python script to retrieve a sequence from a genome or tyranscriptome feasts file.
Usage: RetrieveGene.py -g [name of gene] -f [name og f genome or transcriptome] [options]
| -h, --help | show this help message and exit. |
|---|---|
| -g GENE, --gene=GENE | name of thetranscript, gene or fragment that needs to be retrieved. |
| -f GENOME_FASTA, --genome_fasta=GENOME_FASTA | path and name of genome or transcriptome fasta file, a file containing the the sequence that needs to be retrieved. |
| -o OUTPUT_FILE, --output_file=OUTPUT_FILE | Path and name of the output file the sequence needs to be writen to. If filename is not specified the sequence will be printen in the console. Default = NULL |
| -d DIRECTION, --direction=DIRECTION | This option offers the posibility to chose the orientation of the sequence. Forward for forward, and reverse or rv for reverse and complement of the desired sequence. Default = fw |
| -s START_POSITION, --start_position=START_POSITION | position of the first base of the sequence to beretrieved. If -1, the full transcript, gene, scaffold or chromosome will be retrieved. Default = -1 |
| -e END_POSITION, --end_position=END_POSITION | position of the last base of the sequence to be retrieved. If -1, the full transcript, gene, scaffold or chromosome will be retrieved. Default = -1 |