Adam Witney awitney
awitney
/ gist:7ac35d3fcdecbff5ffc254bd6e526475
Created
June 25, 2019 11:54
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| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_* refseq/Mycobacterium/ | |
| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycolicibacterium_* refseq/Mycolicibacterium/ | |
| mkdir fna | |
| find refseq/Mycobacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| find refseq/Mycolicibacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_rna_from_genomic.fna.gz |
awitney
/ gist:b30c2e7fb6f27c319ebbf9329f842a75
Created
April 23, 2019 12:16
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| Lineage report | |
| -------------- | |
| Lineage Estimated Fraction Family Spoligotype Rd | |
| lineage4 1.000 Euro-American LAM;T;S;X;H None | |
| lineage4.3 1.000 Euro-American (LAM) mainly-LAM None | |
| lineage4.3.4 1.000 Euro-American (LAM) LAM RD174 | |
| lineage4.3.4.2 1.000 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 |
awitney
/ gist:60b49d0a2cb8ab74d3376f955ee03721
Created
January 11, 2019 21:26
mycobacterium build kraken db
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| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_* refseq/Mycobacterium/ | |
| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycolicibacterium_* refseq/Mycolicibacterium/ | |
| mkdir fna | |
| find refseq/Mycobacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| find refseq/Mycolicibacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_rna_from_genomic.fna.gz |
awitney
/ gist:5a7f6ab2024888583ea8
Created
June 18, 2014 13:47
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| print("Testing") |
awitney
/ gist:3c1192a86a1b5f17dd46
Created
June 18, 2014 13:46
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| print("Testing") |
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| #!/usr/bin/env perl | |
| use strict; | |
| use warnings; | |
| use Bio::EnsEMBL::LookUp; | |
| use Bio::SeqIO; | |
| use Bio::Seq; | |
| my $string = $ARGV[0] || 'gyrA'; |