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mpievolbio-scicomp
RepinPop
Commits
2b062f1d
Commit
2b062f1d
authored
Jan 14, 2022
by
frederic.bertels
Browse files
added a parameter to the main function call that sets the group seed sequence distance.
parent
c1056f5f
Pipeline
#266105
failed with stages
in 8 minutes and 10 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
REPIN_ecology/REPIN_ecology/src/REPINpopulations/DetermineFocalSeeds.java
View file @
2b062f1d
...
...
@@ -11,7 +11,7 @@ public class DetermineFocalSeeds {
File
outFolder
=
new
File
(
args
[
1
]);
int
minFreq
=
Integer
.
parseInt
(
args
[
2
]);
int
wordLength
=
Integer
.
parseInt
(
args
[
3
]);
DetermineFocalSeeds
dfs
=
new
DetermineFocalSeeds
(
genome
,
outFolder
,
minFreq
,
wordLength
);
DetermineFocalSeeds
dfs
=
new
DetermineFocalSeeds
(
genome
,
outFolder
,
minFreq
,
wordLength
,
30
);
}
File
genome
;
int
wl
;
...
...
@@ -21,8 +21,9 @@ public class DetermineFocalSeeds {
int
flanking
=
30
;
String
[]
seedSequences
;
File
outFolder
;
public
DetermineFocalSeeds
(
File
genome
,
File
outFolder
,
int
minRepFreq
,
int
wl
)
{
public
DetermineFocalSeeds
(
File
genome
,
File
outFolder
,
int
minRepFreq
,
int
wl
,
int
flanking
)
{
this
.
genome
=
genome
;
this
.
flanking
=
flanking
;
this
.
outFolder
=
outFolder
;
this
.
wl
=
wl
;
genomeFolder
=
genome
.
getParentFile
();
...
...
REPIN_ecology/REPIN_ecology/src/REPINpopulations/DeterminePopulationFrequencies.java
View file @
2b062f1d
...
...
@@ -50,21 +50,22 @@ public class DeterminePopulationFrequencies {
DeterminePopulationFrequencies
dpf
;
String
program
=
"tblastn"
;
int
MCLThreads
=
Integer
.
parseInt
(
args
[
9
]);
int
distanceGroupSeeds
=
Integer
.
parseInt
(
args
[
10
]);
// legacy_blast path not given.
if
(
args
.
length
==
1
0
)
{
dpf
=
new
DeterminePopulationFrequencies
(
inFolder
,
outFolder
,
focalSeedGenome
,
minRepFreq
,
wordlength
,
queryRAYT
,
program
,
treeFile
,
""
,
evalue
,
analyseREPIN
,
MCLThreads
);
if
(
args
.
length
==
1
1
)
{
dpf
=
new
DeterminePopulationFrequencies
(
inFolder
,
outFolder
,
focalSeedGenome
,
minRepFreq
,
wordlength
,
queryRAYT
,
program
,
treeFile
,
""
,
evalue
,
analyseREPIN
,
MCLThreads
,
distanceGroupSeeds
);
dpf
.
print
(
out
);
}
// legacy_blast path given.
else
if
(
args
.
length
==
1
1
)
{
String
legacyBlastPerlLocation
=
args
[
1
0
];
dpf
=
new
DeterminePopulationFrequencies
(
inFolder
,
outFolder
,
focalSeedGenome
,
minRepFreq
,
wordlength
,
queryRAYT
,
program
,
treeFile
,
legacyBlastPerlLocation
,
evalue
,
analyseREPIN
,
MCLThreads
);
else
if
(
args
.
length
==
1
2
)
{
String
legacyBlastPerlLocation
=
args
[
1
1
];
dpf
=
new
DeterminePopulationFrequencies
(
inFolder
,
outFolder
,
focalSeedGenome
,
minRepFreq
,
wordlength
,
queryRAYT
,
program
,
treeFile
,
legacyBlastPerlLocation
,
evalue
,
analyseREPIN
,
MCLThreads
,
distanceGroupSeeds
);
dpf
.
print
(
out
);
}
}
// Workhorse function.
public
DeterminePopulationFrequencies
(
File
inFolder
,
File
outFolder
,
String
focalSeedGenome
,
int
minRepFreq
,
int
wordlength
,
File
queryRAYT
,
String
program
,
File
treeFile
,
String
legacyBlastPerlLocation
,
String
evalue
,
boolean
analyseREPIN
,
int
MCLThreads
){
public
DeterminePopulationFrequencies
(
File
inFolder
,
File
outFolder
,
String
focalSeedGenome
,
int
minRepFreq
,
int
wordlength
,
File
queryRAYT
,
String
program
,
File
treeFile
,
String
legacyBlastPerlLocation
,
String
evalue
,
boolean
analyseREPIN
,
int
MCLThreads
,
int
distanceGroupSeeds
){
this
.
inFolder
=
inFolder
;
this
.
outFolder
=
outFolder
;
this
.
MCLThreads
=
MCLThreads
;
...
...
@@ -72,7 +73,7 @@ public class DeterminePopulationFrequencies {
genomes
=
getFiles
();
this
.
legacyBlastPerlLocation
=
legacyBlastPerlLocation
;
this
.
queryRAYT
=
queryRAYT
;
this
.
focalSeeds
=
getFocalSeeds
(
focalSeedGenome
,
minRepFreq
,
wordlength
);
this
.
focalSeeds
=
getFocalSeeds
(
focalSeedGenome
,
minRepFreq
,
wordlength
,
distanceGroupSeeds
);
this
.
genomeFolder
=
inFolder
;
this
.
analyseREPIN
=
analyseREPIN
;
e
=
evalue
;
...
...
@@ -116,9 +117,9 @@ public class DeterminePopulationFrequencies {
return
list
.
toArray
(
new
String
[
0
]);
}
private
String
[]
getFocalSeeds
(
String
genome
,
int
minRepFreq
,
int
wl
)
{
private
String
[]
getFocalSeeds
(
String
genome
,
int
minRepFreq
,
int
wl
,
int
distanceGroupSeeds
)
{
File
fsg
=
new
File
(
inFolder
+
"/"
+
genome
);
DetermineFocalSeeds
dfs
=
new
DetermineFocalSeeds
(
fsg
,
outFolder
,
minRepFreq
,
wl
);
DetermineFocalSeeds
dfs
=
new
DetermineFocalSeeds
(
fsg
,
outFolder
,
minRepFreq
,
wl
,
distanceGroupSeeds
);
return
dfs
.
getFocalSeeds
();
}
...
...
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