scout-browser 4.88__py3-none-any.whl → 4.89__py3-none-any.whl

scout/commands/load/variants.py

@@ -1,8 +1,10 @@
 import logging
+from typing import Dict, List, Optional
 
 import click
 from flask.cli import with_appcontext
 
+from scout.constants import OMICS_FILE_TYPE_MAP
 from scout.server.extensions import store
 
 LOG = logging.getLogger(__name__)
@@ -21,6 +23,7 @@ LOG = logging.getLogger(__name__)
 )
 @click.option("--mei", is_flag=True, help="Upload clinical MEI variants")
 @click.option("--mei-research", is_flag=True, help="Upload research MEI variants")
+@click.option("--outlier", is_flag=True, help="Upload clinical OMICS outlier variants")
 @click.option("--sv", is_flag=True, help="Upload clinical structural variants")
 @click.option("--sv-research", is_flag=True, help="Upload research structural variants")
 @click.option("--snv", is_flag=True, help="Upload clinical SNV variants")
@@ -34,7 +37,7 @@ LOG = logging.getLogger(__name__)
 @click.option(
     "--rank-treshold",
     default=5,
-    help="Specify the rank score treshold",
+    help="Specify the rank score threshold. Deprecation warning: this parameter name will change in a later release.",
     show_default=True,
 )
 @click.option("-f", "--force", is_flag=True, help="upload without request")
@@ -53,6 +56,7 @@ def variants(
     cancer_sv_research,
     mei,
     mei_research,
+    outlier,
     sv,
     sv_research,
     snv,
@@ -69,7 +73,7 @@ def variants(
 ):
     """Upload variants to a case
 
-    Note that the files has to be linked with the case,
+    Note that the files have to be linked with the case,
     if they are not use 'scout update case'.
     """
     LOG.info("Running scout load variants")
@@ -108,6 +112,14 @@ def variants(
         {"category": "str", "variant_type": "clinical", "upload": str_clinical},
     ]
 
+    omics_files = [
+        {
+            "category": "outlier",
+            "variant_type": "clinical",
+            "upload": outlier,
+        },
+    ]
+
     gene_obj = None
     if hgnc_id or hgnc_symbol:
         if hgnc_id:
@@ -125,55 +137,124 @@ def variants(
     if keep_actions:  # collect all variants with user actions for this case
         old_evaluated_variants = list(adapter.evaluated_variants(case_id, institute_id))
 
-    i = 0
-    for file_type in files:
-        variant_type = file_type["variant_type"]
-        category = file_type["category"]
+    def load_variant_files(
+        case_obj: dict, files: List[Dict], rank_threshold: int, force: bool
+    ) -> int:
+        """Load variants from indicated VCF files. Keep count of files used for logging blank commands."""
+        i = 0
+        for file_type in files:
+            variant_type = file_type["variant_type"]
+            category = file_type["category"]
 
-        if not file_type["upload"]:
-            continue
+            if not file_type["upload"]:
+                continue
+
+            i += 1
+            if variant_type == "research":
+                if not (force or case_obj["research_requested"]):
+                    LOG.warning("research not requested, use '--force'")
+                    raise click.Abort()
+
+            LOG.info(
+                "Delete {0} {1} variants for case {2}".format(
+                    variant_type, category, case_obj["_id"]
+                )
+            )
 
-        i += 1
-        if variant_type == "research":
-            if not (force or case_obj["research_requested"]):
-                LOG.warning("research not requested, use '--force'")
+            adapter.delete_variants(
+                case_id=case_obj["_id"], variant_type=variant_type, category=category
+            )
+
+            LOG.info(
+                "Load {0} {1} variants for case {2}".format(variant_type, category, case_obj["_id"])
+            )
+
+            try:
+                adapter.load_variants(
+                    case_obj=case_obj,
+                    variant_type=variant_type,
+                    category=category,
+                    rank_threshold=rank_threshold,
+                    chrom=chrom,
+                    start=start,
+                    end=end,
+                    gene_obj=gene_obj,
+                    build=case_obj["genome_build"],
+                )
+                # Update case variants count
+                adapter.case_variants_count(case_obj["_id"], institute_id, force_update_case=True)
+
+            except Exception as e:
+                LOG.warning(e)
                 raise click.Abort()
 
