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Fix compilation warnings in _pyrodigal.pyx
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@althonos
althonos committed Sep 18, 2021
1 parent 1ba750c commit 7eda392
Showing 1 changed file with 28 additions and 25 deletions.
53 changes: 28 additions & 25 deletions pyrodigal/_pyrodigal.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ import threading

cdef int IDEAL_SINGLE_GENOME = 100000
cdef int MIN_SINGLE_GENOME = 20000
cdef size_t WINDOW = 120
cdef int WINDOW = 120
cdef size_t MIN_GENES_ALLOC = 8
cdef size_t MIN_NODES_ALLOC = 8 * MIN_GENES_ALLOC
cdef set TRANSLATION_TABLES = set(range(1, 7)) | set(range(9, 17)) | set(range(21, 26))
Expand Down Expand Up @@ -1633,13 +1633,14 @@ cpdef void calc_dicodon_gene(TrainingInfo tinf, Sequence seq, Nodes nodes, int i
tinf.tinf.gene_dc[i] = -5.0

cdef int* calc_most_gc_frame(Sequence seq) nogil except NULL:
cdef size_t i
cdef size_t j
cdef int win
cdef int* fwd
cdef int* bwd
cdef int* tot
cdef int* gp
cdef int i
cdef int j
cdef int win
cdef int* fwd
cdef int* bwd
cdef int* tot
cdef int* gp
cdef int slen = seq.slen

gp = <int*> malloc(seq.slen*sizeof(int));
fwd = <int*> malloc(seq.slen*sizeof(int));
Expand All @@ -1649,29 +1650,30 @@ cdef int* calc_most_gc_frame(Sequence seq) nogil except NULL:
free(gp)
free(bwd)
free(tot)
return NULL
with gil:
raise MemoryError("could not allocate GC frame buffers")

for i in range(seq.slen):
for i in range(slen):
fwd[i] = 0
bwd[i] = 0
tot[i] = 0
gp[i] = -1

for j in range(0, seq.slen):
for j in range(0, slen):
if j < 3:
fwd[j] = seq._is_gc(j)
bwd[seq.slen-j-1] = seq._is_gc(seq.slen-j-1)
else:
fwd[j] = fwd[j-3] + seq._is_gc(j)
bwd[seq.slen-j-1] = bwd[seq.slen-j+2] + seq._is_gc(seq.slen-j-1)
for i in range(seq.slen):
bwd[slen-j-1] = bwd[slen-j+2] + seq._is_gc(slen-j-1)
for i in range(slen):
tot[i] = fwd[i] + bwd[i] - seq._is_gc(i);
if i >= WINDOW//2:
tot[i] -= fwd[i-WINDOW//2]
if i + WINDOW//2 < seq.slen:
tot[i] -= bwd[i+WINDOW//2]
free(bwd);
for i in range(0, seq.slen-2, 3):
for i in range(0, slen-2, 3):
win = sequence.max_fr(tot[i], tot[i+1], tot[i+2])
for j in range(3):
gp[i+j] = win
Expand All @@ -1689,7 +1691,7 @@ cpdef int calc_orf_gc(Nodes nodes, Sequence seq, TrainingInfo tinf) nogil except

# direct strand
gc[0] = gc[1] = gc[2] = 0.0
for i in reversed(range(nodes.length)):
for i in reversed(range(<int> nodes.length)):
if nodes.nodes[i].strand == 1:
phase = nodes.nodes[i].ndx %3
if nodes.nodes[i].type == node_type.STOP:
Expand All @@ -1704,7 +1706,7 @@ cpdef int calc_orf_gc(Nodes nodes, Sequence seq, TrainingInfo tinf) nogil except

