allpy
changeset 229:f85ca82c4965
repeats: fix +-1 problem (interval ends)
| author | boris <bnagaev@gmail.com> |
|---|---|
| date | Sat, 27 Nov 2010 19:50:57 +0300 |
| parents | 0ed41390408f |
| children | 684ff5579345 |
| files | repeats/repeat_joiner.py |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
line diff
1.1 --- a/repeats/repeat_joiner.py Sat Nov 27 19:21:17 2010 +0300 1.2 +++ b/repeats/repeat_joiner.py Sat Nov 27 19:50:57 2010 +0300 1.3 @@ -59,7 +59,7 @@ 1.4 if pos_start >= pos_end: 1.5 return [] 1.6 return filter(lambda r: r != self, self.chromosome.find(pos_start, pos_end)) 1.7 - 1.8 + 1.9 def thick_edge(self): 1.10 """ return thick edge (paired repeat) """ 1.11 if self == self.repeat_pair[0]: 1.12 @@ -137,11 +137,12 @@ 1.13 return "%s: [%i, %i)" % (self.chromosome, self.real_start, self.real_end) 1.14 1.15 def __str__(self): 1.16 + """ returns string to put into table file. IMPORTANT: [start, end] """ 1.17 ori = 1 if self.ori else -1 1.18 if self.group_real_start != None: 1.19 group_ori = 1 if self.group_ori else -1 1.20 return "%s %i %i %i %i %i %i" % (self.chromosome, self.start, 1.21 - self.end, self.group_start, self.group_end, ori, group_ori) 1.22 + self.end-1, self.group_start, self.group_end-1, ori, group_ori) 1.23 else: 1.24 return "%s %i %i %i" % (self.chromosome, self.start, 1.25 self.end, ori)