-        LOG.info("Delete {0} {1} variants for case {2}".format(variant_type, category, case_id))
-
-        adapter.delete_variants(
-            case_id=case_obj["_id"], variant_type=variant_type, category=category
-        )
-
-        LOG.info("Load {0} {1} variants for case {2}".format(variant_type, category, case_id))
-
-        try:
-            adapter.load_variants(
-                case_obj=case_obj,
-                variant_type=variant_type,
-                category=category,
-                rank_threshold=rank_treshold,
-                chrom=chrom,
-                start=start,
-                end=end,
-                gene_obj=gene_obj,
-                build=case_obj["genome_build"],
+        return i
+
+    def load_omics_variant_files(case_obj: dict, omics_files: List[Dict]) -> int:
+        """Load variants from indicated VCF files. Keep count of files used for logging blank commands."""
+        i = 0
+        for file_type in omics_files:
+            variant_type = file_type["variant_type"]
+            category = file_type["category"]
+
+            if not file_type["upload"]:
+                continue
+
+            i += 1
+            LOG.info(
+                "Delete {0} {1} OMICS variants for case {2}".format(
+                    variant_type, category, case_obj["_id"]
+                )
             )
-            # Update case variants count
-            adapter.case_variants_count(case_obj["_id"], institute_id, force_update_case=True)
 
-        except Exception as e:
-            LOG.warning(e)
-            raise click.Abort()
+            adapter.delete_omics_variants_by_category(
+                case_id=case_obj["_id"], variant_type=variant_type, category=category
+            )
+
+            for file_type, omics_file_type in OMICS_FILE_TYPE_MAP.items():
+                if (
+                    omics_file_type["variant_type"] != variant_type
+                    or omics_file_type["category"] != category
+                ):
+                    continue
+
+                i += 1
+                LOG.info(
+                    "Load {0} {1} variants for case {2}".format(
+                        variant_type, category, case_obj["_id"]
+                    )
+                )
+
+                build = case_obj.get("rna_genome_build", case_obj.get("genome_build", "38"))
+
+                try:
+                    adapter.load_omics_variants(
+                        case_obj=case_obj,
+                        file_type=file_type,
+                        build=build,
+                    )
+                    # Update case variants count
+                    adapter.case_variants_count(
+                        case_obj["_id"], institute_id, force_update_case=True
+                    )
+
+                except Exception as e:
+                    LOG.warning(e)
+                    raise click.Abort()
+
+        return i
+
+    i = load_variant_files(case_obj, files, rank_treshold, force)
+    i += load_omics_variant_files(
+        case_obj,
+        omics_files,
+    )
 
     if i == 0:
         LOG.info("No files where specified to upload variants from")
-        return
 
     # update Sanger status for the new inserted variants
-    sanger_updated = adapter.update_case_sanger_variants(
-        institute_obj, case_obj, old_sanger_variants
-    )
+    adapter.update_case_sanger_variants(institute_obj, case_obj, old_sanger_variants)
 
     if keep_actions and old_evaluated_variants:
         adapter.update_variant_actions(institute_obj, case_obj, old_evaluated_variants)

