/scripts/taxonomy/processTaxonomy.sh

https://bitbucket.org/cistrome/cistrome-harvard/ · Shell · 18 lines · 18 code · 0 blank · 0 comment · 0 complexity · b8a83454ffaeb5202ebf5cd19d5e8fbd MD5 · raw file 

    

  1. echo "Getting files from NCBI..."
    2. 

  2. wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
    3. 

  3. wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
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  4. wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz
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  5. echo "Unzipping untarring..."
    6. 

  6. gunzip -c taxdump.tar.gz | tar xvf -
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  7. gunzip gi_taxid_nucl.dmp.gz
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  8. gunzip gi_taxid_prot.dmp.gz
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  9. cat gi_taxid_nucl.dmp gi_taxid_prot.dmp > gi_taxid_all.dmp
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  10. echo "Sorting gi2tax files..."
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  11. sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt
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  12. rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp
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  13. echo "Removing parenthesis from names.dmp"
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  14. cat names.dmp | sed s/[\(\)\'\"]/_/g > names.temporary
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  15. mv names.dmp names.dmp.orig
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  16. mv names.temporary names.dmp
    17.