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TranSyT
transyt-scraper
Commits
c693031a
Commit
c693031a
authored
Jul 05, 2018
by
Davide Lagoa
Browse files
blast operation created
parent
c45bc230
Changes
24
Hide whitespace changes
Inline
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.classpath
View file @
c693031a
...
...
@@ -12,11 +12,7 @@
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
</classpathentry>
<classpathentry
kind=
"con"
path=
"org.eclipse.jdt.launching.JRE_CONTAINER"
>
<attributes>
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
</classpathentry>
<classpathentry
kind=
"con"
path=
"org.eclipse.jdt.launching.JRE_CONTAINER"
/>
<classpathentry
kind=
"con"
path=
"org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"
>
<attributes>
<attribute
name=
"maven.pomderived"
value=
"true"
/>
...
...
src/main/java/betaBarrels/Navigate.java
View file @
c693031a
package
betaBarrels
;
import
java.util.concurrent.TimeUnit
;
import
org.openqa.selenium.By
;
import
org.openqa.selenium.WebDriver
;
import
org.openqa.selenium.WebElement
;
...
...
src/main/java/betaBarrels/main.java
View file @
c693031a
package
betaBarrels
;
import
java.util.HashMap
;
import
java.util.Map
;
public
class
main
{
public
static
void
main
(
String
[]
args
)
{
...
...
src/main/java/blast/Blast.java
0 → 100644
View file @
c693031a
package
blast
;
import
java.io.BufferedReader
;
import
java.io.ByteArrayInputStream
;
import
java.io.File
;
import
java.io.InputStream
;
import
java.io.InputStreamReader
;
import
java.net.URL
;
import
java.util.HashMap
;
import
java.util.Map
;
import
java.util.Observable
;
import
java.util.Observer
;
import
java.util.concurrent.ConcurrentHashMap
;
import
java.util.concurrent.ConcurrentLinkedQueue
;
import
java.util.concurrent.atomic.AtomicBoolean
;
import
java.util.concurrent.atomic.AtomicInteger
;
import
org.biojava.nbio.core.sequence.ProteinSequence
;
import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound
;
import
org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
;
import
org.biojava.nbio.core.sequence.io.FastaReader
;
import
org.biojava.nbio.core.sequence.io.FastaReaderHelper
;
import
org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
;
import
org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
;
import
org.biojava.nbio.core.sequence.template.AbstractSequence
;
import
pt.uminho.ceb.biosystems.merlin.bioapis.externalAPI.ncbi.CreateGenomeFile
;
import
pt.uminho.ceb.biosystems.merlin.local.alignments.core.RunSimilaritySearch
;
import
pt.uminho.ceb.biosystems.merlin.utilities.Enumerators.AlignmentScoreType
;
import
pt.uminho.ceb.biosystems.merlin.utilities.Enumerators.Method
;
import
pt.uminho.ceb.biosystems.merlin.utilities.containers.capsules.AlignmentCapsule
;
import
tcdb.tcdbTransportTypesRetriever.TcdbExplorer
;
public
class
Blast
implements
Observer
{
public
Blast
()
{
try
{
performBlast
();
}
catch
(
Exception
e
)
{
e
.
printStackTrace
();
}
}
private
void
performBlast
()
throws
Exception
{
//BLAST
System
.
out
.
println
(
"INIT BLAST!!"
);
String
filePath
=
"C:/Users/Davide/Documents/reactionsBuilderTriage/temp/"
;
String
tcdbFastaFile
=
filePath
.
concat
(
"tcdbSEQs.txt"
);
Map
<
String
,
AbstractSequence
<?>>
tcdbGenes
=
getTcdbInMapFormat
();
System
.
out
.
println
(
"BIOJAVA TCDB!!"
);
CreateGenomeFile
.
buildFastaFile
(
tcdbFastaFile
,
tcdbGenes
);
System
.
out
.
println
(
"BIOJAVA RENATO!!"
