open_to_read()
f_ninfo.read_all(ninfo)
f_ninfo.close()
ninfo.update_info()
nunit = ninfo.max_unit
# Count the number of contacts or basepairs
data = {}
for i in range(1, nunit + 1):
for j in range(i, nunit + 1):
n_con = len(ninfo.get_contacts_by_unit(i, j))
n_bp = len(ninfo.get_basepairs_by_unit(i, j))
data[(i, j)] = (n_con, n_bp)
data[(j, i)] = (n_con, n_bp)