# Find an item in HailTable by a string representation of a variant **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [April 21, 2021, 6:36pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014 "2021-04-21T18:36:25Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 6:36pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/1 "2021-04-21T18:36:25Z")
I have a HailTable where rows are keyed by locus and alleles fields: ``` In [37]: cidr.describe() ---------------------------------------- Global fields: 'sourceFilePath': str 'genomeVersion': str ---------------------------------------- Row fields: 'locus': locus 'alleles': array 'rsid': str 'qual': float64 'filters': set 'info': struct { AC: array, AF: array, AN: int32 } 'original_alt_alleles': array 'a_index': int32 'was_split': bool ---------------------------------------- Key: ['locus', 'alleles'] ---------------------------------------- ``` I want to select a row given a string ‘20-42077813-A-ATTT’, how to do that? I tried the following but it does not work: ``` pos = hl.Locus.parse('20:42077813', reference_genome='GRCh38') cidr_problem = cidr[hl.struct(locus = pos, alleles = hl.literal(['A', 'ATTT']))].info.AC ``` giving me ‘ExpressionException: Cannot index with a scalar expression’ error ---
**Author:** ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)\ **Post date:** [April 21, 2021, 6:54pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/2 "2021-04-21T18:54:05Z")
You can’t look up a single element of a Table. You could filter to that single element, then collect the resulting table. ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 6:59pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/3 "2021-04-21T18:59:47Z")
And how could I filter it to achieve the ultimate result? ---
**Author:** ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)\ **Post date:** [April 21, 2021, 7:02pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/4 "2021-04-21T19:02:56Z")
`final_results = cidr.filter(cidr.locus == pos).collect()` `final_result = final_results[0] # Assuming there's only one` ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 7:07pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/5 "2021-04-21T19:07:58Z")
> [@johnc1231](#): > > final\_results = cidr.filter(cidr.locus == pos).collect() The first line - `final_results = cidr.filter(cidr.locus == pos).collect()` - gives me: `FatalError: AssertionError: assertion failed` ---
**Author:** ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)\ **Post date:** [April 21, 2021, 7:11pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/6 "2021-04-21T19:11:07Z")
What’s the rest of the error? ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 7:26pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/7 "2021-04-21T19:26:32Z")
``` In [45]: final_results = cidr.filter(cidr.locus == pos).collect() --------------------------------------------------------------------------- FatalError Traceback (most recent call last) in ----> 1 final_results = cidr.filter(cidr.locus == pos).collect() in collect(self, _localize) ~/.conda/envs/py37/lib/python3.7/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper ~/.conda/envs/py37/lib/python3.7/site-packages/hail/table.py in collect(self, _localize) 1918 e = construct_expr(rows_ir, hl.tarray(t.row.dtype)) 1919 if _localize: -> 1920 return Env.backend().execute(e._ir) 1921 else: 1922 return e ~/.conda/envs/py37/lib/python3.7/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed) 96 raise HailUserError(message_and_trace) from None 97 ---> 98 raise e ~/.conda/envs/py37/lib/python3.7/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed) 72 # print(self._hail_package.expr.ir.Pretty.apply(jir, True, -1)) 73 try: ---> 74 result = json.loads(self._jhc.backend().executeJSON(jir)) 75 value = ir.typ._from_json(result['value']) 76 timings = result['timings'] ~/.conda/envs/py37/lib/python3.7/site-packages/py4j/java_gateway.py in __call__ (self, *args) 1255 answer = self.gateway_client.send_command(command) 1256 return_value = get_return_value( -> 1257 answer, self.gateway_client, self.target_id, self.name) 1258 1259 for temp_arg in temp_args: ~/.conda/envs/py37/lib/python3.7/site-packages/hail/backend/py4j_backend.py in deco(*args, **kwargs) 30 raise FatalError('%s\n\nJava stack trace:\n%s\n' 31 'Hail version: %s\n' ---> 32 'Error summary: %s' % (deepest, full, hail. __version__ , deepest), error_id) from None 33 except pyspark.sql.utils.CapturedException as e: 34 raise FatalError('%s\n\nJava stack trace:\n%s\n' FatalError: AssertionError: assertion failed Java stack trace: java.lang.AssertionError: assertion failed at scala.Predef$.assert(Predef.scala:156) at is.hail.variant.ReferenceGenome$.compare(ReferenceGenome.scala:700) at is.hail.variant.ReferenceGenome$.compare(ReferenceGenome.scala:707) at is.hail.variant.ReferenceGenome$$anon$1.compare(ReferenceGenome.scala:112) at is.hail.variant.ReferenceGenome$$anon$1.compare(ReferenceGenome.scala:111) at is.hail.annotations.ExtendedOrdering$$anon$3.compareNonnull(ExtendedOrdering.scala:11) at is.hail.annotations.ExtendedOrdering.compare(ExtendedOrdering.scala:301) at is.hail.rvd.PartitionBoundOrdering$$anon$2.compareNonnull(PartitionBoundOrdering.scala:42) at is.hail.annotations.ExtendedOrdering.compare(ExtendedOrdering.scala:301) at