);
ConcurrentHashMap
<
String
,
AbstractSequence
<?>>
sequences
=
new
ConcurrentHashMap
<
String
,
AbstractSequence
<?>>();
sequences
.
putAll
(
FastaReaderHelper
.
readFastaProteinSequence
(
new
File
(
"C:/Users/Davide/Downloads/nvulgaris_29421_protein.faa"
)));
System
.
out
.
println
(
"BLAST!!"
);
RunSimilaritySearch
run_similaritySearch
=
new
RunSimilaritySearch
(
tcdbGenes
,
0.1
,
Method
.
SmithWaterman
,
sequences
,
new
AtomicBoolean
(
false
),
new
AtomicInteger
(
0
),
new
AtomicInteger
(
0
),
AlignmentScoreType
.
ALIGNMENT
);
run_similaritySearch
.
setTcdbFastaFilePath
(
tcdbFastaFile
);
run_similaritySearch
.
addObserver
(
this
);
run_similaritySearch
.
setCurrentTempFolderDirectory
(
filePath
);
//////set temp directory here!!!
ConcurrentLinkedQueue
<
AlignmentCapsule
>
results
=
null
;
if
(
sequences
.
keySet
().
size
()>
0
)
results
=
run_similaritySearch
.
runBlastSearch
(
true
);
System
.
out
.
println
(
"BLAST PERFORMED!!"
);
}
/**
*
* @param url
* @return
* @throws Exception
*/
public
static
Map
<
String
,
AbstractSequence
<?>>
getTcdbInMapFormat
()
throws
Exception
{
InputStream
tcdbInputStream
=
(
new
URL
(
TcdbExplorer
.
TCDB_FASTA_URL
)).
openStream
();
BufferedReader
br
=
new
BufferedReader
(
new
InputStreamReader
(
tcdbInputStream
));
StringBuilder
sb
=
new
StringBuilder
();
String
line
;
while
((
line
=
br
.
readLine
())
!=
null
)
sb
.
append
(
line
.
concat
(
"\n"
));
String
theString
=
sb
.
toString
().
replace
(
"</p>"
,
""
).
replace
(
"<p>"
,
""
).
replace
(
">gnl|TC-DB|xxxxxx 3.A.1.205.14 \ndsfgdfg"
,
""
);
byte
[]
bytes
=
theString
.
getBytes
(
"utf-8"
);
tcdbInputStream
=
new
ByteArrayInputStream
(
bytes
);
FastaReader
<
ProteinSequence
,
AminoAcidCompound
>
fastaReader
=
new
FastaReader
<
ProteinSequence
,
AminoAcidCompound
>(
tcdbInputStream
,
//tcdbFile,
new
GenericFastaHeaderParser
<
ProteinSequence
,
AminoAcidCompound
>(),
new
ProteinSequenceCreator
(
AminoAcidCompoundSet
.
getAminoAcidCompoundSet
()));
// System.out.println("CHECK3---->"+LocalDateTime.now().getHour()+":"+LocalDateTime.now().getMinute()+":"+LocalDateTime.now().getSecond());
Map
<
String
,
AbstractSequence
<?>>
tcdb
=
new
HashMap
<>();
tcdb
.
putAll
(
fastaReader
.
process
());
return
tcdb
;
}
@Override
public
void
update
(
Observable
arg0
,
Object
arg1
)
{
// TODO Auto-generated method stub
}
}
src/main/java/tcdb/comparison/Compare.java
View file @
c693031a
...
...
@@ -348,6 +348,8 @@ public class Compare {
workbook
.
write
(
fileOut
);
fileOut
.
flush
();
fileOut
.
close
();
workbook
.
close
();
System
.
out
.
println
(
"xlsx containing the comparison results created"
);
...
...
src/main/java/tcdb/reactionsGenerator/GenerateTransportReactions.java
View file @
c693031a
...
...