scout/commands/update/case.py

@@ -17,51 +17,73 @@ LOG = logging.getLogger(__name__)
     "--institute", "-i", help="Case institute ID (case display name should also be provided)"
 )
 @click.option("--collaborator", "-c", help="Add a collaborator to the case")
-@click.option("--vcf", type=click.Path(exists=True), help="path to clinical VCF file to be added")
+@click.option(
+    "--fraser",
+    help="Path to clinical WTS OMICS outlier FRASER TSV file to be added - NB variants are NOT loaded",
+)
+@click.option(
+    "--outrider",
+    help="Path to clinical WTS OMICS outlier OUTRIDER TSV file to be added - NB variants are NOT loaded",
+)
+@click.option(
+    "--rna-genome-build",
+    type=click.Choice(["37", "38"]),
+    help="RNA human genome build - should match RNA alignment files and IGV tracks",
+)
+@click.option(
+    "--vcf",
+    type=click.Path(exists=True),
+    help="Path to clinical VCF file to be added - NB variants are NOT loaded",
+)
 @click.option(
     "--vcf-sv",
     type=click.Path(exists=True),
     help="path to clinical SV VCF file to be added",
 )
+@click.option(
+    "--vcf-str",
+    type=click.Path(exists=True),
+    help="Path to clinical STR VCF file to be added - NB variants are NOT loaded",
+)
 @click.option(
     "--vcf-cancer",
     type=click.Path(exists=True),
-    help="path to clinical cancer VCF file to be added",
+    help="Path to clinical cancer VCF file to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--vcf-cancer-sv",
     type=click.Path(exists=True),
-    help="path to clinical cancer structural VCF file to be added",
+    help="Path to clinical cancer structural VCF file to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--vcf-research",
     type=click.Path(exists=True),
-    help="path to research VCF file to be added",
+    help="Path to research VCF file to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--vcf-sv-research",
     type=click.Path(exists=True),
-    help="path to research VCF with SV variants to be added",
+    help="Path to research VCF with SV variants to be added",
 )
 @click.option(
     "--vcf-cancer-research",
     type=click.Path(exists=True),
-    help="path to research VCF with cancer variants to be added",
+    help="Path to research VCF with cancer variants to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--vcf-cancer-sv-research",
     type=click.Path(exists=True),
-    help="path to research VCF with cancer structural variants to be added",
+    help="Path to research VCF with cancer structural variants to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--vcf-mei",
     type=click.Path(exists=True),
-    help="path to clinical mei variants to be added",
+    help="Path to clinical mei variants to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--vcf-mei-research",
     type=click.Path(exists=True),
-    help="path to research mei variants to be added",
+    help="Path to research mei variants to be added - NB variants are NOT loaded",
 )
 @click.option(
     "--reupload-sv",
@@ -77,8 +99,11 @@ def case(
     case_name,
     institute,
     collaborator,
+    fraser,
+    outrider,
     vcf,
     vcf_sv,
+    vcf_str,
     vcf_cancer,
     vcf_cancer_sv,
     vcf_research,
@@ -89,6 +114,7 @@ def case(
     vcf_mei_research,
     reupload_sv,
     rankscore_treshold,
+    rna_genome_build,
     sv_rankmodel_version,
 ):
     """
@@ -122,6 +148,7 @@ def case(
     for key_name, key in [
         ("vcf_snv", vcf),
         ("vcf_sv", vcf_sv),
+        ("vcf_str", vcf_str),
         ("vcf_cancer", vcf_cancer),
         ("vcf_cancer_sv", vcf_cancer_sv),
         ("vcf_research", vcf_research),
@@ -137,6 +164,25 @@ def case(
         case_obj["vcf_files"][key_name] = key
         case_changed = True
 
