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major rework of pangolin test stage to consolidate to fewer test comm…
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@kapsakcj
kapsakcj committed Nov 22, 2024
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Expand Up @@ -111,109 +111,21 @@ RUN wget https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd
chmod +x datasets && \
mv -v datasets /usr/local/bin

# download assembly for a BA.1 from Florida (https://www.ncbi.nlm.nih.gov/biosample?term=SAMN29506515 and https://www.ncbi.nlm.nih.gov/nuccore/ON924087)
# run pangolin in usher analysis mode
RUN datasets download virus genome accession ON924087.1 --filename ON924087.1.zip && \
unzip ON924087.1.zip && rm ON924087.1.zip && \
mv -v ncbi_dataset/data/genomic.fna ON924087.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin ON924087.1.genomic.fna -o ON924087.1-usher && \
column -t -s, ON924087.1-usher/lineage_report.csv

# test specific for new lineage, XBB.1.16, introduced in pangolin-data v1.19
# using this assembly: https://www.ncbi.nlm.nih.gov/nuccore/2440446687
# biosample here: https://www.ncbi.nlm.nih.gov/biosample?term=SAMN33060589
# one of the sample included in initial pango-designation here: https://github.com/cov-lineages/pango-designation/issues/1723
RUN datasets download virus genome accession OQ381818.1 --filename OQ381818.1.zip && \
unzip -o OQ381818.1.zip && rm OQ381818.1.zip && \
mv -v ncbi_dataset/data/genomic.fna OQ381818.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin OQ381818.1.genomic.fna -o OQ381818.1-usher && \
column -t -s, OQ381818.1-usher/lineage_report.csv

# testing another XBB.1.16, trying to test scorpio functionality. Want pangolin to NOT assign lineage based on pango hash match.
# this test runs as expected, uses scorpio to check for constellation of mutations, then assign using PUSHER placement
RUN datasets download virus genome accession OR177999.1 --filename OR177999.1.zip && \
unzip -o OR177999.1.zip && rm OR177999.1.zip && \
mv -v ncbi_dataset/data/genomic.fna OR177999.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin OR177999.1.genomic.fna -o OR177999.1-usher && \
column -t -s, OR177999.1-usher/lineage_report.csv

## test for BA.2.86
# virus identified in MI: https://www.ncbi.nlm.nih.gov/nuccore/OR461132.1
RUN datasets download virus genome accession OR461132.1 --filename OR461132.1.zip && \
unzip -o OR461132.1.zip && rm OR461132.1.zip && \
mv -v ncbi_dataset/data/genomic.fna OR461132.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin OR461132.1.genomic.fna -o OR461132.1-usher && \
column -t -s, OR461132.1-usher/lineage_report.csv

## test for JN.2 (BA.2.86 sublineage) JN.2 is an alias of B.1.1.529.2.86.1.2
# NY CDC Quest sample: https://www.ncbi.nlm.nih.gov/nuccore/OR598183
RUN datasets download virus genome accession OR598183.1 --filename OR598183.1.zip && \
unzip -o OR598183.1.zip && rm OR598183.1.zip && \
mv -v ncbi_dataset/data/genomic.fna OR598183.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin OR598183.1.genomic.fna -o OR598183.1-usher && \
column -t -s, OR598183.1-usher/lineage_report.csv

## test for JQ.1 (BA.2.86.3 sublineage); JQ.1 is an alias of B.1.1.529.2.86.3.1
# THANK YOU ERIN AND UPHL!! https://www.ncbi.nlm.nih.gov/nuccore/OR716684
# this test is important due to the fact that this lineage was included in the UShER tree, despite being designated after the pangolin-designation 1.23 release
# it previously caused and error/bug in pangolin, but now is fixed
RUN datasets download virus genome accession OR716684.1 --filename OR716684.1.zip && \
unzip -o OR716684.1.zip && rm OR716684.1.zip && \
mv -v ncbi_dataset/data/genomic.fna OR716684.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin OR716684.1.genomic.fna -o OR716684.1-usher && \
column -t -s, OR716684.1-usher/lineage_report.csv