@@ -26,13 +26,18 @@ public class GenerateTransportReactions {
* @param tcdbMetabolites
* @return
*/
public
static
Map
<
String
,
Map
<
String
,
TcNumberContainer
>>
generateReactions
(
Map
<
String
,
TcNumberContainer
>
data
,
Map
<
String
,
TcdbMetabolitesContainer
>
tcdbMetabolites
)
{
public
static
Map
<
String
,
Map
<
String
,
TcNumberContainer
>>
generateReactions
(
Map
<
String
,
TcNumberContainer
>
data
,
Map
<
String
,
TcdbMetabolitesContainer
>
tcdbMetabolites
,
Map
<
String
,
String
>
proteinFamilyDescription
)
{
Map
<
String
,
Map
<
String
,
TcNumberContainer
>>
mainMap
=
new
HashMap
<>();
Synonyms
dictionary
=
new
Synonyms
();
int
noMetabolitesNoReactionsCounter
=
0
;
// Map<String, TcdbMetabolitesContainer> tcdbMetabolites = new HashMap<>();
//
// tcdbMetabolites.put("O51918", tcdbMetabolitessss.get("O51918"));
for
(
String
accession
:
tcdbMetabolites
.
keySet
())
{
...
...
@@ -61,9 +66,12 @@ public class GenerateTransportReactions {
for
(
int
id
:
tcNumberContainer
.
getAllReactionsIds
())
{
ReactionContainer
reactionContainer
=
tcNumberContainer
.
getReactionContainer
(
id
);
TypeOfTransporter
evidence
=
checkForEvidenceOfTransport
(
tcdbMetContainer
.
getDescription
(
tcNumber
),
tcNumber
);
if
(
evidence
==
null
&&
proteinFamilyDescription
.
containsKey
(
tcNumber
.
replaceAll
(
"(\\.\\d+)$"
,
""
)))
evidence
=
checkForEvidenceOfTransport
(
proteinFamilyDescription
.
get
(
tcNumber
.
replaceAll
(
"(\\.\\d+)$"
,
""
)),
tcNumber
);
// System.out.println(accession);
Boolean
antiportOrSymport
=
selectMethodOfMetabolitesDistribution
(
reactionContainer
.
getReaction
(),
reactionContainer
.
getTransportType
(),
dictionary
);
...
...
@@ -83,8 +91,6 @@ public class GenerateTransportReactions {
// Set<String> metabolites = tcdbMetContainer.getMetabolites(tcNumber);
if
(
evidence
==
null
)
{
if
(
reactionContainer
.
getTransportType
().
equals
(
TypeOfTransporter
.
Uniport
)
||
reactionContainer
.
getTransportType
().
equals
(
TypeOfTransporter
.
Symport
))
...
...
@@ -109,7 +115,7 @@ public class GenerateTransportReactions {
newTcContainer
=
processAntiportReactions
(
reactionContainer
,
newTcContainer
,
metabolites
,
dictionary
,
tcNumber
+
" "
+
accession
);
// }
else
else
if
(!
tcNumberContainer
.
evidenceTransportTypeExists
(
evidence
))
newTcContainer
=
correctReaction
(
tcNumber
,
reactionContainer
.
getReaction
(),
"C-1"
,
evidence
,
reactionContainer
.
getProperties
(),
metabolites
,
newTcContainer
);
// System.out.println(tcNumber+" "+accession + " " + evidence + " " + reactionContainer.getTransportType() + " " + reactionContainer.getReaction() + "\t" + metabolites);
...
...
@@ -133,7 +139,8 @@ public class GenerateTransportReactions {
if
(
newTcContainer
.
getAllReactionsIds
().
size
()
==
0
)
//reactions with generic reactions such as
noMetabolitesNoReactionsCounter
++;
//solute1 + solute2 <-> solute1 + solute2 are also included here because no metabolites where found for them
newTcContainer
=
filterUnwantedReactions
(
tcNumber
,
newTcContainer
);
newContainers
.
put
(
tcNumber
,
newTcContainer
);
}
...
...
