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fixup: usvi description
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j23414 committed Jan 30, 2024
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28 changes: 23 additions & 5 deletions phylogenetic/data/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,8 @@ cat blast_output.txt \
| awk -F'\t' '$1~"USVI" , OFS="\t" {print}' \
| grep -Fvf USVI_100_match.txt \
| awk -F'\t' '{print $1}' \
| sort | uniq \
| sort \
| uniq \
> USVI_not_match.txt

head USVI_not_match.txt
Expand All @@ -74,10 +75,27 @@ smof grep -f USVI_not_match.txt zika.fasta > usvi.fasta
augur parse \
--sequences usvi.fasta \
--output-sequences sequences_usvi.fasta \
--output-metadata metadata_usvi.tsv \
--fields strain virus accession date region country division city db segment authors url title journal paper_url \
--prettify-fields region country division city
--output-metadata raw_metadata_usvi.tsv \
--fields strain virus accession date region country division location institution segment authors url title journal paper_url \
--prettify-fields region country division location

# Ah put in accession instead of strain
augur parse \
--sequences usvi.fasta \
--output-sequences sequences_usvi.fasta \
--output-metadata no.tsv \
--fields a b strain c d e f g h i j k l m n

# Add sequence lengths to metadata
echo "accession|length" | tr '|' '\t' > lengths_usvi.tsv
smof stat --length --byseq sequences_usvi.fasta >> lengths_usvi.tsv

tsv-join -H \
--filter-file lengths_usvi.tsv\
--key-fields accession \
--append-fields length \
raw_metadata_usvi.tsv \
| tsv-select -H \
--fields accession,strain,date,region,country,division,location,length,authors,institution,url \
> metadata_usvi.tsv
```

52 changes: 26 additions & 26 deletions phylogenetic/data/metadata_usvi.tsv
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@@ -1,26 +1,26 @@
genbank_accession genbank_accession_rev accession strain date region country division location length host release_date update_date sra_accessions authors institution url
USVI/37/2016 VI37 USVI/37/2016 2016-10-06 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/2/2016 VI2 USVI/2/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/42/2016 VI42 USVI/42/2016 2016-10-26 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/41/2016 VI41 USVI/41/2016 2016-11-10 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/6/2016 VI6 USVI/6/2016 2016-10-19 North America Usvi Saint John Saint John 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/12/2016 VI12 USVI/12/2016 2016-11-04 North America Usvi Saint Croix Saint Croix 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/36/2016 VI36 USVI/36/2016 2016-09-13 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/30/2016 VI30_1d USVI/30/2016 2016-08-07 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/13/2016 VI13 USVI/13/2016 2016-08-13 North America Usvi Saint Thomas Saint Thomas 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/32/2016 VI32_12plex USVI/32/2016 2016-08-11 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/7/2016 VI7 USVI/7/2016 2016-10-27 North America Usvi Saint Thomas Saint Thomas 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/28/2016 VI28_1d USVI/28/2016 2016-11-28 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/34/2016 VI34 USVI/34/2016 2016-08-01 North America Usvi Saint Thomas Saint Thomas 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/45/2016 VI45 USVI/45/2016 2016-08-03 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/3/2016 VI3 USVI/3/2016 2016-09-26 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/1/2016 VI1_1d USVI/1/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/46/2016 VI46 USVI/46/2016 2016-07-15 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/11/2016 VI11 USVI/11/2016 2016-03-22 North America Usvi Saint Thomas Saint Thomas 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/38/2016 VI38 USVI/38/2016 2016-10-25 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/27/2016 VI27_1d USVI/27/2016 2016-08-19 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/20/2016 VI20_12plex USVI/20/2016 2016-10-13 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/39/2016 VI39_12plex USVI/39/2016 2016-11-09 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/44/2016 VI44 USVI/44/2016 2016-10-17 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/19/2016 VI19_12plex USVI/19/2016 2016-11-21 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/23/2016 VI23_12plex USVI/23/2016 2016-07-12 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
accession strain date region country division location length authors institution url
VI44 USVI/44/2016 2016-10-17 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI20_12plex USVI/20/2016 2016-10-13 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/
VI41 USVI/41/2016 2016-11-10 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI32_12plex USVI/32/2016 2016-08-11 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/
VI12 USVI/12/2016 2016-11-04 North America Usvi Saint Croix Saint Croix 10636 Black et al fh https://github.com/blab/zika-usvi/
VI46 USVI/46/2016 2016-07-15 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI23_12plex USVI/23/2016 2016-07-12 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI28_1d USVI/28/2016 2016-11-28 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI45 USVI/45/2016 2016-08-03 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI37 USVI/37/2016 2016-10-06 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI39_12plex USVI/39/2016 2016-11-09 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI36 USVI/36/2016 2016-09-13 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI34 USVI/34/2016 2016-08-01 North America Usvi Saint Thomas Saint Thomas 10792 Black et al fh https://github.com/blab/zika-usvi/
VI11 USVI/11/2016 2016-03-22 North America Usvi Saint Thomas Saint Thomas 10636 Black et al fh https://github.com/blab/zika-usvi/
VI6 USVI/6/2016 2016-10-19 North America Usvi Saint John Saint John 10636 Black et al fh https://github.com/blab/zika-usvi/
VI3 USVI/3/2016 2016-09-26 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI27_1d USVI/27/2016 2016-08-19 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI13 USVI/13/2016 2016-08-13 North America Usvi Saint Thomas Saint Thomas 10636 Black et al fh https://github.com/blab/zika-usvi/
VI7 USVI/7/2016 2016-10-27 North America Usvi Saint Thomas Saint Thomas 10636 Black et al fh https://github.com/blab/zika-usvi/
VI38 USVI/38/2016 2016-10-25 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/
VI19_12plex USVI/19/2016 2016-11-21 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/
VI1_1d USVI/1/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/
VI42 USVI/42/2016 2016-10-26 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI30_1d USVI/30/2016 2016-08-07 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
VI2 USVI/2/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/
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