Separate curated data by L and S segments #12
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| """ | ||
| This part of the workflow handles running Nextclade on the curated metadata | ||
| and sequences to split the sequences into L and S segments. | ||
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| REQUIRED INPUTS: | ||
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| metadata = data/subset_metadata.tsv | ||
| all_metadata = results/all/metadata.tsv | ||
| sequences = results/all/sequences.fasta | ||
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| OUTPUTS: | ||
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| metadata = results/{segment}/metadata.tsv | ||
| sequences = results/{segment}/sequences.fasta | ||
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| See Nextclade docs for more details on usage, inputs, and outputs if you would | ||
| like to customize the rules: | ||
| https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli.html | ||
| """ | ||
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| rule run_nextclade_to_identify_segment: | ||
| input: | ||
| metadata = "data/subset_metadata.tsv", | ||
| sequences = "results/all/sequences.fasta", | ||
| segment_reference = config["nextclade"]["segment_reference"], | ||
| output: | ||
| sequences = "results/{segment}/sequences.fasta", | ||
| params: | ||
| min_seed_cover = config["nextclade"]["min_seed_cover"], | ||
| shell: | ||
| """ | ||
| nextclade run \ | ||
|
There was a problem hiding this comment. I'm curious what the decision process was around There was a problem hiding this comment. Good question! At least in dengue, 
I admit I haven't done the same comparison for lassa data, mostly just wanted one that worked and didn't seem noticeably slow. |
||
| --input-ref {input.segment_reference} \ | ||
| --output-fasta {output.sequences} \ | ||
| --min-seed-cover {params.min_seed_cover} \ | ||
| --silent \ | ||
| {input.sequences} | ||
| """ | ||
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| rule subset_metadata_by_segment: | ||
| input: | ||
| metadata = "results/all/metadata.tsv", | ||
| sequences = "results/{segment}/sequences.fasta", | ||
| output: | ||
| metadata = "results/{segment}/metadata.tsv", | ||
| params: | ||
| strain_id_field = config["curate"]["output_id_field"], | ||
| shell: | ||
| """ | ||
| augur filter \ | ||
| --sequences {input.sequences} \ | ||
| --metadata {input.metadata} \ | ||
| --metadata-id-columns {params.strain_id_field} \ | ||
| --output-metadata {output.metadata} | ||
| """ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| >KM822127_REF | ||
| caccaaccccagcagagagcccccacaacacagccaagcccacccagcccccagaaccgc | ||
| ccacatcagcaggcatgggcaacaagcagaccaggtccccacccaaaccagagcacccca | ||
| gaccaaccctgctacccgacgcatcccacctgggcccccaattctgcaagagctgctggt | ||
| ttgagaacaagggactggtggagtgtaataaccattacctctgtctaaactgtctcacac | ||
| tgcttctcagcgtgagcgacagatgtcctatttgtaagatgcccctccccaccaagctgg | ||
| cagtccgaacccaaccaagtgcacccccactcaaccagggcaacactcaatcctccccgc | ||
| ccccctacagcccctaactctcccaagacgggcccgcaccccacacccaggaacccaacc | ||
