add variant effect dataloader for framepool

Framepool/VariantEffect/dataloader.py

@@ -0,0 +1,14 @@
+from kipoiseq.dataloaders import SingleVariantUTRDataLoader
+
+class SingleVariantFramepoolDataloader(SingleVariantUTRDataLoader):
+    def __init__(self, gtf_file, fasta_file, vcf_file, vcf_file_tbi=None, infer_from_cds=False, on_error_warn=True, **kwargs):
+        kwargs["feature_type"] = "5UTR"
+        super().__init__(
+            gtf_file=gtf_file,
+            fasta_file=fasta_file,
+            vcf_file=vcf_file,
+            vcf_file_tbi=vcf_file_tbi,
+            infer_from_cds=infer_from_cds,
+            on_error_warn=on_error_warn,
+            **kwargs
+        )

Framepool/VariantEffect/dataloader.yaml

@@ -1,85 +1,80 @@
-defined_as: kipoiseq.dataloaders.SingleVariantUTRDataLoader
+defined_as: dataloader.py::SingleVariantFramepoolDataloader
 
 type: SampleIterator
-
 args:
-  gtf_file:
-    doc: file path; Genome annotation GTF file
-    example:
-      url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22_ENST00000319363.gtf?raw=true
-      md5: 8a1f158e17379773fcab21628fc3910f
-      name: gtf_file.gtf
-  fasta_file:
-    doc: Reference Genome sequence in fasta format
-    example:
-      url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22.fa.gz?raw=true
-      md5: 5ebe034256ecc5689989a96387c5a65e
-      name: fasta_file.fa.gz
-  vcf_file:
-    doc: Genomic variants to evaluate in VCF format
-    example:
-      url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22_ENST00000319363.vcf.gz?raw=true
-      md5: c45e75fb75326c2be514d2dcea52e585
-      name: vcf_file.vcf.gz
-  vcf_file_tbi:
-    doc: tabix index of vcf (just to make kipoi tests work - leave as None in normal usage)
-    example:
-      url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22_ENST00000319363.vcf.gz.tbi?raw=true
-      md5: 9aebc88287a3d6b8517ace9e0fc427af
-      name: vcf_file.vcf.gz.tbi
-  feature_type:
-    doc: >
-      Needs to be "5UTR"
-    default: 5UTR
-    example: 5UTR
-    type: str
-  infer_from_cds:
-    doc: infer UTR regions from coding sequence
-    optional: True
-    default: False
-    type: bool
-  on_error_warn:
-    doc: print warning instead of throwing an error on malformed input
-    optional: True
-    default: True
-    type: bool
-default_args:
-  feature_type: 5UTR
+    gtf_file:
+        doc: file path; Genome annotation GTF file
+        example:
+            url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22_ENST00000319363.gtf?raw=true
+            md5: 8a1f158e17379773fcab21628fc3910f
+            name: gtf_file.gtf
+    fasta_file:
+        doc: Reference Genome sequence in fasta format
+        example:
+            url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22.fa.gz?raw=true
+            md5: 5ebe034256ecc5689989a96387c5a65e
+            name: fasta_file.fa.gz
+    vcf_file:
+        doc: Genomic variants to evaluate in VCF format
+        example:
+            url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22_ENST00000319363.vcf.gz?raw=true
+            md5: c45e75fb75326c2be514d2dcea52e585
+            name: vcf_file.vcf.gz
+    vcf_file_tbi:
+        doc: tabix index of vcf (just to make kipoi tests work - leave as None in normal usage)
+        optional: True
+        example:
+            url: https://github.com/kipoi/kipoiseq/blob/ddeb4eefc15ebf8a9b88fca4ce99d9b315d54f34/tests/data/chr22_ENST00000319363.vcf.gz.tbi?raw=true
+            md5: 9aebc88287a3d6b8517ace9e0fc427af
+            name: vcf_file.vcf.gz.tbi
+    infer_from_cds:
+        doc: infer UTR regions from coding sequence
+        optional: True
+        default: False
+        example: False
+        type: bool
+    on_error_warn:
+        doc: print warning instead of throwing an error on malformed input
+        optional: True
+        default: True
+        example: True
+        type: bool
 
 output_schema:
-  inputs:
-    ref_seq:
-      name: ref_seq
-      shape: ()
-      special_type: DNAStringSeq
-      doc: reference sequence of UTR
-      associated_metadata: ranges
-    alt_seq:
-      name: alt_seq
-      doc: alternative sequence of 5' UTR
-      shape: ()
-      special_type: DNAStringSeq
-      associated_metadata: ranges, variants
-  metadata:
-    transcript_id:
-      type: str
-      doc: transcript id
-    variant:
-      chrom:
-        type: str
-        doc: chromsome of variant
-      pos:
-        type: int
-        doc: variant position
-      ref:
-        type: str
-        doc: variant reference
-      alt:
-        type: str
-        doc: variant alternative string
-      id:
-        type: str
-        doc: variant id
-      str:
-        type: str
-        doc: string representation of the variant
+    inputs:
+        ref_seq:
+            name: ref_seq
+            shape: ()
+            special_type: DNAStringSeq
+            doc: reference sequence of 5' UTR
+            associated_metadata: ranges
+        alt_seq:
+            name: alt_seq
+            doc: alternative sequence of 5' UTR
+            shape: ()
+            special_type: DNAStringSeq
+            associated_metadata: ranges, variants
+    metadata:
+        transcript_id:
+            type: str
+            doc: transcript id
+        variant:
+            chrom:
+                type: str
+                doc: chromsome of variant
+            pos:
+                type: int
+                doc: variant position
+            ref:
+                type: str
+                doc: variant reference
+            alt:
+                type: str
+                doc: variant alternative string
+            id:
+                type: str
+                doc: variant id
+            str:
+                type: str
+                doc: string representation of the variant
+