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Added new tests for the MITAB 2.8 format and refactored old ones (psi…
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…mitab module)
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@bblodfon
bblodfon committed Jul 16, 2018
1 parent 3788d25 commit 2369338
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129 changes: 105 additions & 24 deletions psimitab-parser/src/test/java/psidev/psi/mi/tab/PsimiTabIteratorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,29 +21,6 @@
*/
public class PsimiTabIteratorTest {

@Test
public void getInteractionsProcessedCount() throws Exception {

String[] lines = {
"uniprotkb:P23367 uniprotkb:P06722 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR004230|uniprotkb:Q9R2X2|uniprotkb:Q9R3A8|uniprotkb:Q9R411|uniprotkb:Q9S6P5|uniprotkb:Q9S6P6|uniprotkb:Q9S6P7|go:\"GO:0005515\"|intact:EBI-545170 gene name:mutL|locus name:b4170 gene name:mutH|gene name synonym:mutR|gene name synonym:prv|locus name:b2831 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P23367 uniprotkb:P06722 - - - - - - - taxid:562 taxid:562 - - - -\n",
"uniprotkb:P23909 uniprotkb:P23909 interpro:IPR005748|interpro:IPR000432|interpro:IPR007860|interpro:IPR007696|interpro:IPR007861|interpro:IPR007695|uniprotkb:P71279|go:\"GO:0005515\"|intact:EBI-554920 interpro:IPR005748|interpro:IPR000432|interpro:IPR007860|interpro:IPR007696|interpro:IPR007861|interpro:IPR007695|uniprotkb:P71279|go:\"GO:0005515\"|intact:EBI-554920 gene name:mutS|gene name synonym:fdv|locus name:b2733 gene name:mutS|gene name synonym:fdv|locus name:b2733 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P23367 uniprotkb:P23367 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 gene name:mutL|locus name:b4170 gene name:mutL|locus name:b4170 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P23367 uniprotkb:P09184 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR004603|intact:EBI-765033 gene name:mutL|locus name:b4170 gene name:vsr|locus name:b1960 two hybrid:\"MI:0018\"|adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P06722 uniprotkb:P23367 interpro:IPR004230|uniprotkb:Q9R2X2|uniprotkb:Q9R3A8|uniprotkb:Q9R411|uniprotkb:Q9S6P5|uniprotkb:Q9S6P6|uniprotkb:Q9S6P7|go:\"GO:0005515\"|intact:EBI-545170 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 gene name:mutH|gene name synonym:mutR|gene name synonym:prv|locus name:b2831 gene name:mutL|locus name:b4170 two hybrid:\"MI:0018\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n"
};


psidev.psi.mi.tab.io.PsimiTabReader reader = new PsimiTabReader();
Iterator<BinaryInteraction> iterator = reader.iterate(TestHelper.HEADER_TAB_11585365);
int i = 0;
while (iterator.hasNext()) {
assertEquals(lines[i], MitabWriterUtils.buildLine(iterator.next(), PsimiTabVersion.v2_5));
i++;
}
assertEquals(6, ((PsimiTabIterator) iterator).getInteractionsProcessedCount());
}

@Test
public void next() throws Exception {
psidev.psi.mi.tab.io.PsimiTabReader reader = new PsimiTabReader();
Expand Down Expand Up @@ -84,7 +61,30 @@ public void hasNext() throws Exception {
}

@Test
public void getInteractionsProcessedCountWithoutHeader() throws Exception {
public void getInteractionsProcessedCountMitab25() throws Exception {

String[] lines = {
"uniprotkb:P23367 uniprotkb:P06722 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR004230|uniprotkb:Q9R2X2|uniprotkb:Q9R3A8|uniprotkb:Q9R411|uniprotkb:Q9S6P5|uniprotkb:Q9S6P6|uniprotkb:Q9S6P7|go:\"GO:0005515\"|intact:EBI-545170 gene name:mutL|locus name:b4170 gene name:mutH|gene name synonym:mutR|gene name synonym:prv|locus name:b2831 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P23367 uniprotkb:P06722 - - - - - - - taxid:562 taxid:562 - - - -\n",
"uniprotkb:P23909 uniprotkb:P23909 interpro:IPR005748|interpro:IPR000432|interpro:IPR007860|interpro:IPR007696|interpro:IPR007861|interpro:IPR007695|uniprotkb:P71279|go:\"GO:0005515\"|intact:EBI-554920 interpro:IPR005748|interpro:IPR000432|interpro:IPR007860|interpro:IPR007696|interpro:IPR007861|interpro:IPR007695|uniprotkb:P71279|go:\"GO:0005515\"|intact:EBI-554920 gene name:mutS|gene name synonym:fdv|locus name:b2733 gene name:mutS|gene name synonym:fdv|locus name:b2733 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P23367 uniprotkb:P23367 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 gene name:mutL|locus name:b4170 gene name:mutL|locus name:b4170 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P23367 uniprotkb:P09184 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR004603|intact:EBI-765033 gene name:mutL|locus name:b4170 gene name:vsr|locus name:b1960 two hybrid:\"MI:0018\"|adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
"uniprotkb:P06722 uniprotkb:P23367 interpro:IPR004230|uniprotkb:Q9R2X2|uniprotkb:Q9R3A8|uniprotkb:Q9R411|uniprotkb:Q9S6P5|uniprotkb:Q9S6P6|uniprotkb:Q9S6P7|go:\"GO:0005515\"|intact:EBI-545170 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 gene name:mutH|gene name synonym:mutR|gene name synonym:prv|locus name:b2831 gene name:mutL|locus name:b4170 two hybrid:\"MI:0018\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n"
};