@@ -155,6 +162,24 @@ public class GenerateTransportReactions {
}
private
static
TcNumberContainer
filterUnwantedReactions
(
String
tcNumber
,
TcNumberContainer
newTcContainer
)
{
Set
<
TypeOfTransporter
>
set
=
newTcContainer
.
getAllTransportTypesAssociated
();
if
(
set
.
size
()
>
1
)
{
for
(
int
id
:
newTcContainer
.
getAllReactionsIds
())
{
ReactionContainer
container
=
newTcContainer
.
getReactionContainer
(
id
);
if
(!
container
.
getTransportType
().
equals
(
TypeOfTransporter
.
Uniport
))
newTcContainer
.
removeReaction
(
id
);
}
}
return
newTcContainer
;
}
/**
* Process metabolites associated to the wrong transport types.
*
...
...
@@ -256,18 +281,26 @@ public class GenerateTransportReactions {
* @return
*/
private
static
TypeOfTransporter
checkForEvidenceOfTransport
(
String
description
,
String
tcNumber
)
{
if
(
tcNumber
.
equals
(
"2.A.1.4.8"
))
return
TypeOfTransporter
.
Uniport
;
if
(
description
.
matches
(
"(?i).*uniporte*r*[\\s*\\.*].*"
))
return
TypeOfTransporter
.
Uniport
;
else
if
(
description
.
matches
(
"(?i).*symporte*r*[\\s*\\.*].*"
))
return
TypeOfTransporter
.
Symport
;
else
if
(
description
.
matches
(
"(?i).*antiporte*r*[\\s*\\.*]"
))
return
TypeOfTransporter
.
Antiport
;
try
{
if
(
tcNumber
.
equals
(
"2.A.1.4.8"
))
return
TypeOfTransporter
.
Uniport
;
if
(
description
.
matches
(
"(?i).*uniporte*r*[\\s*\\.*]*.*"
))
return
TypeOfTransporter
.
Uniport
;
else
if
(
description
.
matches
(
"(?i).*symporte*r*[\\s*\\.*]*.*"
))
return
TypeOfTransporter
.
Symport
;
else
if
(
description
.
matches
(
"(?i).*antiporte*r*[\\s*\\.*]*.*"
))
return
TypeOfTransporter
.
Antiport
;
}
catch
(
Exception
e
)
{
System
.
out
.
println
(
tcNumber
);
System
.
out
.
println
(
description
);
e
.
printStackTrace
();
}
return
null
;
}
...
...
@@ -745,7 +778,7 @@ public class GenerateTransportReactions {
reactant
=
aux
[
1
];
product
=
aux
[
2
];
Set
<
String
>
reactions
=
getAllPossibleReactions
(
originalReaction
,
reactant
,
product
,
reactionContainer
.
get
Reversible
(),
tc
);
Set
<
String
>
reactions
=
getAllPossibleReactions
(
originalReaction
,
reactant
,
product
,
reactionContainer
.
is
Reversible
(),
tc
);
// if(tc.equals("2.A.20.1.2 P43676")) {
// System.out.println("Areactions " + reactions);
...
...
@@ -757,7 +790,7 @@ public class GenerateTransportReactions {
// System.out.println(react);
String
[]
newReaction
;
if
(
reactionContainer
.
get
Reversible
())
if
(
reactionContainer
.
is
Reversible
())
newReaction
=
react
.
split
(
ReactionContainer
.
REV_TOKEN
);
else
newReaction
=
react
.
split
(
ReactionContainer
.
IRREV_TOKEN
);
...
...
@@ -785,7 +818,7 @@ public class GenerateTransportReactions {
// System.out.println();
// }
ReactionContainer
newReactContainer
=
new
ReactionContainer
(
result
[
0
],
result
[
1
],
reactionContainer
.
get
Reversible
());
ReactionContainer
newReactContainer
=
new
ReactionContainer
(
result
[
0
],
result
[
1
],
reactionContainer
.
is
Reversible
());
newReactContainer
.
setTransportType
(
reactionContainer
.
getTransportType
());
newReactContainer
.
setProperties
(
reactionContainer
.
getProperties
());
...
