[issue/273] Add chromosome renaming script for dbSNP2 files #304
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poneill
approved these changes
Oct 20, 2023
| @@ -0,0 +1,30 @@ | |||
| # Check if the correct number of arguments are provided | |||
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I'd vote for starting all scripts with set -e, wdyt?
| for k in *assembly_report.txt | ||
| do | ||
| out=$(echo $k | sed 's/.txt/.chrnames/') | ||
| grep -e '^[^#]' $k | awk '{ print $7, $1 }' > $out |
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would gloss what these column positions represent in case the format changes at some later date
|
Addressed |
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This script works tested on GCF_000001405.25.gz (hg19) and GCF_000001405.39.gz (hg38); in a future PR will wrap into utility that can be run through bystro-utils.pl; will add test at that time.
With this we have a fully working DbSNP 2 transformation; I have already tested building dbSNP 2, works well.