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ORG.Asm
ORG.Asm
Commits
ce8a9a7a
Commit
ce8a9a7a
authored
Apr 13, 2016
by
Eric Coissac
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Swich to the new version of the progress bar
parent
089f0892
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4 changed files
with
15 additions
and
11 deletions
+15
-11
VERSION
VERSION
+1
-1
_ahocorasick.pyx
python/orgasm/backtranslate/_ahocorasick.pyx
+8
-5
_multi.pyx
python/orgasm/multialign/_multi.pyx
+5
-4
version.py
python/orgasm/version.py
+1
-1
No files found.
VERSION
View file @
ce8a9a7a
0.2.0
0.2.0
2
python/orgasm/backtranslate/_ahocorasick.pyx
View file @
ce8a9a7a
# cython: language_level=3
from ._ahocorasick cimport *
from orgasm.utils._progress cimport progressBar
from orgasm.apps.progress cimport ProgressBar
from orgasm.utils.dna import reverseComplement
from ._bitvector cimport BitVector
...
...
@@ -977,6 +978,7 @@ cdef class ProtAhoCorasick(AhoCorasick):
cdef size_t offset
cdef double* shanonTable = buildShanonTable(readsize,&offset)
cdef double* shanonLine
cdef ProgressBar pb
# mid is the number of read frame globally available for each
# protein stored in the automata
...
...
@@ -997,7 +999,8 @@ cdef class ProtAhoCorasick(AhoCorasick):
nuc4 = records + i * (recordsize)
if (progress):
progressBar(1,readcount,True)
pb=ProgressBar(readcount)
# progressBar(1,readcount,True)
while i < readcount:
...
...
@@ -1100,7 +1103,7 @@ cdef class ProtAhoCorasick(AhoCorasick):
i+=1
if (progress):
p
rogressBar(i,readcount
)
p
b(i
)
while (i< readcount and
samereads(nuc4, nuc4bis, readsize64)):
...
...
@@ -1269,7 +1272,7 @@ cdef class NucAhoCorasick(AhoCorasick):
nuc4 = records + i * (recordsize)
if (progress):
p
rogressBar(1,readcount,True
)
p
b=ProgressBar(readcount
)
while i < readcount:
...
...
@@ -1342,7 +1345,7 @@ cdef class NucAhoCorasick(AhoCorasick):
i+=1
if (progress):
p
rogressBar(i,readcount
)
p
b(i
)
while (i< readcount and
samereads(nuc4, nuc4bis, readsize64)):
...
...
python/orgasm/multialign/_multi.pyx
View file @
ce8a9a7a
...
...
@@ -3,7 +3,7 @@
from collections import Counter
from orgasm.
utils._progress cimport progressBar
from orgasm.
apps.progress cimport ProgressBar
from ._dynamic cimport EndGapFree
from orgasm.indexer._orgasm cimport Index
from collections import Counter
...
...
@@ -177,6 +177,7 @@ cdef list alignReads(readids,Index index,size_t kmer=12,int smin=10,size_t delta
cdef size_t h2
cdef bytes s
cdef int j # @DuplicatedSignature
cdef ProgressBar pb
# We dereplicate the sequences
for j in readids:
...
...
@@ -191,12 +192,12 @@ cdef list alignReads(readids,Index index,size_t kmer=12,int smin=10,size_t delta
nali = nseq * (nseq-1) // 2
hashes =[hashSeq(s,kmer) for s in seqs]
p
rogressBar(1,nali,reset=True,head=bytes("Pairwise alignment %6d x %6d " % (0,0),encoding='ascii'
))
p
b = ProgressBar(nali,head="Pairwise alignment %6d x %6d " % (0,0
))
for h1 in range(nseq):
for h2 in range(h1+1,nseq):
p
rogressBar(pos,nali,reset=False,head=bytes("Pairwise alignment %6d x %6d " % (h1,h2),encoding='ascii')
)
pb.head="Pairwise alignment %6d x %6d " % (h1,h2)
p
b(pos
)
pos+=1
ali = alignSequence(seqs[h1],seqs[h2],
...
...
python/orgasm/version.py
View file @
ce8a9a7a
major
=
0
minor
=
'2'
serial
=
'0
1
'
serial
=
'0
2
'
version
=
"
%
d.
%
s.
%
s"
%
(
major
,
minor
,
serial
)
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