...
@@ -1667,7 +1700,7 @@ public class GenerateTransportReactions {
// System.out.println();
// }
ReactionContainer
newReactContainer
=
new
ReactionContainer
(
result
[
0
],
result
[
1
],
reactionContainer
.
get
Reversible
());
ReactionContainer
newReactContainer
=
new
ReactionContainer
(
result
[
0
],
result
[
1
],
reactionContainer
.
is
Reversible
());
newReactContainer
.
setTransportType
(
reactionContainer
.
getTransportType
());
newReactContainer
.
setProperties
(
reactionContainer
.
getProperties
());
...
...
src/main/java/tcdb/tcdbTransportTypesRetriever/FindTransportTypes.java
View file @
c693031a
...
...
@@ -39,15 +39,15 @@ public class FindTransportTypes {
* @throws IOException
* @throws Exception
*/
public
static
Map
<
String
,
TcNumberContainer
>
getAllTCNumbersInformation
()
throws
IOException
,
Exception
{
public
static
Map
<
String
,
TcNumberContainer
>
getAllTCNumbersInformation
(
Set
<
String
>
toSearch
)
throws
IOException
,
Exception
{
Map
<
String
,
TcNumberContainer
>
data
=
new
HashMap
<>();
//
Set<String> toSearch = TcdbExplorer.getTcNumbers();
Set
<
String
>
toSearch
=
new
HashSet
<>();
toSearch
.
add
(
"2.A.37"
);
//
Set<String> toSearch = TcdbExplorer.getTcNumbers();
//
////
Set<String> toSearch = new HashSet<>();
//
////
toSearch.add("2.A.37");
List
<
String
>
searched
=
new
ArrayList
<>();
...
...
src/main/java/tcdb/tcdbTransportTypesRetriever/FindTransporters.java
View file @
c693031a
...
...
@@ -30,7 +30,7 @@ import tcdb.capsules.TcNumberContainer;
public
class
FindTransporters
{
public
static
final
int
LIMIT
=
10
;
private
static
final
String
URL
=
"http://www.tcdb.org/search/result.php?tc="
;
public
static
final
List
<
String
>
REVERSIBLES
=
List
.
of
(
"⇌"
,
"⇌ "
,
"↔"
,
"⇌"
,
"⇋"
);
public
static
final
List
<
String
>
IRREVERSIBLES
=
List
.
of
(
"→"
,
"%u21CC"
,
"%u2192"
,
"-->"
,
"→"
,
"Æ"
,
"à"
);
...
...
@@ -90,7 +90,7 @@ public class FindTransporters {
while
(
attempt
<
LIMIT
&&
!
found
)
{
if
(
conn
.
getCodeConnection
(
URL
.
concat
(
tc
))
==
200
){
if
(
conn
.
getCodeConnection
(
TcdbExplorer
.
TCDB_TCNUMBER_
URL
.
concat
(
tc
))
==
200
){
FilesUtils
.
webPageSaver
(
conn
.
getPageOpenStream
(),
out
);
...
...
@@ -122,7 +122,7 @@ public class FindTransporters {
if
(
attempt
==
LIMIT
&&
!
found
){
System
.
out
.
println
(
"results not found for query: "
+
URL
.
concat
(
tc
));
System
.
out
.
println
(
"results not found for query: "
+
TcdbExplorer
.
TCDB_TCNUMBER_
URL
.
concat
(
tc
));
failed
.
add
(
tc
);
}
...
...
@@ -973,5 +973,5 @@ public class FindTransporters {
return
null
;
}
}
src/main/java/tcdb/tcdbTransportTypesRetriever/ReadFastaTcdb.java
View file @
c693031a
...
...