PsimiTabReader reader = new PsimiTabReader();
Iterator<BinaryInteraction> iterator = reader.iterate(TestHelper.HEADER_TAB_11585365);
int i = 0;
while (iterator.hasNext()) {
assertEquals(lines[i], MitabWriterUtils.buildLine(iterator.next(), PsimiTabVersion.v2_5));
i++;
}
assertEquals(6, ((PsimiTabIterator) iterator).getInteractionsProcessedCount());
}

@Test
public void getInteractionsProcessedCountMitab25WithoutHeader() throws Exception {

String[] lines = {
"uniprotkb:P23367 uniprotkb:P06722 interpro:IPR003594|interpro:IPR002099|go:\"GO:0005515\"|intact:EBI-554913 interpro:IPR004230|uniprotkb:Q9R2X2|uniprotkb:Q9R3A8|uniprotkb:Q9R411|uniprotkb:Q9S6P5|uniprotkb:Q9S6P6|uniprotkb:Q9S6P7|go:\"GO:0005515\"|intact:EBI-545170 gene name:mutL|locus name:b4170 gene name:mutH|gene name synonym:mutR|gene name synonym:prv|locus name:b2831 adenylate cyclase:\"MI:0014\" - pubmed:11585365 taxid:562 taxid:562 physical interaction:\"MI:0218\" - - -\n",
Expand All @@ -106,6 +106,87 @@ public void getInteractionsProcessedCountWithoutHeader() throws Exception {
assertEquals(6, ((PsimiTabIterator) iterator).getInteractionsProcessedCount());
}

@Test
public void getInteractionsProcessedCountMitab26() throws Exception {
String[] mitab26line = {
"uniprotkb:Q9Y5J7|intact:EBI-123456\tuniprotkb:Q9Y584\tuniprotkb:TIMM9(gene name)\tuniprotkb:TIMM22(gene name)\t" +
"uniprotkb:TIM9\tuniprotkb:TEX4\t" +
"psi-mi:\"MI:0006\"(anti bait coip)\tPeter et al (2010)\tpubmed:14726512\ttaxid:9606(human)\ttaxid:9606(human)\t" +
"psi-mi:\"MI:0218\"(physical interaction)\tpsi-mi:\"MI:0469\"(intact)\tintact:EBI-1200556\t-\t" +
"psi-mi:\"MI:xxxx\"(spoke)\tpsi-mi:\"MI:0499\"(unspecified role)\tpsi-mi:\"MI:0499\"(unspecified role)\t" +
"psi-mi:\"MI:0497\"(bait)\tpsi-mi:\"MI:0498\"(prey)\tpsi-mi:\"MI:0326\"(protein)\tpsi-mi:\"MI:0326\"(protein)\t" +
"interpro:IPR004046(GST_C)\t" +
"go:\"GO:0004709\"(\"F:MAP kinase kinase kinase act\")\tgo:\"GO:xxxxx\"\t" +
"caution:AnnotA\tcaution:AnnotB\tdataset:Test\ttaxid:9606(human-293t)\tkd:2.0\t2009/03/09\t2010/03/30\t" +
"seguid:checksumA\tseguid:checksumB\tseguid:checksumI\tfalse\n"
};

psidev.psi.mi.tab.io.PsimiTabReader reader = new PsimiTabReader();
Iterator<BinaryInteraction> iterator = reader.iterate(TestHelper.MITAB26_LINE_HEADER);
int i = 0;
while (iterator.hasNext()) {
assertEquals(mitab26line[i], MitabWriterUtils.buildLine(iterator.next(), PsimiTabVersion.v2_6));
i++;
}
assertEquals(1, ((PsimiTabIterator) iterator).getInteractionsProcessedCount());