# reverse strand
gc[0] = gc[1] = gc[2] = 0.0
for i in range(nodes.length):
for i in range(<int> nodes.length):
if nodes.nodes[i].strand == -1:
phase = nodes.nodes[i].ndx % 3
if nodes.nodes[i].type == node_type.STOP:
Expand Down Expand Up @@ -1755,12 +1757,12 @@ cpdef int dynamic_programming(Nodes nodes, TrainingInfo tinf, bint final=False)
if nodes.length == 0:
return -1

for i in range(nodes.length):
for i in range(<int> nodes.length):
nodes.nodes[i].score = 0
nodes.nodes[i].traceb = -1
nodes.nodes[i].tracef = -1

for i in range(nodes.length):
for i in range(<int> nodes.length):
# Set up distance constraints for making connections,
# but make exceptions for giant ORFS.
min = 0 if i < dprog.MAX_NODE_DIST else i - dprog.MAX_NODE_DIST
Expand All @@ -1774,7 +1776,7 @@ cpdef int dynamic_programming(Nodes nodes, TrainingInfo tinf, bint final=False)
for j in range(min, i):
dprog.score_connection(nodes.nodes, j, i, tinf.tinf, final)

for i in reversed(range(nodes.length)):
for i in reversed(range(<int> nodes.length)):
if nodes.nodes[i].strand == 1 and nodes.nodes[i].type != node_type.STOP:
continue
if nodes.nodes[i].strand == -1 and nodes.nodes[i].type == node_type.STOP:
Expand Down Expand Up @@ -2000,8 +2002,9 @@ cpdef void rbs_score(Nodes nodes, Sequence seq, TrainingInfo tinf) nogil:
cdef int i
cdef int j
cdef int cur_sc[2]
cdef int slen = seq.slen

for i in range(nodes.length):
for i in range(<int> nodes.length):
if nodes.nodes[i].type == node_type.STOP or nodes.nodes[i].edge:
continue
nodes.nodes[i].rbs[0] = nodes.nodes[i].rbs[1] = 0
Expand All @@ -2017,11 +2020,11 @@ cpdef void rbs_score(Nodes nodes, Sequence seq, TrainingInfo tinf) nogil:
if cur_sc[1] > nodes.nodes[i].rbs[1]:
nodes.nodes[i].rbs[1] = cur_sc[1]
else:
for j in range(seq.slen - nodes.nodes[i].ndx - 21, seq.slen - nodes.nodes[i].ndx - 6):
if j > seq.slen-1:
for j in range(slen - nodes.nodes[i].ndx - 21, slen - nodes.nodes[i].ndx - 6):
if j + 1 > slen:
continue
cur_sc[0] = shine_dalgarno_exact(seq, j, seq.slen-1-nodes.nodes[i].ndx, tinf, strand=-1)
cur_sc[1] = shine_dalgarno_mm(seq, j, seq.slen-1-nodes.nodes[i].ndx, tinf, strand=-1)
cur_sc[0] = shine_dalgarno_exact(seq, j, slen-1-nodes.nodes[i].ndx, tinf, strand=-1)
cur_sc[1] = shine_dalgarno_mm(seq, j, slen-1-nodes.nodes[i].ndx, tinf, strand=-1)
if cur_sc[0] > nodes.nodes[i].rbs[0]:
nodes.nodes[i].rbs[0] = cur_sc[0]
if cur_sc[1] > nodes.nodes[i].rbs[1]:
Expand Down Expand Up @@ -2117,7 +2120,7 @@ cpdef void score_nodes(Nodes nodes, Sequence seq, TrainingInfo tinf, bint closed
if nodes.nodes[j].edge and nodes.nodes[i].stop_val == nodes.nodes[j].stop_val:
nodes.nodes[i].uscore += node.EDGE_UPS*tinf.tinf.st_wt
break
elif i >= nodes.length - 500 and nodes.nodes[i].strand == -1:
elif i + 500>= nodes.length and nodes.nodes[i].strand == -1:
for j in range(i+1, nodes.length):
if nodes.nodes[j].edge and nodes.nodes[i].stop_val == nodes.nodes[j].stop_val:
nodes.nodes[i].uscore += node.EDGE_UPS*tinf.tinf.st_wt
Expand Down

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