# Accessing fields in structure type

**URL:** <https://discuss.hail.is/t/accessing-fields-in-structure-type/316>\
**Category:** Help \[0.1\]\
**Created:** [October 12, 2017, 1:13pm UTC](https://discuss.hail.is/t/accessing-fields-in-structure-type/316 "2017-10-12T13:13:06Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![drhod](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@drhod](https://discuss.hail.is/u/drhod)\
**Post date:** [October 12, 2017, 1:13pm UTC](https://discuss.hail.is/t/accessing-fields-in-structure-type/316/1 "2017-10-12T13:13:06Z")

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Hi,  
I am attempting to filter data from the gnomad exomes vds keeping only loss of function instances. My attempts have brought me to the following:  
vds.filter\_intervals(Interval.parse(‘22’)).filter\_variants\_expr(‘va.vep.transcript\_consequences.lof == None’, keep=False).count\_variants()

I get:  
Error summary: HailException: `Array[Struct{allele_num:Int,amino_acids:String,biotype:String,canonical:Int,ccds:String,cdna_start:Int,cdna_end:Int,cds_end:Int,cds_start:Int,codons:String,consequence_terms:Array[String],distance:Int,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int,gene_symbol:String,gene_symbol_source:String,hgnc_id:Int,hgvsc:String,hgvsp:String,hgvs_offset:Int,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int,polyphen_prediction:String,polyphen_score:Double,protein_end:Int,protein_start:Int,protein_id:String,sift_prediction:String,sift_score:Double,strand:Int,swissprot:String,transcript_id:String,trembl:String,uniparc:String,variant_allele:String}]' has no field or method`lof’

lof is contained within the struct ‘transcript\_consequences’.  
How can I access that lof field and just keep data without ‘None’ in that field?

Thanks

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<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [October 12, 2017, 1:37pm UTC](https://discuss.hail.is/t/accessing-fields-in-structure-type/316/2 "2017-10-12T13:37:49Z")

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This is a bit more complicated because it’s not just a structure, it’s an `Array[Struct{...}]`.

If you want to just select the one canonical transcript per variant, then here’s a bit of discourse on that:  
[Parsing VEP output](http://discuss.hail.is/t/parsing-vep-output/41/5)

If you wanted to remove variants where `lof` was None for every transcript, then here’s the code to do that:

```python
print(vds.filter_intervals(Interval.parse('22'))
.filter_variants_expr('va.vep.transcript_consequences.forall(tc => isMissing(tc.lof))')
.count_variants())

```

You might want to see the distribution of values for all transcripts:

```python
print(vds.filter_intervals(Interval.parse('22'))
.query_variants('variants.flatMap(v => va.vep.transcript_consequences.map(tc => tc.lof)).counter()'))

```

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<div class="post-metadata">

**Author:** ![drhod](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@drhod](https://discuss.hail.is/u/drhod)\
**Post date:** [October 12, 2017, 3:15pm UTC](https://discuss.hail.is/t/accessing-fields-in-structure-type/316/3 "2017-10-12T15:15:54Z")

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Thank you, the latter is what I was looking for. I am trying to export this information to a tsv, however this means I run into the same problem of not being able to refer directly to the lof fields. The line below works but results in a tonne of extraneous info.  
vds\_result.export\_variants(‘test.tsv’, ‘v, va.vep.transcript\_consequences.\*’)  
Is there restricting annotation output in that way?

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<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [October 12, 2017, 3:44pm UTC](https://discuss.hail.is/t/accessing-fields-in-structure-type/316/4 "2017-10-12T15:44:09Z")

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You could map it to the list of LOF things, comma delimit that, and export the result:

```python
vds_result.export_variants('test.tsv', 
    'v, va.vep.transcript_consequences.map(tc => tc.lof).mkString(",")')

```