## test for JN.1.22 (BA.2.86.x sublineage; full unaliased lineage is B.1.1.529.2.86.1.1.22)
# see here for commit where it was designated https://github.com/cov-lineages/pango-designation/commit/a90c8e31c154621ed86c985debfea09e17541cda
# Here's the genome on NCBI, which was used to designate JN.1.22 lineage
RUN datasets download virus genome accession PP189069.1 --filename PP189069.1.zip && \
unzip -o PP189069.1.zip && rm PP189069.1.zip && \
mv -v ncbi_dataset/data/genomic.fna PP189069.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin PP189069.1.genomic.fna -o PP189069.1-usher && \
column -t -s, PP189069.1-usher/lineage_report.csv

## test for JN.1.48 (BA.2.86.x sublineage; full unaliased lineage is B.1.1.529.2.86.1.1.48)
# this lineages which was designated in pango-designation v1.27: https://github.com/cov-lineages/pango-designation/releases/tag/v1.27
# see here for commit where it was designated https://github.com/cov-lineages/pango-designation/commit/67f48bf24283999f1940f3aee8159f404124ff3f
# Here's the genome on NCBI: https://www.ncbi.nlm.nih.gov/nuccore/PP218754
RUN datasets download virus genome accession PP218754.1 --filename PP218754.1.zip && \
unzip -o PP218754.1.zip && rm PP218754.1.zip && \
mv -v ncbi_dataset/data/genomic.fna PP218754.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin PP218754.1.genomic.fna -o PP218754.1-usher && \
column -t -s, PP218754.1-usher/lineage_report.csv

# new lineage LK.1 that was introduced in pango-designation v1.28: https://github.com/cov-lineages/pango-designation/commit/922795c90de355e67200cf4d379e8e5ff22472e4
# thank you Luis, Lorraine, Marcos & team from PR Sci Trust for sharing your data!
# genome on NCBI: https://www.ncbi.nlm.nih.gov/nuccore/2728145425
RUN datasets download virus genome accession PP770375.1 --filename PP770375.1.zip && \
unzip -o PP770375.1.zip && rm PP770375.1.zip && \
mv -v ncbi_dataset/data/genomic.fna PP770375.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin PP770375.1.genomic.fna -o PP770375.1-usher && \
column -t -s, PP770375.1-usher/lineage_report.csv

# new lineage KP.3.3.2 that was introduced in pango-designation v1.29: https://github.com/cov-lineages/pango-designation/commit/7125e606818312b78f0756d7fcab6dba92dd0a9e
# genome on NCBI: https://www.ncbi.nlm.nih.gov/nuccore/PQ073669
RUN datasets download virus genome accession PQ073669.1 --filename PQ073669.1.zip && \
unzip -o PQ073669.1.zip && rm PQ073669.1.zip && \
mv -v ncbi_dataset/data/genomic.fna PQ073669.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin PQ073669.1.genomic.fna -o PQ073669.1-usher && \
column -t -s, PQ073669.1-usher/lineage_report.csv

