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Taxonomy.md

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To extract taxonomy information using Diamond blast report (when using IMG/VR db) and using IMGVR_all_Sequence_information.tsv file:

Note: It should be run in the root folder where the SOVAP pipeline is executed.

This is a shell script that loops over all directories (indicated by */) in the current directory, extracts information from a file called output.diamond.tsv, and joins it with information from a file called IMGVR_all_Sequence_information.tsv.

for folder in */; do \
    parent_dir=${folder%/}; \
    cut -f1,2 ${folder%}6_Diamond-Taxonomy/output.diamond.tsv | cut -d "|" -f1 | \
        paste <(cut -f2) <(cut -f1) | \
        sort -k1,1 | \
        join -t $'\t' -a1 - /path/to/IMGVR_all_Sequence_information.tsv > ${folder%}6_Diamond-Taxonomy/$parent_dir.taxo ; \
done

Details: The script loops through each subdirectory in the root folder and performs the following steps for each subdirectory:

  • Define the parent_dir variable as the subdirectory name without the trailing slash.
  • Extract the first and second columns from the output.diamond.tsv file using cut command and separate taxonomic information up to the first "|" character using cut again.
  • Merge the taxonomic information into a single column using the paste command.
  • Sort the merged column using sort command.
  • Use the join command to join the sorted merged column with IMGVR_all_Sequence_information.tsv file. The -t option specifies the tab as the delimiter, and the -a1 option tells join to print unpairable lines from the first file. The - character specifies to use standard input as the first file for join.
  • Write the output to a file named after the subdirectory and with the extension .taxo.
  • The resulting output files will contain taxonomic information for each sequence in the subdirectory's output.diamond.tsv file.

Due to the large size of IMGVR_all_Sequence_information.tsv file, this step is provided as an optional side script. However, it is recommended to perform this step for reproducing graphs in the manuscript and analyzing data in R for taxonomy, diversity indices, and etc.

IMGVR_all_Sequence_information.tsv: a table listing the characteristics of each viral sequence such as its origin, affiliation, and predicted host (tsv format).

More information: https://genome.jgi.doe.gov/portal/IMG_VR/IMG_VR.home.html