@@ -50,10 +50,10 @@ public class ReadFastaTcdb {
String
accession
=
""
,
tcNumber
=
""
,
organism
=
""
,
description
=
""
;
Map
<
String
,
Integer
>
distributions1
=
new
TreeMap
<>();
Map
<
String
,
Integer
>
distributions2
=
new
TreeMap
<>();
Map
<
String
,
Integer
>
distributions3
=
new
TreeMap
<>();
Map
<
String
,
Integer
>
distributions4
=
new
TreeMap
<>();
//
Map<String, Integer> distributions1 = new TreeMap<>();
//
Map<String, Integer> distributions2 = new TreeMap<>();
//
Map<String, Integer> distributions3 = new TreeMap<>();
//
Map<String, Integer> distributions4 = new TreeMap<>();
Map
<
String
,
Integer
>
distributions5
=
new
TreeMap
<>();
...
...
@@ -115,53 +115,53 @@ public class ReadFastaTcdb {
// System.out.println("tc--" + tcNumber);
String
[]
newTcNumber
=
tcNumber
.
split
(
"\\."
);
// System.out.println(newTcNumber.length);
String
newTc
=
newTcNumber
[
0
].
concat
(
"."
).
concat
(
newTcNumber
[
1
]).
concat
(
"."
).
concat
(
newTcNumber
[
2
]).
concat
(
"."
).
concat
(
newTcNumber
[
3
]);
if
(
distributions4
.
containsKey
(
newTc
))
{
int
count
=
distributions4
.
get
(
newTc
);
distributions4
.
put
(
newTc
,
count
+
1
);
}
else
distributions4
.
put
(
newTc
,
1
);
newTc
=
newTcNumber
[
0
].
concat
(
"."
).
concat
(
newTcNumber
[
1
]).
concat
(
"."
).
concat
(
newTcNumber
[
2
]);
if
(
distributions3
.
containsKey
(
newTc
))
{
int
count
=
distributions3
.
get
(
newTc
);
distributions3
.
put
(
newTc
,
count
+
1
);
}
else
distributions3
.
put
(
newTc
,
1
);
newTc
=
newTcNumber
[
0
].
concat
(
"."
).
concat
(
newTcNumber
[
1
]);
if
(
distributions2
.
containsKey
(
newTc
))
{
int
count
=
distributions2
.
get
(
newTc
);
distributions2
.
put
(
newTc
,
count
+
1
);
}
else
distributions2
.
put
(
newTc
,
1
);
newTc
=
newTcNumber
[
0
];
if
(
distributions1
.
containsKey
(
newTc
))
{
int
count
=
distributions1
.
get
(
newTc
);
distributions1
.
put
(
newTc
,
count
+
1
);
}
else
distributions1
.
put
(
newTc
,
1
);
//
String[] newTcNumber = tcNumber.split("\\.");
//
//
// System.out.println(newTcNumber.length);
//
//
String newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]).concat(".").concat(newTcNumber[2]).concat(".").concat(newTcNumber[3]);
//
//
if(distributions4.containsKey(newTc)) {
//
//
int count = distributions4.get(newTc);
//
distributions4.put(newTc, count+1);
//
}
//
//
else
//
distributions4.put(newTc, 1);
//
//
newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]).concat(".").concat(newTcNumber[2]);
//
//
if(distributions3.containsKey(newTc)) {
//
//
int count = distributions3.get(newTc);
//
distributions3.put(newTc, count+1);
//
}
//
//
else
//
distributions3.put(newTc, 1);
//
//
newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]);
//
//
if(distributions2.containsKey(newTc)) {
//
//
int count = distributions2.get(newTc);
//
distributions2.put(newTc, count+1);
//
}
//
//
else
//
distributions2.put(newTc, 1);
//
//
newTc = newTcNumber[0];
//
//
if(distributions1.containsKey(newTc)) {
//
//
int count = distributions1.get(newTc);
//
distributions1.put(newTc, count+1);
//
}
//
//
else
//
distributions1.put(newTc, 1);
description
=
""
;
...
...