}

@Test
public void getInteractionsProcessedCountMitab27() throws Exception {
String[] mitab27line = {
"uniprotkb:Q9Y5J7|intact:EBI-123456\tuniprotkb:Q9Y584\tuniprotkb:TIMM9(gene name)\tuniprotkb:TIMM22(gene name)\t" +
"uniprotkb:TIM9\tuniprotkb:TEX4\t" +
"psi-mi:\"MI:0006\"(anti bait coip)\tPeter et al (2010)\tpubmed:14726512\ttaxid:9606(human)\ttaxid:9606(human)\t" +
"psi-mi:\"MI:0218\"(physical interaction)\tpsi-mi:\"MI:0469\"(intact)\tintact:EBI-1200556\t-\t" +
"psi-mi:\"MI:xxxx\"(spoke)\tpsi-mi:\"MI:0499\"(unspecified role)\tpsi-mi:\"MI:0499\"(unspecified role)\t" +
"psi-mi:\"MI:0497\"(bait)\tpsi-mi:\"MI:0498\"(prey)\tpsi-mi:\"MI:0326\"(protein)\tpsi-mi:\"MI:0326\"(protein)\t" +
"interpro:IPR004046(GST_C)\t" +
"go:\"GO:0004709\"(\"F:MAP kinase kinase kinase act\")\tgo:\"GO:xxxxx\"\t" +
"caution:AnnotA\tcaution:AnnotB\tdataset:Test\ttaxid:9606(human-293t)\tkd:2.0\t2009/03/09\t2010/03/30\t" +
"seguid:checksumA\tseguid:checksumB\tseguid:checksumI\tfalse\t" +
"tag:?-?\t-\t-\t-\tpsi-mi:\"MI:0102\"(sequence tag identification)\tpsi-mi:\"MI:0102\"(sequence tag identification)\n"
};

psidev.psi.mi.tab.io.PsimiTabReader reader = new PsimiTabReader();
Iterator<BinaryInteraction> iterator = reader.iterate(TestHelper.MITAB27_LINE_HEADER);
int i = 0;
while (iterator.hasNext()) {
assertEquals(mitab27line[i], MitabWriterUtils.buildLine(iterator.next(), PsimiTabVersion.v2_7));
i++;
}
assertEquals(1, ((PsimiTabIterator) iterator).getInteractionsProcessedCount());

}

@Test
public void getInteractionsProcessedCountMitab28() throws Exception {
String[] mitab28line = {
"uniprotkb:Q9Y5J7|intact:EBI-123456\tuniprotkb:Q9Y584\tuniprotkb:TIMM9(gene name)\tuniprotkb:TIMM22(gene name)\t" +
"uniprotkb:TIM9\tuniprotkb:TEX4\t" +
"psi-mi:\"MI:0006\"(anti bait coip)\tPeter et al (2010)\tpubmed:14726512\ttaxid:9606(human)\ttaxid:9606(human)\t" +
"psi-mi:\"MI:0218\"(physical interaction)\tpsi-mi:\"MI:0469\"(intact)\tintact:EBI-1200556\t-\t" +
"psi-mi:\"MI:xxxx\"(spoke)\tpsi-mi:\"MI:0499\"(unspecified role)\tpsi-mi:\"MI:0499\"(unspecified role)\t" +
"psi-mi:\"MI:0497\"(bait)\tpsi-mi:\"MI:0498\"(prey)\tpsi-mi:\"MI:0326\"(protein)\tpsi-mi:\"MI:0326\"(protein)\t" +
"interpro:IPR004046(GST_C)\t" +
"go:\"GO:0004709\"(\"F:MAP kinase kinase kinase act\")\tgo:\"GO:xxxxx\"\t" +
"caution:AnnotA\tcaution:AnnotB\tdataset:Test\ttaxid:9606(human-293t)\tkd:2.0\t2009/03/09\t2010/03/30\t" +
"seguid:checksumA\tseguid:checksumB\tseguid:checksumI\tfalse\t" +
"tag:?-?\t-\t-\t-\tpsi-mi:\"MI:0102\"(sequence tag identification)\tpsi-mi:\"MI:0102\"(sequence tag identification)\t" +
"-\t-\tpsi-mi:\"MI:2247\"(transcriptional regulation)\tpsi-mi:\"MI:2236\"(up-regulates activity)\n"
};

psidev.psi.mi.tab.io.PsimiTabReader reader = new PsimiTabReader();
Iterator<BinaryInteraction> iterator = reader.iterate(TestHelper.MITAB28_LINE_HEADER);
int i = 0;
while (iterator.hasNext()) {
assertEquals(mitab28line[i], MitabWriterUtils.buildLine(iterator.next(), PsimiTabVersion.v2_8));
i++;
}
assertEquals(1, ((PsimiTabIterator) iterator).getInteractionsProcessedCount());

}

@Test
public void readEmptyFile() throws Exception {

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