Pull metadata from EBI's ENA database for given accession numbers and save resistance status with the metadata.
Usage: resistome.py
####add
add data to database. Input files should take the format:
aac_1_AJ628983 aminoglycoside
aac_3_I_1_AJ877225 aminoglycoside
aac_3_Ia_1_X15852 aminoglycoside
i.e.
gene_name_ACCNO123 resistance
Options:
-f|file input file
-d|database name of database to add data to
The update function will collect metadata from ENA based on the acc# and add it to the database
Example:
resistome.py add -f database.file.txt -d resistome1
####update add additional information to entries. Input should take the format:
ACCNO123 This is my note for accession ACCNO123
ACCNO456 Here is another note
Options:
-f|file input file
-t|type type of info (Notes, Sequence, etc)
-d|database name of database
Example:
resistome.py update -f note_list.txt -t Notes -d resistome1
####query query information from the database. Input may be a search term or a file of search terms (one per line). Searches on accession number as default.
Options:
-q|query search term
-f|file file of search terms
-t|type specify a different search field.
-d|database name of database
-o|query-output output file name
Example:
resistome.py query -q ACCNO123 -d resistome1
resistome.py query -f file_of_accessions.txt -d resistome1
resistome.py query -q aminoglycoside -t Resistance -d resistome1
Note: for queries (or types) with more than one word, use "". Example:
resistome.py query -q "genomic DNA" -t "Molecule Type" -d resistome1
####save save data to a CSV file.
Options:
-f|file CSV output file
-d|database name of database
Example:
resistome.py save -f output_db.csv -d resistome1
####avail list available databases
Example:
resistome.py avail
####help Show this help menu