+    for key_name, key in [
+        ("fraser", fraser),
+        ("outrider", outrider),
+    ]:
+        if key is None:
+            continue
+        LOG.info(f"Updating '{key_name}' to {key}")
+
+        if "omics_files" not in case_obj or case_obj["omics_files"] is None:
+            case_obj["omics_files"] = {}
+
+        case_obj["omics_files"][key_name] = key
+        case_obj["has_outliers"] = True
+        case_changed = True
+
+    if rna_genome_build:
+        case_obj["rna_genome_build"] = rna_genome_build
+        case_changed = True
+
     if case_changed:
         institute_obj = store.institute(case_obj["owner"])
         store.update_case_cli(case_obj, institute_obj)
@@ -148,7 +194,7 @@ def case(
             updates["sv_rank_model_version"] = str(sv_rankmodel_version)
         if vcf_sv:
             updates["vcf_files.vcf_sv"] = vcf_sv
-        if vcf_sv:
+        if vcf_sv_research:
             updates["vcf_files.vcf_sv_research"] = vcf_sv_research
 
         updated_case = store.case_collection.find_one_and_update(

scout/constants/case_tags.py

@@ -3,6 +3,11 @@ ANALYSIS_TYPES = ("external", "mixed", "ogm", "panel", "panel-umi", "unknown", "
 # keys are used in the load report cli, while key_name is saved in case database documents
 CUSTOM_CASE_REPORTS = {
     "delivery": {"key_name": "delivery_report", "format": "HTML", "pdf_export": True},
+    "rna_delivery_report": {
+        "key_name": "rna_delivery_report",
+        "format": "HTML",
+        "pdf_export": True,
+    },
     "cnv": {"key_name": "cnv_report", "format": "PDF", "pdf_export": False},
     "cov_qc": {"key_name": "coverage_qc_report", "format": "HTML", "pdf_export": True},
     "exe_ver": {"key_name": "pipeline_version", "format": "YAML", "pdf_export": True},

scout/constants/disease_parsing.py

@@ -1,7 +1,7 @@
 import re
 
-MIMNR_PATTERN = re.compile("[0-9]{6,6}")
-ENTRY_PATTERN = re.compile("\([1,2,3,4]\)")
+MIMNR_PATTERN = re.compile(r"[0-9]{6,6}")
+ENTRY_PATTERN = re.compile(r"\([1-4]\)")
 
 DISEASE_INHERITANCE_TERMS = [
     "Autosomal recessive",

scout/constants/igv_tracks.py

@@ -4,11 +4,11 @@ HG19REF_URL = (
 )
 HG19REF_INDEX_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta.fai"
 HG19CYTOBAND_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"
-HG19ALIAS_URL = "https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_alias.tab"
+HG19ALIAS_URL = "https://igv.org/genomes/data/hg19/hg19_alias.tab"
 
 HG38REF_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa"
 HG38REF_INDEX_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai"
-HG38ALIAS_URL = "https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab"
+HG38ALIAS_URL = "https://igv.org/genomes/data/hg38/hg38_alias.tab"
 HG38CYTOBAND_URL = (
     "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt"
 )

scout/constants/indexes.py

@@ -145,11 +145,18 @@ INDEXES = {
     "case": [
         IndexModel([("synopsis", TEXT)], default_language="english", name="synopsis_text"),
         IndexModel([("causatives", ASCENDING)], name="causatives"),
+        IndexModel([("suspects", ASCENDING)], name="suspects"),
         IndexModel(
             [("collaborators", ASCENDING), ("status", ASCENDING), ("updated_at", ASCENDING)],
             name="collaborators_status_updated_at",
         ),
-        IndexModel([("owner", ASCENDING), ("display_name", ASCENDING)], name="owner_display_name"),
+        IndexModel(
+            [
+                ("owner", ASCENDING),
+                ("display_name", ASCENDING),
+            ],
+            name="owner_display_name",
+        ),
     ],
     "managed_variant": [
         IndexModel(

scout/demo/643594.config.yaml

@@ -142,6 +142,7 @@ peddy_sex: scout/demo/643594.sex_check.csv
 
 delivery_report: scout/demo/delivery_report.html
 gene_fusion_report: scout/demo/draw-fusions-example.pdf
+rna_delivery_report: scout/demo/delivery_report.html
 exe_ver: scout/demo/exe_ver.yaml
 reference_info: scout/demo/reference_info.yaml
 

