A collection of tools to merge, summarize and update genbank record annotations.
The genbankSummary.py file will return a list of features and qualifiers for each record in a genbank file.
usage: genbankSummary.py [-h] -g GENBANK [-i ID]
Summarize the contents of a genbank file or record
optional arguments:
-h, --help show this help message and exit
-g GENBANK, --genbank GENBANK
Genbank file to summarize
-i ID, --id ID Limit to only the record with this ID
required
For the path to the .gb file. This can either be a single record, or multiple genbank records concatenated together. The summary will be reported for each record independently if it is a multi-genbank file.
default = all
For the ID of a genbank record if you only want to report one record within a multi-genbank file.
This is just a count of feature types within the record.
Currently, the feature types are limited to only CDS, rRNA and tRNA types, but this can be edited in the script in the featureTypePrint list.
This is a count of all of the qualifier types within the features. Many features have overlapping qualifiers, for example, the same locus_tag is found the CDS, gene and misc_features feature types, and probably many more. In parentheses is the non-redundant count for these features within the record.
The qualifiers displayed is also limited to those within the qualifierTypePrint list, and can be modified to show other types if necessary. It currently only shows locus_tag, db_xref, translation, EC_number and product.
Since db_xref is the catch-all for different types of annotations, they are all listed out here. Each db_xref record has a TYPE:VALUE format, and these are summarized for total counts, as well as for unique values (two CDSs with the same TYPE:VALUE).
The mergeGenbank.py script takes a “secondary” genbank file, and merges its qualifiers into a “master” genbank file. It currently finds similar CDS features between the two genbank files solely on source length and feature position. This is because genbank files generated from some sources (such as RAST) often remove all CDS identifiers such as locus_tag or protein_id, and only location information is preserved.
usage: mergeGenbank.py [-h] -m MASTER -s SECONDARY [-f FOLDER]
Merge CDS qualifiers of a secondary (-s) Genbank file into a Master (-m)
optional arguments:
-h, --help show this help message and exit
-m MASTER, --master MASTER
Master genbank file
-s SECONDARY, --secondary SECONDARY
Genbank file to merge into master
-f FOLDER, --folder FOLDER
Output folder, defaults to mergedOutput + timestamp
required
The “master” genbank file. Nothing will be removed from this record, and it will act as a backbone for adding additional annotations.
required
The “secondary” genbank file. Qualifiers from this record will be moved to the “master”.
default = mergedOutput_timestamp
The output folder that the records will be saved to.
This script will save all records as their own .gbk file. To merge into a single concatenated record called merged.gbk,, from the command line type
cat *.gbk > merged.gbk`
The updateGenbankAnnotations.py script will take a tab-delimited file of annotations, and add or overwrite a genbank file.
usage: updateGenbankAnnotations.py [-h] -g GENBANK -a ANNOTATIONS [-m METHOD]
[-i IDENTIFIER] [-q QUALIFIER]
[-x DB_XREF_TYPE] [-f FOLDER]
Add or overwrite annotations in a genbank file
optional arguments:
-h, --help show this help message and exit
-g GENBANK, --genbank GENBANK
Genbank file to update
-a ANNOTATIONS, --annotations ANNOTATIONS
File with annotations (col1=identifier, col2=new
annotation)
-m METHOD, --method METHOD
'o'=overwite, 'a'=append/add
-i IDENTIFIER, --identifier IDENTIFIER
Type of annotation from column 1 of annotations file
(ex. 'locus_tag', 'GI') to look for in the genbank
file
-q QUALIFIER, --qualifier QUALIFIER
Qualifier to add new annotations to (ex. 'product',
'db_xref')
-x DB_XREF_TYPE, --db_xref_type DB_XREF_TYPE
If using -q db_xref this option will prepend
annotations with this variable, if your annotations
file is missing it (ex. 'GO', 'SEED')
-f FOLDER, --folder FOLDER
Output folder, defaults to updatedOutput + timestamp
required
The filepath of the genbank file.
required
The filepath to the annotations file. This should be a 2-column, tab-delimited file with the identifier in column 1, and the annotation in column 2.
default = a
The method for updating. If set to “o”, it will overwrite the qualifier in the genbank file. If set to “a”, it will add or append to the genbank file.
default = locus_tag
Due to their being different ways to map a feature in the genbank file with the feature in the annotations file, the script uses an identifier to map between the two files. For example, if your both your genbank and annotations file use locus_tag, then ‘locus_tag’ would be the identifier.
default = product
The qualifier that you want column 2 to be mapped to. For example, the default is product, so after identifying the correct genbank entry based on the identifier, the product will be updated with the annotation in column 2.
default = none
If -q is db_xref, this option can add an additional prefix to the beginning of the annotations. For example, suppose you had the following annotations file of locus_tag and GO terms:
Gal_00002 0003887
Gal_00007 0003918
Gal_00019 0003677
Use the flags -i locus_tag to match the locus_tags between records, -q db_xref to add the column 2 annotations to a db_xref qualifier, and -x GO to prefix annotations with GO: (no need to add the “:”). This will add the following lines to the appropriate locus tags in the genbank file:
/db_xref="GO:0003887”
/db_xref="GO:0003918”
/db_xref="GO:0003677”
This can also be used for custom annotation types, such as signalP, transporter, or anything else you may want to add.
default=updatedOutput_timestamp
This is the output folder that the new genbank files will be written to.
New genbank files, one for each record. See above for concatenation code.