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gad-public
vihgo
Commits
39c51b1b
Commit
39c51b1b
authored
Jan 22, 2021
by
Yannis Duffourd
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Adding full cs sequence capabilities
parent
1efacb84
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1 changed file
with
11 additions
and
34 deletions
+11
-34
Vihgo.cpp
cpp/Vihgo.cpp
+11
-34
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cpp/Vihgo.cpp
View file @
39c51b1b
...
...
@@ -1740,44 +1740,20 @@ void Vihgo::writeFullConsensus() {
cerr
<<
"Writing full consensus sequence ... "
<<
endl
;
ofstream
csStream
;
csStream
.
open
((
this
->
getConsensusFile
()).
c_str
(),
ios
::
out
);
csStream
<<
">"
<<
"full_cs_sequence"
<<
endl
;
map
<
string
,
map
<
int
,
map
<
string
,
int
>>>::
iterator
myIterA
;
map
<
int
,
map
<
string
,
int
>>::
iterator
myIterB
;
map
<
string
,
int
>::
iterator
myIterC
;
map
<
string
,
map
<
int
,
string
>>::
iterator
myIterE
;
map
<
int
,
string
>::
iterator
myIterF
;
for
(
myIterE
=
this
->
protCodon
.
begin
();
myIterE
!=
this
->
protCodon
.
end
();
myIterE
++
)
{
string
prot
=
myIterE
->
first
;
string
chrom
=
getChrFromProt
(
prot
);
if
(
!
(
this
->
sampleData
.
count
(
chrom
)
>
0
))
{
continue
;
}
csStream
<<
">"
<<
prot
<<
endl
;
for
(
myIterF
=
(
myIterE
->
second
).
begin
();
myIterF
!=
(
myIterE
->
second
).
end
();
myIterF
++
)
{
int
aaPosition
=
myIterF
->
first
;
int
gPosition
;
map
<
int
,
int
>
tmpMap
=
this
->
refProtCorresp
[
prot
];
map
<
int
,
int
>::
iterator
myIterG
;
for
(
myIterG
=
tmpMap
.
begin
();
myIterG
!=
tmpMap
.
end
();
myIterG
++
)
{
if
(
myIterG
->
second
==
aaPosition
)
{
gPosition
=
myIterG
->
first
;
break
;
}
}
// cerr << "ppos : " << aaPosition << " ; genomic position is : " <<
// gPosition << endl;
map
<
string
,
map
<
int
,
string
>>::
iterator
myIterA
;
map
<
int
,
string
>::
iterator
myIterB
;
// determine most frequent codon
for
(
myIterA
=
this
->
referenceCodon
.
begin
();
myIterA
!=
this
->
referenceCodon
.
end
();
myIterA
++
)
{
string
chrom
=
myIterA
->
first
;
for
(
myIterB
=
(
myIterA
->
second
).
begin
();
myIterB
!=
(
myIterA
->
second
).
end
();
myIterB
++
)
{
int
gPosition
=
myIterB
->
first
;
// determine most frequent codon at this position
string
codon
=
"NNN"
;
int
count
=
0
;
if
(
this
->
sampleData
[
chrom
].
count
(
gPosition
)
>
0
)
{
map
<
string
,
int
>
tmpMapCodon
;
tmpMapCodon
=
this
->
sampleData
[
chrom
][
gPosition
];
...
...
@@ -1790,6 +1766,7 @@ void Vihgo::writeFullConsensus() {
}
}
}
// write codon : if found will be a true codon, other wise will be a NNN
csStream
<<
codon
;
}
csStream
<<
endl
;
...
...
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