| aaacacacacacacagacaaacacatagaaagacacacacacacgcacacacacccacag | ||
| tccccacccgcacccccggggggaccccccgccgggggcccccccggggggctcagaggc | ||
| tggcatcactcaatgtcctctacctgcaccagtgtgtcgaacaatttaatgcacgtcctt | ||
| cccttcaatctcagctttccactgcttgactggatcatcacttcttttagtgacttacta | ||
| taacacagtgagtagcccttgaaatccacccagtcaccaactgcttcaagaagccgaaca | ||
| agaattggtctttgcaattctaacacagtcttcttcaacacagaaacaatgtcgacatcc | ||
| acccagtgcttcttgagcttcaatctgtcagaaaacattgagatcagtgcctctatcaaa | ||
| agatcttgggaaccatccctaacctcccttatgaacaactccaagtcttgatcgtgaatt | ||
| gctggggtaaaagtagcaagtctgctgtcacattcccaaagggctcctctactgatcact | ||
| aatggtacaggttcaatttcaggccccaccagtgtgaaatcatactgtgaaaactgcagc | ||
| ttcctcagatcaacaactatctcaatgggggttacaggccctaattctttagtgtcctct | ||
| aggaactcattaatgacctcagtatcgacaaaccatgcagatttccccttgaaaacagat | ||
| ccagacagcacaagcctccagcagtcaggcagcacacattggttgactgatccggaaaac | ||
| atggcttcaacattatcaactaaatacttaccctgatgatttattgagccaatgaaatta | ||
| agatgaatagaaaaattttctttaaaacttgcgtcttggcttctgatttggaatcttatt | ||
| gtctggctgaatctcactgaaccaactggtagttcactgattccatctaagaagtcttca | ||
| agacatttaaatttgacatcagttaacccacacatgatcaactgactgtaattgagtttt | ||
| gctggttctaaatcataatcaatccatgcataacccatcatcaaatcatatttgaacata | ||
| ggtctttctatacctttgtataccaccttctcaacaaaagaggaaaaggggccaagtctc | ||
| tgcaaaccttcaccctctgggatagaggttttatgagggaaccatgtaaatgatccaagc | ||
| gttctagttgttgcaacaaacgatctgatgtacgactcaaaataaatctgtctcataaaa | ||
| ttatcaacaacgtcactcgagctgacaaccctttcttctatcatgggttcatgtgtcctg | ||
| gtgtgtgacaatctcagctcagatgaaagcactatgtagtgttcctctctcttccacttc | ||
| actatgtgcgagacaagagatagtgcctcgcaattcacatctagtgcaacacaaagatct | ||
| agaaatttaattctaggtgaccacttcattttagtcgaggccaaatcactcatgaagggc | ||
| aacaaatgtttctcaaacagactggggtacagtctccttaatgagtgtattatatggttc | ||
| atgccaactctatcttctagcaatttagaagcagtaggttttaagggaaagtagtcacat | ||
| gggttatgtttgaaaaactccagctgtcctgctggcttagggttccctagaacccatgcc | ||
| cccaactctatcgctgttgataatgaaatgcacatataatcccataacaaagatctgaaa | ||
| taagataggacactcttcccttcagactcttctcttaccctcattgggaccctccaaatc | ||
| tggactccaaggtcgttagttaaacactcaacgccctgaattgccaggacctcagattgc | ||
| agtgatttgatgtataggttttccttgttagaccccctcacacacttgctgccaagtgtt | ||
| ctgcataatcctacaaagcctgaagcgattgaactttggaaagcagatttatttatggcc | ||
| tcagatagcagtttctgagctcctctagtgaatgtagaagacaatttattctgaatggtt | ||
| ttcactattgttggtattctctcatcatctaaactcactgccccagcataaatcaccttc | ||
| tgtctcagcaccattcttaatgggtgatgtgtagccagattcaaccaacaaatttctaga | ||
| tcagagtcatccaacatctcagtacccattaactcgcataaattccttaatgaagaaaca | ||
| tgttcacctgacagataattggtggtaaattcctcatgcaactcacctgtctttaatttg | ||
| ttaaacaactttcttagcattgatcttaccttactacaagcctctggggccaactcttca | ||
| atcagtctcatgatcctgtaactacggttgccgtcaacccaatccctaacatctgtgttg | ||
| caattgagtaagaatgggtcaatggggtacctcgcatacttcagcaagttcaaagttctc | ||
| ttctgaataagattacataggctaactggaacaccgttagcaatggactgatcaattatg | ||
| gtgtcaattgtctctgctaactggtgtggttctttacacttaacattatgtagcgcagca | ||
| gccacaaacttcgtcaagaggggaacctcatcaccccagacataaaatcttgatttaaat | ||
| tctgctacaaatcttccaatcacacttttcgggctgacaaacttatttaactgatcactc | ||
| atatagtaatgaaattctaacagggttttaaactcatcttggtctctagacattaactct | ||