# new lineage MC.2 that was introduced in pango-designation v1.30: https://github.com/cov-lineages/pango-designation/commit/c64dbc47fbfbfd7f4da011deeb1a88dd6baa45f1#diff-a121ea4b8cbeb4c0020511b5535bf24489f0223cc83511df7b8209953115d329R2564181
# genome on NCBI: https://www.ncbi.nlm.nih.gov/nuccore/PQ034842.1
RUN datasets download virus genome accession PQ034842.1 --filename PQ034842.1.zip && \
unzip -o PQ034842.1.zip && rm PQ034842.1.zip && \
mv -v ncbi_dataset/data/genomic.fna PQ034842.1.genomic.fna && \
rm -vr ncbi_dataset/ README.md && \
pangolin PQ034842.1.genomic.fna -o PQ034842.1-usher && \
column -t -s, PQ034842.1-usher/lineage_report.csv
# testing the following lineages:
# BA.1 | ON924087.1 | from Florida https://www.ncbi.nlm.nih.gov/biosample?term=SAMN29506515 and https://www.ncbi.nlm.nih.gov/nuccore/ON924087
# XBB.1.16 | OQ381818.1 | introduced in p-data 1.19, https://www.ncbi.nlm.nih.gov/nuccore/2440446687 and https://www.ncbi.nlm.nih.gov/biosample?term=SAMN33060589 and https://github.com/cov-lineages/pango-designation/issues/1723
# another XBB.1.16 | OR177999.1 | https://www.ncbi.nlm.nih.gov/nuccore/OR177999.1
# BA.2.86 | OR461132.1 | from Michigan https://www.ncbi.nlm.nih.gov/nuccore/OR461132.1
# JN.2 (BA.2.86 sublineage) JN.2 is an alias of B.1.1.529.2.86.1.2 | OR598183.1 | NY CDC Quest sample https://www.ncbi.nlm.nih.gov/nuccore/OR598183
# JQ.1 (BA.2.86.3 sublineage); JQ.1 is an alias of B.1.1.529.2.86.3.1 | OR716684.1 | THANK YOU ERIN AND UPHL!! https://www.ncbi.nlm.nih.gov/nuccore/OR716684 this test is important due to the fact that this lineage was included in the UShER tree, despite being designated after the pangolin-designation 1.23 release it previously caused and error/bug in pangolin, but now is fixed
# JN.1.22 (BA.2.86.x sublineage; full unaliased lineage is B.1.1.529.2.86.1.1.22) | PP189069.1 | https://github.com/cov-lineages/pango-designation/commit/a90c8e31c154621ed86c985debfea09e17541cda
# JN.1.48 (BA.2.86.x sublineage; full unaliased lineage is B.1.1.529.2.86.1.1.48) | PP218754.1 | https://github.com/cov-lineages/pango-designation/releases/tag/v1.27 and https://github.com/cov-lineages/pango-designation/commit/67f48bf24283999f1940f3aee8159f404124ff3f and https://www.ncbi.nlm.nih.gov/nuccore/PP218754
# LK.1 | PP770375.1 | introduced in pango-designation 1.28 https://github.com/cov-lineages/pango-designation/commit/922795c90de355e67200cf4d379e8e5ff22472e4 and https://www.ncbi.nlm.nih.gov/nuccore/2728145425 thank you Luis, Lorraine, Marcos & team from PR Sci Trust for sharing your data!
# KP.3.3.2 | PQ073669.1 | introduced in pango-designation 1.29 https://github.com/cov-lineages/pango-designation/commit/7125e606818312b78f0756d7fcab6dba92dd0a9e and https://www.ncbi.nlm.nih.gov/nuccore/PQ073669
# MC.2 | PQ034842.1 | introduced in pango-designation 1.30 https://github.com/cov-lineages/pango-designation/commit/c64dbc47fbfbfd7f4da011deeb1a88dd6baa45f1#diff-a121ea4b8cbeb4c0020511b5535bf24489f0223cc83511df7b8209953115d329R2564181 and https://www.ncbi.nlm.nih.gov/nuccore/PQ034842
# XEC.3 | PQ277908.1 | introduced in pango-designation 1.31 https://github.com/cov-lineages/pango-designation/commit/ba3711a5615956ed97150288eb68356aa0fe7cdd#diff-a121ea4b8cbeb4c0020511b5535bf24489f0223cc83511df7b8209953115d329R2572545 and https://www.ncbi.nlm.nih.gov/nuccore/PQ277908.1
RUN datasets download virus genome accession ON924087.1,OQ381818.1,OR177999.1,OR461132.1,OR598183.1,OR716684.1,PP189069.1,PP218754.1,PP770375.1,PQ073669.1,PQ034842.1,PQ277908.1 && \
unzip -o ncbi_dataset.zip && \
rm -v ncbi_dataset.zip && \
pangolin ncbi_dataset/data/genomic.fna && \
column -t -s, lineage_report.csv

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