scout/demo/panel_1.txt

@@ -267,3 +267,5 @@
 10542	SBF1						SBF1
 10604	SCO2						SCO2
 713	ARSA						ARSA
+11117	SMN1						SMN1
+11118	SMN2						SMN2

scout/demo/resources/ensembl_exons_37_reduced.txt

@@ -15570,6 +15570,141 @@ Chromosome/scaffold name	Gene stable ID	Transcript stable ID	Exon stable ID	Exon
 5	ENSG00000170458	ENST00000401743	ENSE00001862834	140011313	140012565			140011313	140011440	-1	3
 5	ENSG00000170458	ENST00000401743	ENSE00001429397	140012654	140012877	140012657	140012877			-1	2
 5	ENSG00000170458	ENST00000401743	ENSE00001554029	140013116	140013286	140013116	140013286			-1	1
+5	ENSG00000172062	ENST00000503079	ENSE00001922009	70220857	70221011	70220857	70220930			1	1
+5	ENSG00000172062	ENST00000503079	ENSE00001688516	70234666	70234737					1	2
+5	ENSG00000172062	ENST00000503079	ENSE00001638255	70237216	70237335					1	3
+5	ENSG00000172062	ENST00000503079	ENSE00001766361	70238185	70238385					1	4
+5	ENSG00000172062	ENST00000503079	ENSE00003576392	70238545	70238697					1	5
+5	ENSG00000172062	ENST00000503079	ENSE00001593733	70241893	70242003					1	6
+5	ENSG00000172062	ENST00000503079	ENSE00002062475	70247768	70248174			70247819	70248174	1	7
+5	ENSG00000172062	ENST00000380707	ENSE00001922009	70220857	70221011	70220857	70220930			1	1
+5	ENSG00000172062	ENST00000380707	ENSE00001688516	70234666	70234737					1	2
+5	ENSG00000172062	ENST00000380707	ENSE00001638255	70237216	70237335					1	3
+5	ENSG00000172062	ENST00000380707	ENSE00001766361	70238185	70238385					1	4
+5	ENSG00000172062	ENST00000380707	ENSE00003576392	70238545	70238697					1	5
+5	ENSG00000172062	ENST00000380707	ENSE00003611930	70240485	70240580					1	6
+5	ENSG00000172062	ENST00000380707	ENSE00001593733	70241893	70242003					1	7
+5	ENSG00000172062	ENST00000380707	ENSE00003693452	70247768	70247821			70247819	70247821	1	8
+5	ENSG00000172062	ENST00000380707	ENSE00001885073	70248266	70248839			70248266	70248839	1	9
+5	ENSG00000172062	ENST00000514951	ENSE00002034950	70220883	70221011	70220883	70220930			1	1
+5	ENSG00000172062	ENST00000514951	ENSE00001688516	70234666	70234737					1	2
+5	ENSG00000172062	ENST00000514951	ENSE00001638255	70237216	70237335					1	3
+5	ENSG00000172062	ENST00000514951	ENSE00003576392	70238545	70238697					1	4
+5	ENSG00000172062	ENST00000514951	ENSE00003611930	70240485	70240580					1	5
+5	ENSG00000172062	ENST00000514951	ENSE00001593733	70241893	70242003					1	6
+5	ENSG00000172062	ENST00000514951	ENSE00002045198	70247768	70248394			70247819	70248394	1	7
+5	ENSG00000172062	ENST00000506239	ENSE00002073998	70220902	70221011	70220902	70220930			1	1
+5	ENSG00000172062	ENST00000506239	ENSE00001688516	70234666	70234737					1	2
+5	ENSG00000172062	ENST00000506239	ENSE00001638255	70237216	70237335					1	3
+5	ENSG00000172062	ENST00000506239	ENSE00001766361	70238185	70238385					1	4
+5	ENSG00000172062	ENST00000506239	ENSE00003576392	70238545	70238697					1	5
+5	ENSG00000172062	ENST00000506239	ENSE00003611930	70240485	70240580					1	6