| gtcaggttctggtcaaaaagagaaatttggtcatcactagaagtgtaagcatcaacttgc | ||
| cctccacaaacacaactcacagcatagtttataaatctctccgaaatgagtccataaaag | ||
| tctgaagtgttgtgcagaataccttgccccatgtcaaggatggaacttatatgagatggc | ||
| acaacacccaaatgaaagtttgagtaaaagaaatcttctgttagtgtctgagatgtactc | ||
| tttctcaacccaagttgtgcctttatataagatttcatcattgctgacactacattaaag | ||
| ggaatttctaccatcttgtgcatgtgccatgccaatagtgttgagagataatcctttcct | ||
| ttggcatcagcctgagtgtccccagtgagtagaattaagttctgtagggttgcaaggaat | ||
| aggaatgggcacatcataggaccccatttgctgtggtccatgctgtaggatacatgtgct | ||
| tgtgagacatttaatttcattgacaaaattgcattctcaaactctctttcatcatttaaa | ||
| caacttcccgagaattgcgtcgtcaatgcttcaaaataatcctctatcaatcttgtgaac | ||
| attttggtcctaaggtctccaatataaagttctctattacctccaacctgctctttgtat | ||
| gacagcgagaattttagtctccctgtatcaggaccaactgagttgaatgattgtggagat | ||
| tcctggctataaaaacacagatttttcaacatggcagttgtgcaatttgttagtgagagt | ||
| gctttactaagtgcttcggagttgctctctctttcacttattctagtgtcggttgacagt | ||
| ttgtctgtgtcaaatttgaaattgagacacttcgacttatagtgggtatacctccccatc | ||
| aacctgttgccattcatcaacaagagaattgatttgaaacacaggaaatattcctgatct | ||
| gaataagtcctggttacaactgcttttgttagttcaccaatagggcaagacaccatgggt | ||
| ccacaataaaagtacttctgcttaaactcttggtggtgatacactatgtcacagaactct | ||
| ttataaaaagtgtcagggagtgtgttataatcaaagtcctccaccatgtggtttgagagt | ||
| tcccctttaatcaatctgatgtacagtttttccttaacaatctcatttaaatcgtcaatt | ||
| gaacaaatctccccggttgttgagcgctggtccggtcctttcagatctctatactgatcc | ||
| acaattttttctatagtttcttttaactcatcaaaatatgacatcgcattcccttcaagc | ||
| aatatctcatccaggtcggccctgtctgtttctacatctttcccttgagaccccaaaacc | ||
| aaattgctcatagcctgctggactttgtactcatagtcttgcttatctaataaatactta | ||
| cctttccttgaaaaaacctcggtcaattgtgtaactgctaaggctgttagcttgttgaaa | ||
| tcataatttaagaccctacatccatctgtgtacttattaatcacaacactcttattgctt | ||
| gccagatctaaagcagtcgcacagccactggttgacagagggtcttttaattctttcctc | ||
| acttcttttcctttaaagagtgaaccattgttaaaagaagatgtaagcaaggacaagtac | ||
| ttcttggagacaccaggtttcttgtaccttatttcagctgattccacacagcattcctta | ||
| cctaagaactttttagcgttgtacaccatttcactcaactcatccgactctgcatgatcc | ||
| agaggattgacgctaacatgcccaaactctagttttggttctaagaatttctcaaagcac | ||
| ttgatctgatctgttagtctatcaggggtttccttagtgataaaatgacacatgtaagaa | ||
| atgttcaaaacaaatttgaacctgtttgttagcatactagtcacattaggagataaaaca | ||
| gtgcttaacagggctcttaccactctgaaaagcaagtactcaacatctgtaatcagcttc | ||
| tctttgatcttgttgattaagtctttgtgataataatcagagacaaaggccattatgaag | ||
| tatctaagattttgcaaaaacttctgacatcgcttactagggtgggtcaagattaaaacc | ||
| aaaatcattttggttagcactttaattgaggatatatcatccttaagctcagaacaatct | ||
| tcaatccagctgaccatgacttctaccacctttgtcagaacttcactggaaaagattgcg | ||
| gggaaaaacctcttgggatccgcataaaaggaacagacttcaccaactaagttgttgttt | ||
| accgcataacattttgaacactcgcccgttttttgataaagtaagctatattccactcca | ||
| tctatgaagaactgttgacagtatgcttctttgcatcttaccttctggtatcttgctgct | ||
| ccaagctcattttgcctcaacttaacagtggaggaagtcttcattgaattcaccaatgca | ||
| agactcaatgttgagagcctttcaagatcagctgactctgaaacgctcactgtgcccatt | ||
| gagtagggaaacagtccttcgtcagacttttgataagacattgttggcacaacacctgat | ||
| gcctcacagttcataactttactaaatacatgcccatccagaattgttagatcaacccca | ||
| taggtgtccacatttacatttaggtctttgagggcacttattgctttggtaacagttttc | ||