@@ -187,7 +187,7 @@ public class ReadFastaTcdb {
System
.
out
.
println
(
"Number of different accessions: "
+
accessions
.
size
());
return
distributions
3
.
keySet
();
return
distributions
5
.
keySet
();
}
catch
(
IOException
e
)
{
e
.
printStackTrace
();
...
...
@@ -213,7 +213,7 @@ public class ReadFastaTcdb {
LinkConnection
conn
=
new
LinkConnection
();
if
(
conn
.
getCodeConnection
(
"http://www.tcdb.org/public/tcdb"
)
==
200
)
{
if
(
conn
.
getCodeConnection
(
TcdbExplorer
.
TCDB_FASTA_URL
)
==
200
)
{
webPageSaver
(
conn
.
getPageOpenStream
(),
out
);
...
...
src/main/java/tcdb/tcdbTransportTypesRetriever/Retriever.java
View file @
c693031a
...
...
@@ -6,6 +6,7 @@ import java.util.Map;
import
java.util.Scanner
;
import
java.util.Set
;
import
files.FilesUtils
;
import
files.JSONFilesUtils
;
import
files.ReadExcelFile
;
import
tcdb.capsules.TcNumberContainer
;
...
...
@@ -26,16 +27,24 @@ public class Retriever {
@SuppressWarnings
(
"resource"
)
Scanner
reader
=
new
Scanner
(
System
.
in
);
// Set<String> toSearch = new HashSet<>();
//
// toSearch = TcdbExplorer.getTcNumbers();
System
.
out
.
println
(
"Retrieving TCDB FASTA file..."
);
Set
<
String
>
tcNumbers
=
TcdbExplorer
.
getTcNumbers
();
Set
<
String
>
toSearch
=
TcdbExplorer
.
generateTCsFamily
(
tcNumbers
);
// toSearch.add("2.A.75");
////
// System.out.println("Retrieving data from TCDB...");
// Map<String, TcNumberContainer> data = FindTransporters.getAllTCNumbersInformation(toSearch);
// Map<String, String> proteinFamilyDescription = TcdbExplorer.getProteinsBelongingToFamilyDescription(tcNumbers);
//
// System.out.println("COMPLETE...");
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\proteinFamilyDescriptions.txt", proteinFamilyDescription);
Map
<
String
,
String
>
proteinFamilyDescription
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\proteinFamilyDescriptions.txt"
);
System
.
out
.
println
(
"SEARCH COMPLETE..."
);
//
int
n
=
1
;
...
...
@@ -52,7 +61,7 @@ public class Retriever {
//
//
///////////////DESCOMENTAR
Map
<
String
,
TcNumberContainer
>
data
=
JSONFilesUtils
.
readJSONExceptionsFile
();
//the reader that reads exceptios can also read normal data
...
...
@@ -64,10 +73,15 @@ public class Retriever {
Map
<
String
,
TcdbMetabolitesContainer
>
tcdbMetabolites
=
ProcessTcdbMetabolitesExcel
.
processData
(
excel
);
Map
<
String
,
Map
<
String
,
TcNumberContainer
>>
transportReactions
=
GenerateTransportReactions
.
generateReactions
(
data
,
tcdbMetabolites
);
Map
<
String
,
Map
<
String
,
TcNumberContainer
>>
transportReactions
=
GenerateTransportReactions
.
generateReactions
(
data
,
tcdbMetabolites
,
proteinFamilyDescription
);
JSONFilesUtils
.
writeJSONtcReactions
(
transportReactions
);
///////////////DESCOMENTAR
// checkDescriptions(tcdbMetabolites);
...
...
src/main/java/tcdb/tcdbTransportTypesRetriever/TcdbExplorer.java
View file @
c693031a
package
tcdb.tcdbTransportTypesRetriever
;
import
java.io.BufferedReader
;
import
java.util.ArrayList
;
import
java.util.HashMap
;
import
java.util.HashSet
;
import
java.util.List
;
import
java.util.Map
;
import
java.util.Set
;
import
java.util.concurrent.TimeUnit
;