+5	ENSG00000172062	ENST00000506239	ENSE00001593733	70241893	70242003					1	7
+5	ENSG00000172062	ENST00000506239	ENSE00002042046	70242534	70242642			70242585	70242642	1	8
+5	ENSG00000172062	ENST00000506239	ENSE00002052357	70248266	70248843			70248266	70248843	1	9
+5	ENSG00000172062	ENST00000506163	ENSE00002033586	70220922	70221011	70220922	70220930			1	1
+5	ENSG00000172062	ENST00000506163	ENSE00001688516	70234666	70234737					1	2
+5	ENSG00000172062	ENST00000506163	ENSE00001638255	70237216	70237335					1	3
+5	ENSG00000172062	ENST00000506163	ENSE00001766361	70238185	70238385					1	4
+5	ENSG00000172062	ENST00000506163	ENSE00003576392	70238545	70238697					1	5
+5	ENSG00000172062	ENST00000506163	ENSE00003611930	70240485	70240580					1	6
+5	ENSG00000172062	ENST00000506163	ENSE00001593733	70241893	70242003					1	7
+5	ENSG00000172062	ENST00000506163	ENSE00002025434	70248266	70248867			70248281	70248867	1	8
+5	ENSG00000172062	ENST00000518504	ENSE00002115234	70238299	70238385					1	1
+5	ENSG00000172062	ENST00000518504	ENSE00003586477	70238545	70238697					1	2
+5	ENSG00000172062	ENST00000518504	ENSE00002067240	70241893	70242105					1	3
+5	ENSG00000172062	ENST00000507905	ENSE00002065935	70238335	70238385					1	1
+5	ENSG00000172062	ENST00000507905	ENSE00003576392	70238545	70238697					1	2
+5	ENSG00000172062	ENST00000507905	ENSE00002019326	70240276	70240392			70240312	70240392	1	3
+5	ENSG00000172062	ENST00000507905	ENSE00003477349	70240485	70240580			70240485	70240580	1	4
+5	ENSG00000172062	ENST00000507905	ENSE00002110817	70241893	70241906			70241893	70241906	1	5
+5	ENSG00000172062	ENST00000513228	ENSE00002053468	70238345	70238385					1	1
+5	ENSG00000172062	ENST00000513228	ENSE00003586477	70238545	70238697					1	2
+5	ENSG00000172062	ENST00000513228	ENSE00003477349	70240485	70240580					1	3
+5	ENSG00000172062	ENST00000513228	ENSE00002065580	70241893	70242101					1	4
+5	ENSG00000172062	ENST00000510679	ENSE00002063740	70241916	70242003					1	1
+5	ENSG00000172062	ENST00000510679	ENSE00003581587	70247768	70247821					1	2
+5	ENSG00000172062	ENST00000510679	ENSE00002068209	70248266	70248407					1	3
+5	ENSG00000172062	ENST00000510679	ENSE00002084907	70249009	70249769					1	4
+5	ENSG00000172062	ENST00000351205	ENSE00001695536	70220768	70221011	70220768	70220930			1	1
+5	ENSG00000172062	ENST00000351205	ENSE00001688516	70234666	70234737					1	2
+5	ENSG00000172062	ENST00000351205	ENSE00001638255	70237216	70237335					1	3
+5	ENSG00000172062	ENST00000351205	ENSE00001766361	70238185	70238385					1	4
+5	ENSG00000172062	ENST00000351205	ENSE00003576392	70238545	70238697					1	5
+5	ENSG00000172062	ENST00000351205	ENSE00001593733	70241893	70242003					1	6
+5	ENSG00000172062	ENST00000351205	ENSE00003693452	70247768	70247821			70247819	70247821	1	7
+5	ENSG00000172062	ENST00000351205	ENSE00001731510	70248266	70248841			70248266	70248841	1	8
+5	ENSG00000205571	ENST00000380743	ENSE00001904512	69345439	69345593	69345439	69345512			1	1