| tgcaacatgcaactcaagatttgatttctatctaatctaacggagtgagtgcttgatgct | ||
| gattttgaacattcagattgcaatcttctatcaacccaccttttcaggtccctcttagtg | ||
| tattctaaagacaccaagcggtcattcacactgataaaactggatcctaaccagccttcc | ||
| tgagcttgatcttcacatttaatcttgtccctctcataagcaaggagaatcattacatca | ||
| aaaatcaatagaagtttccttcttgtgttcaaaattctcaaagatttgactttgttgagg | ||
| aatgacctccaacaatgcatctgactgctgtttgtgggtgatgatctatcaaccccattg | ||
| gttaaatctgcatacaagaatttcaacacaggagaggctcttttaaaggaatacatcaat | ||
| tcttccactccatcttcattagaaaccatttcagaatcatacaagcagtgaaattctttt | ||
| aacagtctttctttgtcaactttaacaaattgatcttctatttggccctgccttaacttg | ||
| tttctgaatatctgatactcctcctcaatctgattcttaacctcatgggcagtcattttg | ||
| ttgttgatgccttgatggcagctggcaattatatcatcaaaatggttggttcgtttatct | ||
| aataacacattgatgctttctatacctgaaaaccggctagtgctgactgaaagagattcg | ||
| cataatctagagtactcagactcttcaaagagtgaattgctctcctgagcatatttcatc | ||
| aaggagaatagtgtatctctgagtttgtcattcacccagtccggaatttgttcattataa | ||
| aatgtagttcttccgtcaataagtggtattaggtttatatcaattgacttcaagtcattc | ||
| tttagttgctctaacttctttaagtcctctaggtacttctgctcaaagttcactggggat | ||
| gatctcacaaagcactcaaggagtatgaggacattcccattcaatttgaagccatcaggc | ||
| acaacaaagcataatgatggtgttaaaatccctaattcatggagaattacctcaacagag | ||
| cgtgcattgctgttgtgctcacaaccattggccttgcaggaatcaacctctatacataag | ||
| gataaaagttttagtccttccatcaacaacatcctcggctcagtctgcaccaagaatgcc | ||
| aatttttgtctagataatctctcatcatcagaaagatattttgaaacaagatcttttaca | ||
| taagctatctcctcctccattaaagaagttgtcaacaatagagcgtctaaatgcctagga | ||
| tcctcggtgcgc |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| >GU481068_REF | ||
| atttaggattgcgcttcaaagagacctttgtgtgactgagctttatcaaaccatgggaca | ||
| aatagtaacattctttcaggaagttcctcatgtcatagaagaggtaatgaatattgtcct | ||
| aattgctcttagtctcctggcgatactgaaggggatttacaatgttgccacttgtggcct | ||
| ttttgggctgatctcctttcttcttctgtgtggaagatcatgctcaacaacctacaaagg | ||
| tgtctatgagctacaaactctggagttggacatggcaaacctcaacatgactatgcctct | ||
| atcttgtacaaaaaacagcagccatcactatatcatggttgggaatgaaacaggcctaga | ||
| actgaccttgacaaacacaagtataatcaatcacaagttctgcaacctttctgatgcaca | ||
| caagaagaatctttatgatcatgccttgatgagcatcatttcaactttccacttatccat | ||
| tccaaatttcaatcagtatgaagcaatgagttgtgactttaatggagggaaaataagtgt | ||
| gcaatacaatctcagtcatgcttatgctgtagatgcagccaaccactgtgggaccattgc | ||
| caacggtgtcctacagactttcatgagaatggcttggggcggcagttacatagcacttga | ||
| ttctggaaaagggaactgggattgcataatgacttcctatcagtacttgattatccaaaa | ||
| caccacctgggaagatcactgtcagttttcccgcccgtcccctattggatacctaggact | ||
| gttatcacaaaggactagagatatttacattagtcggagacttcttggaactttcacctg | ||
| gaccctctctgactctgagggcaatgaggcacccggtggatactgccttactagatggat | ||
| gctaattgaagctgaattgaagtgctttgggaacacagccattgcgaagtgtaatgagaa | ||
| gcacgatgaggaattctgtgacatgttgagacttttcgacttcaacaaacaagccataaa | ||
| aaggctaaaagcagaagcacagatgagcatccaattgataaataaagcagtaaatgcact | ||
| aatcaatgaccaattgatcatgaagaaccacttgagggatatcatggggattccctattg | ||
| caattacagcaagtactggtatctgaaccatactgtgacagggaaaacatcattgccaag | ||
| gtgttggcttatttcaaatggttcttacctaaatgagacacatttctccgatgatattga | ||
| acagcaagcagataacatgataacagaactgctgcaaaaggagtatatggacaggcaggg | ||
| gaaaacacccttagggttagtggatctttttgttttcagcactagcttttatctcataag | ||
