def align_pairwise(genomes, new_align, r_root_dir, g_root_dir,dirs, run, max_size, chop_mode, mauve_exec, mtype, segtype, min_size):
"""Make a pairwise alignment."""
# set up directories
aln_dir = r_root_dir+run+dirs['aln_segs']
map_dir = r_root_dir+run+dirs['maps']
# load inputs and process genomes
seq_dir = g_root_dir
ref = [Noodle(genome, seq_dir) for genome in genomes
if genome['order'] == 1][0]
query = [Noodle(genome, seq_dir) for genome in genomes
if genome['order'] == 2][0]
# align if needed
print "Aligning", ref.name, "and", query.name, "...",
if new_align:
mauve_pw_align(ref, query, r_root_dir, g_root_dir, dirs, run, max_size, chop_mode, mauve_exec, mtype)
# process data segments
print "Processing segments ..",
seg_file = aln_dir+ref.name+"_"+query.name+"_segs.txt"
pair_data = process_segdata(seg_file, ref, query, segtype)
print "OK"
# map of query aligned to reference
print "Mapping ...",
map_file = map_dir+run+"_"+ref.name+"_vs_"+query.name+".pdf"
pairwise_draw(ref, query, pair_data, map_file, 'dual', 'dual', 'm',
'fct', 'fct', idpt, fct_flags, fct_colors, min_size)
print "OK\n"
def align_multi(genomes, new_align, r_root_dir, g_root_dir, dirs, run, max_size, chop_mode, mauve_exec, mtype, segtype, idpt, fct_flags, fct_colors, min_size):
"""Make a multiple alignment."""
# set up directories
aln_dir = r_root_dir+run+dirs['aln_segs']
map_dir = r_root_dir+run+dirs['maps']
# load inputs, process and pair up genomes
seq_dir = g_root_dir
g_pairs = []
counter = 1
while counter < len(genomes):
g_pairs.append(([Noodle(genome, seq_dir) for genome in genomes if
genome['order'] == counter][0],
[Noodle(genome, seq_dir) for genome in genomes if
genome['order'] == counter+1][0]))
counter +=1
# process pairs
for (ref, query) in g_pairs:
# align if needed
print "Aligning", ref.name, "and", query.name, "...",
if new_align:
mauve_pw_align(ref, query, r_root_dir, g_root_dir, dirs, run, max_size, chop_mode,
mauve_exec, mtype)
# traverse genome pairs
segdata_list = []
counter = 0
for (ref, query) in g_pairs:
counter +=1
# process data segments
print "Processing pair", counter, "segments ...",
p_seg_file = aln_dir+ref.name+"_"+query.name+"_segs.txt"
pair_data = process_segdata(p_seg_file, ref, query, segtype)
segdata_list.append(pair_data)
print "OK"
# make a pairwise map while we're at it
print "Mapping pair", counter, "...",
p_map_file = map_dir+run+"_"+ref.name+"_vs_"+query.name+".pdf"
pairwise_draw(ref, query, pair_data, p_map_file, 'dual', 'dual', 'm',
'fct', 'fct', idpt, fct_flags, fct_colors, min_size)
print "OK"
# map of query aligned to reference
print "Mapping multiple alignment...",
map_file = map_dir+run+".pdf"
multi_draw(g_pairs, segdata_list, map_file, idpt, fct_flags, fct_colors, min_size)
print "OK\n"
def align_multi(genomes, new_align, dirs, run):
"""Make a multiple alignment."""
# load inputs, process and pair up genomes
seq_dir = dirs['seqfiles']
g_pairs = []
counter = 1
while counter < len(genomes):
g_pairs.append(([Noodle(genome, seq_dir) for genome in genomes if
genome['order'] == counter][0],
[Noodle(genome, seq_dir) for genome in genomes if
genome['order'] == counter+1][0]))
counter +=1
# process pairs
for (ref, query) in g_pairs:
# align if needed
print "Aligning", ref.name, "and", query.name, "...",
if new_align:
mauve_pw_align(ref, query, dirs)
# traverse genome pairs
segdata_list = []
counter = 0
for (ref, query) in g_pairs:
counter +=1
# process data segments
print "Processing pair", counter, "segments ...",
p_seg_file = dirs['aln_segs']+"/"+ref.name+"_"+query.name+"_segs.txt"
pair_data = process_segdata(p_seg_file, ref, query)
segdata_list.append(pair_data)
print "OK"
# make a pairwise map while we're at it
print "Mapping pair", counter, "...",
p_map_file = dirs['maps']+run+"_"+ref.name+"_vs_"+query.name+".pdf"
pairwise_draw(ref, query, pair_data, p_map_file, 'dual', 'dual', 'm',
'fct', 'fct')
print "OK"
# map of query aligned to reference
print "Mapping multiple alignment...",
map_file = dirs['maps']+run+".pdf"
multi_draw(g_pairs, segdata_list, map_file)
print "OK\n"
def align_pairwise(genomes, new_align, dirs, run):
"""Make a pairwise alignment."""
# load inputs and process genomes
seq_dir = dirs['seqfiles']
ref = [Noodle(genome, seq_dir) for genome in genomes
if genome['order'] == 1][0]
query = [Noodle(genome, seq_dir) for genome in genomes
if genome['order'] == 2][0]
# align if needed
print "Aligning", ref.name, "and", query.name, "...",
if new_align:
mauve_pw_align(ref, query, dirs)
# process data segments
print "Processing segments ..",
seg_file = dirs['aln_segs']+"/"+ref.name+"_"+query.name+"_segs.txt"
pair_data = process_segdata(seg_file, ref, query)
print "OK"
# map of query aligned to reference
print "Mapping ...",
map_file = dirs['maps']+run+"_"+ref.name+"_vs_"+query.name+".pdf"
pairwise_draw(ref, query, pair_data, map_file, 'dual', 'dual', 'm',
'fct', 'fct')
print "OK\n"