is.hail.rvd.PartitionBoundOrdering$$anon$2$$anon$1.compareIntervalEndpoints(PartitionBoundOrdering.scala:121) at is.hail.annotations.IntervalEndpointOrdering.compareNonnull(ExtendedOrdering.scala:431) at is.hail.annotations.ExtendedOrdering.ltNonnull(ExtendedOrdering.scala:282) at is.hail.annotations.ExtendedOrdering.gtNonnull(ExtendedOrdering.scala:288) at is.hail.annotations.ExtendedOrdering.gt(ExtendedOrdering.scala:351) at is.hail.rvd.RVDPartitioner$$anonfun$6.apply(RVDPartitioner.scala:163) at is.hail.rvd.RVDPartitioner$$anonfun$6.apply(RVDPartitioner.scala:163) at scala.collection.IndexedSeqOptimized$$anonfun$indexWhere$1.apply(IndexedSeqOptimized.scala:204) at scala.collection.IndexedSeqOptimized$$anonfun$indexWhere$1.apply(IndexedSeqOptimized.scala:204) at scala.collection.IndexedSeqOptimized$class.segmentLength(IndexedSeqOptimized.scala:195) at scala.collection.mutable.ArrayBuffer.segmentLength(ArrayBuffer.scala:48) at scala.collection.IndexedSeqOptimized$class.indexWhere(IndexedSeqOptimized.scala:204) at scala.collection.mutable.ArrayBuffer.indexWhere(ArrayBuffer.scala:48) at is.hail.rvd.RVDPartitioner.is$hail$rvd$RVDPartitioner$$firstPast$1(RVDPartitioner.scala:163) at is.hail.rvd.RVDPartitioner$$anonfun$7.apply(RVDPartitioner.scala:167) at is.hail.rvd.RVDPartitioner$$anonfun$7.apply(RVDPartitioner.scala:166) at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:241) at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:241) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:241) at scala.collection.mutable.ArrayOps$ofRef.flatMap(ArrayOps.scala:186) at is.hail.rvd.RVDPartitioner.subdivide(RVDPartitioner.scala:166) at is.hail.rvd.RVDPartitioner$.generate(RVDPartitioner.scala:397) at is.hail.rvd.RVDPartitioner$.generate(RVDPartitioner.scala:385) at is.hail.rvd.RVDPartitioner.extendKey(RVDPartitioner.scala:133) at is.hail.rvd.IndexedRVDSpec2.read(AbstractRVDSpec.scala:467) at is.hail.expr.ir.RVDComponentSpec.read(AbstractMatrixTableSpec.scala:112) at is.hail.expr.ir.TableNativeReader.apply(TableIR.scala:882) at is.hail.expr.ir.TableRead.execute(TableIR.scala:1143) at is.hail.expr.ir.TableKeyBy.execute(TableIR.scala:1255) at is.hail.expr.ir.Interpret$.run(Interpret.scala:813) at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53) at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$1.apply(InterpretNonCompilable.scala:25) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.AbstractTraversable.map(Traversable.scala:104) at is.hail.expr.ir.InterpretNonCompilable$.rewriteChildren$1(InterpretNonCompilable.scala:25) at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:54) at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58) at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:67) at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15) at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15) at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13) at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62) at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:14) at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:12) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35) at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:12) at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28) at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:362) at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:346) at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:343) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1$$anonfun$apply$1.apply(ExecuteContext.scala:48) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1$$anonfun$apply$1.apply(ExecuteContext.scala:48) at is.hail.utils.package$.using(package.scala:618) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:48) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:618) at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:13) at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:47) at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:256) at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:343) at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:387) at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:385) at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52) at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:385) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.lang.Thread.run(Thread.java:748) Hail version: 0.2.63-cb767a7507c8 Error summary: AssertionError: assertion failed ``` ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [April 21, 2021, 7:38pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/8 "2021-04-21T19:38:03Z")
Hey @NLSVTN , sorry you’re running into this assertion error. That’s a bad error message. It seems like at least one locus has an invalid chromosome. From where did you get `cidr`? If you run `cidr.write('/tmp/foo.t')`, do you also get an error message? ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 8:41pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/9 "2021-04-21T20:41:59Z")
It does not work not only for cidr, but for other datasets too. I get ‘connection refused’ error for the write operation. The datasets I am just importing using various functions: import\_vcf, read\_table, read\_matrix\_table, etc. So, is it because there is no such position in the dataset? ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [April 21, 2021, 8:48pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/10 "2021-04-21T20:48:07Z")