| tatcttcctccacttagtcaaaatcccgacccataggcacattgtagggagaccttgccc | ||
| caagccacacagactcaaccacatgggcatatgctcatgtggtttgtacaaacatcctgg | ||
| tgtaccagtcaagtggaagagatagaaatagacccattaacgggcccccgtgacccaccg | ||
| ccgaaaggcggtgggtcacgggggcgtccatttacaggacgactttgggacttgaagttc | ||
| tgaacaccatatctcttgggagaacagctctcaagattggtatattgagtcctcctgaca | ||
| cagctgcgtcaaacattatgcaatccattaaagcacaatgtggagtgatctcctctttgc | ||
| ctcctctcttctttttctcaacaaccactccagtgtgcatgtgacacaaatctttacact | ||
| gatcccagacagcattttcaaatctcctagaatcagccttatttaatgagatgtcaatga | ||
| gcttgatgtcccttctcccctgagaatccaagagttttttaatgtcgtctgaaccttggc | ||
| acgtcaacaccatgttgcgggggagagcctcaatgactgcactggttagaccaggctgag | ||
| cagaaaagagatctgtcacatcaatcccatgagaatatttggcatcttgtttgaactgtt | ||
| ttaaatccgttggttctctgaagaaatgtatataacagcctgacataggttggtaaagag | ||
| ctatctcaacagggtcttctggacgaccttcaatgtctatccaggttttggcgcttgggt | ||
| caagttgcatcattgaatctttgagtgtcatcagttgagaataggtcagccctgttggga | ||
| acccagcagattgcagagatttgttggatccagcagtacccactttctgtggtttcccat | ||
| ctgactcaaggtctacagtggtattctcccaagctctacccacaatggaggttcttgaag | ||
| ctatgtagggccagccgtccccagagagacaaattttgtaaagtatgttttcataagggt | ||
| ttctttcaccaggtgtgtctgaaacaaacattcccagggacctttttacctttagaatag | ||
| acttcagaatgccatccattgtctgaggcgtcaccttgatagtttccaacatgttacccc | ||
| catcgagcatgcaagctccggccttcactgcagctcccaaactaaaattataaccagaaa | ||
| tatttagggagctcttcttggtatctaccatattcagtataggatggctctgggaaagtc | ||
| tgtctaggtcggaactattggggtatttagctgtgtatattaatcccaagtctgttagcg | ||
| ccagaacggcgtcatttaagtcaacctgaccctgtttagtgagacatgctagcgttaaac | ||
| taggcatggtgccaaattggttgttgaggaggtccgggtttttgacatcccacactctga | ||
| caactccgtctcttccaggttgggttccctgagcaccaccgaccatgcctatcatactca | ||
| acaacgccttcctctgctcaagttgttgtgtgctcaagttccccatatacacacctgaac | ||
| ttaatggtctctccgtcctaataacctttgacttcaatttctctagatcagctgctaaag | ||
| tcagcaagtcgtctgaggtcaatgttccaaccctcagaacactcttttgttgtgttgact | ||
| tgagctcgacaaggttgttaactgcctgatttaggtctctaagacgttttaggtcaccgt | ||
| catctcttttctgtttgcgcatcaagcgctggacattgctgacctcagagaagtcgagac | ||
| catgcagaagggcctgagcatccttgaccacttggagttttatattagagcaatagcctg | ||
| aaagctctctcctcaatgactgtgtccaaaggaatgatttcacttccttggaagcactca | ||
| tcctggttgatgttgatcggaactcactggttgaaagtgttatccagtaaatcaacagta | ||
| gtaggcgcaatctaaaa |
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[using this line just to organise discussion into a thread]
The 2018 Nextstrain Lassa builds have the majority of the strains matched up. Was this using a subset of the data? Or were we perhaps not considering strain name duplications and so the matching may be incorrect?
Matching samples across segments is a key part of segmented analyses. Absolutely fine to not be part of this PR, and perhaps is something we can never generalise, but is something we should certainly keep revisiting.
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Good question. I have no idea how the underlying data for those builds were processed. The early README implies the data came from fauna, but I don't see any lassa table in fauna...
For sure, feel free to add thoughts on segment analysis to nextstrain/pathogen-repo-guide#59.