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GenGraphToolkit functions
Jambler edited this page Jun 3, 2019
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Creates a fasta file for the isolate requested from the genome graph.
python ./gengraph.py extract_fasta_file --graph_file <graph.xml> --isolate <isolate required> --out_file_name <file name for fasta>
Extract a region of a sequence for an isolate (For example to return the sequence of a gene).
python ./gengraph.py extract_region --graph_file <graph.xml> --isolate <isolate required> --extract_sequence_range <start position> <stop position>
Generates a pan-transriptome in fasta format using the annotations provided in the sequence file. A .csv file is also created containing genes identified to be homologous.
python ./gengraph.py extract_pan_transcriptome --graph_file <graph.xml> --seq_file <sequence_input_file.txt> --out_file_name <prefix for output files>
Generates a hypothetical ancestral genome and adds the path to the genome graph. The ancestral genome can then be extracted as a fasta file.
python ./gengraph.py extract_ancesteral_genome --out_file_name <prefix for output files> --graph_file <graph.xml>