writer.write(line.upper())
else:
writer.write(line)
original_backbone = MutableAlignment()
done = original_backbone.read_filepath(new_backbone_file)
# all query sequences
original_frag_file = (
'/Users/gillianchu/warnow/bin/gitrepos/smirarab-sepp-17a33aa/trial/all_query.txt'
)
original_frag = MutableAlignment()
done = original_frag.read_filepath(original_frag_file)
# First build extended alignment on entire fragment set
extendedAlignment = ExtendedAlignment(original_frag.get_sequence_names())
dir = '/Users/gillianchu/warnow/bin/gitrepos/smirarab-sepp-17a33aa/trial/'
for a in [1, 2]:
a = str(a)
print("Working on HMM %s\n" % a)
# query sequences
aligned_files = glob.glob(str(dir) + 's' + str(a) + '_query.aln')
if a == '1':
sequence_files = glob.glob(str(dir) + 'query_x.txt')
elif a == '2':
sequence_files = glob.glob(str(dir) + 'query_y.txt')
# sequences your hmm was trained on. Ensure you didn't just take the backbone alignment and
# restrict the subset of sequences. This file must not have any gaps in it.
from sepp.scheduler import JobPool
from multiprocessing import Pool, Manager
from sepp.alignment import ExtendedAlignment
import glob
job_joiner = JoinAlignJobs
original_backbone_file = '/projects/sate8/namphuon/ultra_large/1000000/sate.fasta'
original_backbone = MutableAlignment()
done = original_backbone.read_filepath(original_backbone_file)
original_frag_file = '/projects/sate8/namphuon/ultra_large/1000000/initial.fas.100'
original_frag = MutableAlignment()
done = original_frag.read_filepath(original_frag_file)
#First build extended alignment on entire fragment set
extendedAlignment = ExtendedAlignment(original_frag.get_sequence_names())
dirs = glob.glob('/projects/sate8/namphuon/ultra_large/1000000/upp_100_10_new/temp/upp.1_HNlM/root/P_0/A_0_*/')
dirs.reverse()
for dir in dirs:
print "Working on %s\n" % dir
aligned_files = glob.glob('%sFC_*/hmmalign.results.*' % dir)
sequence_files = glob.glob('%sFC_*/hmmalign.frag.*' % dir)
base_alignment_file = glob.glob('%s/*.fasta' % dir)
base_alignment = MutableAlignment()
done = base_alignment.read_filepath(base_alignment_file[0])
subbackbone = original_backbone.get_soft_sub_alignment(base_alignment.get_sequence_names())
frags = MutableAlignment()
sequence_names = []
for file in sequence_files:
from sepp.problem import SeppProblem
import glob
job_joiner = JoinAlignJobs
original_backbone_file = ('/projects/sate8/namphuon/ultra_large/1000000/'
'sate.fasta')
original_backbone = MutableAlignment()
done = original_backbone.read_filepath(original_backbone_file)
original_frag_file = ('/projects/sate8/namphuon/ultra_large/1000000/'
'initial.fas.100')
original_frag = MutableAlignment()
done = original_frag.read_filepath(original_frag_file)
# First build extended alignment on entire fragment set
extendedAlignment = ExtendedAlignment(original_frag.get_sequence_names())
dirs = glob.glob('/projects/sate8/namphuon/ultra_large/1000000/upp_100_10_new/'
'temp/upp.1_HNlM/root/P_0/A_0_*/')
dirs.reverse()
for dir in dirs:
print("Working on %s\n" % dir)
aligned_files = glob.glob('%sFC_*/hmmalign.results.*' % dir)
sequence_files = glob.glob('%sFC_*/hmmalign.frag.*' % dir)
base_alignment_file = glob.glob('%s/*.fasta' % dir)
base_alignment = MutableAlignment()
done = base_alignment.read_filepath(base_alignment_file[0])
subbackbone = original_backbone.get_soft_sub_alignment(
base_alignment.get_sequence_names())
frags = MutableAlignment()
