rjcorb commented 5 months ago

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #234. This PR renames the rs_id column as variant_ids to reflect cases where multiple variant ID sources are listed. The & separator is also replaced with ;

What was your approach?

What GitHub issue does your pull request address?

234

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please run the custom test samples through AutoGVP , and confirm variant_id column is present and, when applicable, that variant ids are separated by ;

bash run_autogvp.sh --workflow="custom" \
--vcf=data/test_VEP.vcf \
--clinvar=data/clinvar.vcf.gz \
--intervar=data/test_VEP.hg38_multianno.txt.intervar \
--multianno=data/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=data/test_autopvs1.txt \
--outdir=results \
--out="test_custom"

Is there anything that you want to discuss further?

No

Documentation Checklist

[ ] The function has examples to showcase the usage
[ ] Added a vignette

jharenza commented 5 months ago

I had to clone the repo from scratch, but running the command above gives an error:

(base) ubuntu@X:~/AutoGVP$ bash run_autogvp.sh --workflow="custom"
.
select ClinVar submission file not specified. Running select-ClinVar-submissions Rscript...
variant summary and/or submission_summary file(s) not specified. Checking if files exist in data/...
variant_summary and/or submission_summary files not found. Downloading latest versions from ClinVar...
Warning: Illegal date format for -z, --time-cond (and not a file name). 
Warning: Disabling time condition. See curl_getdate(3) for valid date syntax.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   166  100   166    0     0   2721      0 --:--:-- --:--:-- --:--:--  2721
Downloading clinvar.vcf.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 77.8M  100 77.8M    0     0  59.6M      0  0:00:01  0:00:01 --:--:-- 59.6M
Downloading submission_summary.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  190M  100  190M    0     0  46.1M      0  0:00:04  0:00:04 --:--:-- 46.1M
Downloading variant_summary.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  200M  100  200M    0     0  63.2M      0  0:00:03  0:00:03 --:--:-- 63.2M
Checking MD5 hashes...
clinvar.vcf.gz: OK
submission_summary.txt.gz: OK
variant_summary.txt.gz: OK
resolving ClinVar conflicts using default parameters...
run_autogvp.sh: line 143: Rscript: command not found
(base) ubuntu@X:~/AutoGVP$ --vcf=data/test_VEP.vcf
-bash: --vcf=data/test_VEP.vcf: No such file or directory
(base) ubuntu@X:~/AutoGVP$ --clinvar=data/clinvar.vcf.gz
-bash: --clinvar=data/clinvar.vcf.gz: No such file or directory
(base) ubuntu@X:~/AutoGVP$ --intervar=data/test_VEP.hg38_multianno.txt.intervar
-bash: --intervar=data/test_VEP.hg38_multianno.txt.intervar: No such file or directory
(base) ubuntu@X:~/AutoGVP$ --multianno=data/test_VEP.vcf.hg38_multianno.txt
-bash: --multianno=data/test_VEP.vcf.hg38_multianno.txt: No such file or directory
(base) ubuntu@X:~/AutoGVP$ --autopvs1=data/test_autopvs1.txt
-bash: --autopvs1=data/test_autopvs1.txt: No such file or directory
(base) ubuntu@X:~/AutoGVP$ --outdir=results
--outdir=results: command not found

jharenza commented 5 months ago

actually - scratch that, I needed to make the command one line from above since it did not have the line separators and it is running now

naqvia commented 5 months ago

It ran to completion, and I can confirm there's no longer & symbols, but agree with above comments.