Every time you `write` a dataset you get a connection refused error? Are you using Hail in Google Dataproc, on a laptop, on a virtual machine, or on a custom Spark cluster? I’m not sure what the problem is. What happens if you run `cidr._force_count()`? ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 8:52pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/11 "2021-04-21T20:52:54Z")
I am just using `ipython` on a server. Seems so, I never write it since no need to. It just counts and returns some number: `638372`. ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [April 21, 2021, 9:10pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/12 "2021-04-21T21:10:44Z")
Can you share the full script you ran that triggers the assertion error? ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 21, 2021, 9:24pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/13 "2021-04-21T21:24:45Z")
> [@NLSVTN](#): > > `final_results = cidr.filter(cidr.locus == pos).collect()` ``` cidr = hl.read_table('file:///cidr_batch1_and_batch2_cleaned.ht') pos = hl.Locus.parse('20:42077813', reference_genome='GRCh38') final_results = cidr.filter(cidr.locus == pos).collect() ``` Thats it. But I actually need to get a specific allele, not just everything at position `20:42077813`. ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [April 21, 2021, 9:44pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/14 "2021-04-21T21:44:19Z")
Regarding matching to a specific variant, you’re probably looking for [`hl.parse_variant`](https://hail.is/docs/0.2/functions/genetics.html#hail.expr.functions.parse_variant) ```auto var = hl.parse_variant('20:42077813:A:ATTT') cidr.filter((cidr.locus = var.locus) & (cidr.alleles = var.alleles)).collect() ``` Your original attempt would also work if you changed like this: ```auto pos = hl.Locus.parse('20:42077813', reference_genome='GRCh38') cidr.filter( (cidr.locus = var.locus) & (cidr.alleles = hl.literal(['A', 'ATTT'])) ).collect() ``` I’m still not sure why you’re getting the AssertionError. I’ll ask someone from the compiler team to improve the error message so that we can get more useful information next time. ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 22, 2021, 12:30am UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/15 "2021-04-22T00:30:21Z")
This line - `cidr.filter((cidr.locus = var.locus) & (cidr.alleles = var.alleles)).collect()` - gives me `SyntaxError: invalid syntax`: ``` In [8]: cidr.filter((cidr.locus = var.locus) & (cidr.alleles = var.alleles)).collect() File "", line 1 cidr.filter((cidr.locus = var.locus) & (cidr.alleles = var.alleles)).collect() ^ SyntaxError: invalid syntax ``` In the second case you mean `pos.locus`, not `var.locus`, right? ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 22, 2021, 12:42am UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/16 "2021-04-22T00:42:01Z")
Ok, just after changing **=** to **==** it started to work. But I faced another issue with the following code: ``` var = hl.parse_variant('20:42077813:A:ATTT', reference_genome='GRCh38') cidr.filter((cidr.locus == var.locus) & (cidr.alleles == var.alleles)).collect() ``` `Error summary: HailException: Invalid locus '20:42077813' found. Contig '20' is not in the reference genome 'GRCh38'` ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 22, 2021, 12:48am UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/17 "2021-04-22T00:48:40Z")
> [@NLSVTN](#): > > is not in the reference genome ‘GRCh38’ Ok, parse\_variant example works well with GRCh38, just needed to prepend chr: ``` var = hl.parse_variant('chr20:42077813:A:ATTT', reference_genome='GRCh38') cidr.filter((cidr.locus == var.locus) & (cidr.alleles == var.alleles)).collect() ``` With pos needed to do some corrections too: ``` pos = hl.Locus.parse('chr20:42077813', reference_genome='GRCh38') cidr.filter( (cidr.locus == pos) & (cidr.alleles == hl.literal(['A', 'ATTT'])) ).collect() ``` Thank you very much! ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 22, 2021, 3:37pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/18 "2021-04-22T15:37:24Z")
The Connection Refused error was happening because there are issues with my hadoop cluster and it is trying to write to it. How could I write locally? I tried using `file:///` prefix but it does not seem to work, e.g.: `mt.a_index.export('file:///mt_aIndex.tsv')` ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [April 22, 2021, 3:51pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/19 "2021-04-22T15:51:05Z")
The `file://` prefix is what I expect to work. If you’re using a Hadoop cluster, then your workers are presumably on different machines from the leader machine. That means each worker is writing to their own local filesystem. That’s probably not what you want. ---
**Author:** ![NLSVTN](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/nlsvtn/32/339_2.png) [@NLSVTN](https://discuss.hail.is/u/NLSVTN)\ **Post date:** [April 22, 2021, 4:35pm UTC](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014/20 "2021-04-22T16:35:38Z")
Currently I just launched `ipython`. I can read in the file with `file:///` but I can’t export it with the same prefix somehow. [Next page](https://discuss.hail.is/t/find-an-item-in-hailtable-by-a-string-representation-of-a-variant/2014.md?page=2)