def create_merged_seq(self):
"""Writes merged target-ordered query sequence"""
align = pd.read_table(os.path.join(self.out_dir, "longest_segments.txt"))
align.sort(columns=["target_name", "target_final_start"], inplace=True)
out = open(os.path.join(self.out_dir, "merged_seq.fa"), "w")
curr_target_name = ""
i = 0
start = 0
for row in align.iterrows():
query = row[1]['query_name']
target = row[1]['target_name']
fa = FastaHack(self.query_fas[query])
if curr_target_name != target:
if i > 0:
out.write("\n")
i = 1
out.write(">{0}\n".format(target))
curr_target_name = target
fasub = fa.get_sequence(query)
if row[1]['query_strand'] == "-":
fasub = futil.reverse_complement(fasub)
fasub1, start = futil.format_fasta(fasub, start)
[out.write(x) for x in fasub1]
ns = "N" * 1000
ns1, start = futil.format_fasta(ns, start)
[out.write(x) for x in ns1]
out.write("\n")
class FastaTestMore(FastaHackTest):
def setUp(self):
self.fa = FastaHack(FA)
def test_query(self):
self.assertEqual(self.fa.get_sub_sequence("1", 0, 4), "TAACC")
self.assertEqual(self.fa.get_sequence("1:1-5"), "TAACC")
self.assertEqual(self.fa["1:1-5"], "TAACC")
self.assertEqual(self.fa["1:4-5"], "CC")
print >>stderr,"done "
curr_chr=None
curr_wnd_bin=0
for xi in xrange(len(regions_chrms)):
chr=regions_chrms[xi]
start,end= regions_coords[xi]
wnds = regions_wnds[xi]
#if chr!="chr20": continue
if curr_chr!=chr:
curr_chr=chr
curr_wnd_bin=0
seq_str = (fa.get_sequence(curr_chr)[:]).upper()
char_seq_str = np.array(seq_str,'c')
GC = (char_seq_str=="G")|(char_seq_str=="C")
notN = (char_seq_str!="N")
print "chr %s total GC %f"%(curr_chr, np.sum(GC)/float(np.sum(notN)))
csum_GC = np.cumsum(GC).astype(np.float)
print "REGION",chr,start,end,wnds.shape, o.wnd_width
bp_starts, bp_ends = wnds[:,0]+start, wnds[:,1]+start
real_lens = bp_ends-bp_starts
curr_GC = (csum_GC[bp_ends] - csum_GC[bp_starts])/real_lens
#@regressions=g_data.get_regression(chr,start,end,wnds,mask,int(o.wnd_width))
##l_regressions=regressions.shape[0]
l=wnds.shape[0]
print wnds.shape
