Fix #4469 - parse TRGT STR VCF #4566
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## main #4566 +/- ##
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- Coverage 84.61% 84.53% -0.09%
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Files 310 310
Lines 18679 18744 +65
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+ Hits 15805 15845 +40
- Misses 2874 2899 +25 ☔ View full report in Codecov by Sentry. |
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Ok, actually working! There are a couple of small things missing in Stranger now (Clinical-Genomics/stranger#58), but once they are in place we can release it, and make sure we are parsing the release version ok with this PR.
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Would be nice to add this one to the new release. Who's with the missing things in STranger? Otherwise in the next release? |
Well, feel free to review: it would be nice with some input. In my mind right now the further additions would be in STRanger and possibly the reference files, but I conservatively kept this on hold since having things like the REF count visible has been useful in the past. Not that it’s strictly needed. |
| @@ -11,9 +11,11 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) | |||
| - STR variant information card with database links, replacing empty frequency panel | |||
| - Display paging and number of HPO terms available in the database on Phenotypes page | |||
| - On case page, typeahead hints when searching for a disease using substrings containing source ("OMIM:", "ORPHA:") | |||
| t | |||
| - Button to monitor the status of submissions on ClinVar Submissions page | ||
| - Option to filter cancer variants by number of observations in somatic and germline archived database | ||
| - Documentation for integrating chanjo2 | ||
| - Parse TRGT STR VCF |
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| - Parse TRGT STR VCF | |
| - Parse Tandem repeat genotyping (TRGT) tags from STR VCFs |
| @@ -199,7 +199,12 @@ def build_variant( | |||
| variant_obj["str_pathologic_min"] = variant.get("str_pathologic_min") | |||
| variant_obj["str_ref"] = variant.get("str_ref") | |||
| variant_obj["str_repid"] = variant.get("str_repid") | |||
| variant_obj["str_trid"] = variant.get("str_trid") | |||
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I know that we have long lists of key/values in this build_variant function, but without making huge changes to it, what about having all these strs keys/values into a constant and then call a specific function (outside this one) to assign these values in a loop? It would be less code and more readable
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I think this kind of transformation should be done using a class, why not a Pydantic one since we have started using them. I would prefer to do that as a separate PR, knowing that we tend to introduce some issues with empty and missing values when we convert to Pydantic if it's ok with you.
| @@ -103,6 +103,14 @@ def parse_genotype(variant, ind, pos): | |||
| (flanking_ref, flanking_alt) = _parse_format_entry(variant, pos, "ADFL") | |||
| (inrepeat_ref, inrepeat_alt) = _parse_format_entry(variant, pos, "ADIR") | |||
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| # TRGT long read STR specific | |||
| (mc_ref, mc_alt) = _parse_format_entry_trgt_mc(variant, pos) | |||
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| (mc_ref, mc_alt) = _parse_format_entry_trgt_mc(variant, pos) | |
| (_, mc_alt) = _parse_format_entry_trgt_mc(variant, pos) |
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Seems like it's not used downstream?
| @@ -395,14 +403,15 @@ def get_str_so(variant, pos): | |||
| return str_so | |||
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| def _parse_format_entry(variant, pos, format_entry_name): | |||
| def _parse_format_entry(variant, pos, format_entry_name, number_format=int): | |||
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| def _parse_format_entry(variant, pos, format_entry_name, number_format=int): | |
| def _parse_format_entry(variant: cyvcf2.Variant, pos: int, format_entry_name: str, number_format:Optional[Union[float. int]]=int) -> Tuple(Union[float, int]): |
| values = list(value.split("/")) | ||
| values = variant.format(format_entry_name)[pos] | ||
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| new_values = [] |
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Otherwise this could also work
values = re.split("/|,", values)
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| ref_value = None | ||
| alt_value = None | ||
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| if len(values) > 1: | ||
| ref_value = int(values[0]) | ||
| alt_value = int(values[1]) | ||
| ref_value = (number_format)(values[0]) |
| if ref_value >= 0: | ||
| ref = ref_value | ||
| if alt_value >= 0: | ||
| alt = alt_value | ||
| except (ValueError, TypeError) as _ignore_error: | ||
| pass | ||
| return (ref, alt) | ||
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| def _parse_format_entry_trgt_mc(variant, pos): |
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Add type hints and return type instead of having the long docstring. Instead the docstring couls contain a better explanation of what MC is
| pathologic_struc = variant.INFO.get("PathologicStruc", None) | ||
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| pathologic_counts = 0 |
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| pathologic_struc = variant.INFO.get("PathologicStruc", None) | |
| pathologic_counts = 0 | |
| pathologic_struc = variant.INFO.get("PathologicStruc", None) | |
| pathologic_counts = 0 |
These 2 could be moved down, after line 468 perhaps?
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This PR adds a functionality or fixes a bug.
OR
This PR marks a new Scout release. We apply semantic versioning. This is a major/minor/patch release for reasons.
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout.targetsystemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: