extract metadata from genomic gbff files - metadata

Question

I have >1000 .gbff.gz genomic files and I want to extract metadata from each and have metadata entries in separate columns.

Answer 1

In Matlab you can make use of genbankread of the Bioinformatics Toolbox. Here is an example of how to achieve what you want:
results = [];
% unzip data
gunzip('*.gbff.gz');
% process each file
files = dir('*.gbff');
for file = {files.name}
data = genbankread(char(file));
% process each file entry
for i = 1:size(data, 2)
LocusName = '';
Definition = '';
Organism = '';
GenesTotal = NaN;
GenesCoding = NaN;
RRNAs = '';
TRNAs = NaN;
IsolationSource = '';
Country = '';
% copy fields
if isfield(data(i), 'LocusName')
LocusName = data(i).LocusName;
end
if isfield(data(i), 'Definition')
Definition = data(i).Definition;
end
if isfield(data(i), 'Source')
Organism = data(i).Source;
end
% parse comments
if isfield(data(i), 'Comment')
for j = 1:size(data(i).Comment, 1)
tokens = regexp(data(i).Comment(j, :), ...
'^\s*([^\s].*[^\s])\s*::\s*([^\s].*[^\s])\s*$', 'tokens');
if ~isempty(tokens)
switch tokens{1}{1}
case 'Genes (total)'
GenesTotal = str2double(tokens{1}{2});
case 'Genes (coding)'
GenesCoding = str2double(tokens{1}{2});
case 'rRNAs'
RRNAs = tokens{1}{2};
case 'tRNAs'
TRNAs = str2double(tokens{1}{2});
end
end
end
end
% parse features
if isfield(data(i), 'Features')
Feature = '';
for j = 1:size(data(i).Features, 1)
tokens = regexp(data(i).Features(j, :), '^(\w+)', 'tokens');
if isempty(tokens)
tokens = regexp(data(i).Features(j, :), ...
'^\s+/(\w+)="([^"]+)"', 'tokens');
if ~isempty(tokens)
switch Feature
case 'source'
switch tokens{1}{1}
case 'isolation_source'
IsolationSource = tokens{1}{2};
case 'country'
Country = tokens{1}{2};
end
end
end
else
Feature = tokens{1}{1};
end
end
end
% append entries to results
results = [results; struct( ...
'File', char(file), 'LocusName', LocusName, 'Definition', Definition, ...
'Organism', Organism, 'GenesTotal', GenesTotal, ...
'GenesCoding', GenesCoding, 'RRNAs', RRNAs, 'TRNAs', TRNAs, ...
'IsolationSource', IsolationSource, 'Country', Country)];
end
end
% data is in variable results