+5	ENSG00000205571	ENST00000380743	ENSE00001725187	69359242	69359313					1	2
+5	ENSG00000205571	ENST00000380743	ENSE00003668426	69361792	69361911					1	3
+5	ENSG00000205571	ENST00000380743	ENSE00003579743	69362761	69362961					1	4
+5	ENSG00000205571	ENST00000380743	ENSE00003698225	69363121	69363273					1	5
+5	ENSG00000205571	ENST00000380743	ENSE00003550962	69365062	69365157					1	6
+5	ENSG00000205571	ENST00000380743	ENSE00003620900	69366468	69366578					1	7
+5	ENSG00000205571	ENST00000380743	ENSE00003698693	69372348	69372401			69372399	69372401	1	8
+5	ENSG00000205571	ENST00000380743	ENSE00001812360	69372846	69373419			69372846	69373419	1	9
+5	ENSG00000205571	ENST00000511812	ENSE00002054021	69345465	69345593	69345465	69345512			1	1
+5	ENSG00000205571	ENST00000511812	ENSE00001725187	69359242	69359313					1	2
+5	ENSG00000205571	ENST00000511812	ENSE00003668426	69361792	69361911					1	3
+5	ENSG00000205571	ENST00000511812	ENSE00003698225	69363121	69363273					1	4
+5	ENSG00000205571	ENST00000511812	ENSE00003550962	69365062	69365157					1	5
+5	ENSG00000205571	ENST00000511812	ENSE00003620900	69366468	69366578					1	6
+5	ENSG00000205571	ENST00000511812	ENSE00002055618	69372348	69372533			69372399	69372533	1	7
+5	ENSG00000205571	ENST00000506734	ENSE00002041070	69345484	69345593	69345484	69345512			1	1
+5	ENSG00000205571	ENST00000506734	ENSE00001725187	69359242	69359313					1	2
+5	ENSG00000205571	ENST00000506734	ENSE00003668426	69361792	69361911					1	3
+5	ENSG00000205571	ENST00000506734	ENSE00003579743	69362761	69362961					1	4
+5	ENSG00000205571	ENST00000506734	ENSE00003698225	69363121	69363273					1	5
+5	ENSG00000205571	ENST00000506734	ENSE00003550962	69365062	69365157					1	6
+5	ENSG00000205571	ENST00000506734	ENSE00003620900	69366468	69366578					1	7
+5	ENSG00000205571	ENST00000506734	ENSE00002038304	69367109	69367217			69367160	69367217	1	8
+5	ENSG00000205571	ENST00000506734	ENSE00002033350	69372846	69373423			69372846	69373423	1	9
+5	ENSG00000205571	ENST00000380742	ENSE00001897950	69345491	69345593	69345491	69345512			1	1
+5	ENSG00000205571	ENST00000380742	ENSE00001725187	69359242	69359313					1	2
+5	ENSG00000205571	ENST00000380742	ENSE00003668426	69361792	69361911					1	3
+5	ENSG00000205571	ENST00000380742	ENSE00003579743	69362761	69362961					1	4
+5	ENSG00000205571	ENST00000380742	ENSE00003698225	69363121	69363273					1	5
+5	ENSG00000205571	ENST00000380742	ENSE00003620900	69366468	69366578					1	6
+5	ENSG00000205571	ENST00000380742	ENSE00003698693	69372348	69372401			69372399	69372401	1	7
+5	ENSG00000205571	ENST00000380742	ENSE00001812360	69372846	69373419			69372846	69373419	1	8
+5	ENSG00000205571	ENST00000503678	ENSE00002056052	69359238	69359313					1	1
+5	ENSG00000205571	ENST00000503678	ENSE00003685383	69361792	69361911					1	2
+5	ENSG00000205571	ENST00000503678	ENSE00003650356	69362761	69362961					1	3
+5	ENSG00000205571	ENST00000503678	ENSE00003700892	69363121	69363273					1	4
+5	ENSG00000205571	ENST00000503678	ENSE00003668557	69365062	69365157					1	5
+5	ENSG00000205571	ENST00000503678	ENSE00002064131	69366468	69366582					1	6
+5	ENSG00000205571	ENST00000511873	ENSE00002038537	69362911	69362961					1	1
+5	ENSG00000205571	ENST00000511873	ENSE00003698225	69363121	69363273					1	2
+5	ENSG00000205571	ENST00000511873	ENSE00002050020	69364853	69364969			69364889	69364969	1	3
+5	ENSG00000205571	ENST00000511873	ENSE00003668557	69365062	69365157			69365062	69365157	1	4
+5	ENSG00000205571	ENST00000511873	ENSE00003697649	69366468	69366481			69366468	69366481	1	5
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+5	ENSG00000205571	ENST00000509805	ENSE00003700892	69363121	69363273					1	2
+5	ENSG00000205571	ENST00000509805	ENSE00003668557	69365062	69365157					1	3
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+5	ENSG00000205571	ENST00000505346	ENSE00002067458	69362926	69362961					1	1
+5	ENSG00000205571	ENST00000505346	ENSE00003700892	69363121	69363273					1	2
+5	ENSG00000205571	ENST00000505346	ENSE00003529016	69366468	69366578					1	3
+5	ENSG00000205571	ENST00000505346	ENSE00002073006	69372348	69372754					1	4
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+5	ENSG00000205571	ENST00000514914	ENSE00003668557	69365062	69365157					1	2
+5	ENSG00000205571	ENST00000514914	ENSE00003529016	69366468	69366578					1	3
+5	ENSG00000205571	ENST00000514914	ENSE00003696722	69372348	69372401					1	4
+5	ENSG00000205571	ENST00000514914	ENSE00002023398	69372846	69373078					1	5
+5	ENSG00000205571	ENST00000508258	ENSE00002032527	69365060	69365157					1	1
+5	ENSG00000205571	ENST00000508258	ENSE00002041684	69366468	69366580					1	2
+5	ENSG00000205571	ENST00000507458	ENSE00002036578	69366491	69366578					1	1
+5	ENSG00000205571	ENST00000507458	ENSE00003698693	69372348	69372401			69372399	69372401	1	2
+5	ENSG00000205571	ENST00000507458	ENSE00002067548	69372846	69372987			69372846	69372987	1	3
+5	ENSG00000205571	ENST00000507458	ENSE00002085226	69373589	69374349			69373589	69374349	1	4
+5	ENSG00000205571	ENST00000380741	ENSE00001792916	69345350	69345593	69345350	69345512			1	1
+5	ENSG00000205571	ENST00000380741	ENSE00001725187	69359242	69359313					1	2
+5	ENSG00000205571	ENST00000380741	ENSE00003668426	69361792	69361911					1	3
+5	ENSG00000205571	ENST00000380741	ENSE00003579743	69362761	69362961					1	4
+5	ENSG00000205571	ENST00000380741	ENSE00003698225	69363121	69363273					1	5
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+5	ENSG00000205571	ENST00000380741	ENSE00003620900	69366468	69366578					1	7
+5	ENSG00000205571	ENST00000380741	ENSE00002235176	69372846	69373421			69372861	69373421	1	8
 6	ENSG00000118503	ENST00000421450	ENSE00001636894	138188351	138188679	138188351	138188679			1	1
 6	ENSG00000118503	ENST00000421450	ENSE00001724607	138192350	138192441	138192350	138192364			1	2
 6	ENSG00000118503	ENST00000420009	ENSE00001680250	138188459	138188655	138188459	138188655			1	1