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View Code? Open in Web Editor NEWThis script can be used for searching a sequence in a fasta-format file.
This script can be used for searching a sequence in a fasta-format file.
usage: SeqFindPy [-h] -f FASTA [-k MATCHKEY] [-g GFF | -b BED] [-o OPTFILE] [-l LOCATION] [-n NCNUMBER] [-m {bedtools,selftools}] [-ep EXPRESSION_P] [-en EXPRESSION_N] To get the location and anotation of a sequence. First-writtern@20190716 by ZhenLi. optional arguments: -h, --help show this help message and exit -f FASTA, --fasta FASTA The genome sequence,fasta format. -k MATCHKEY, --matchkey MATCHKEY type in the key pattern. -g GFF, --gff GFF The anotation file,gff3 format. -b BED, --bed BED The anotation file,bed format. -o OPTFILE, --optfile OPTFILE The filename of output result. -l LOCATION, --location LOCATION The start and end of the sequence you wanna find. Example:205-225 -n NCNUMBER, --ncnumber NCNUMBER The sequence id. -m {bedtools,selftools}, --method {bedtools,selftools} choice the method of intersecting method. -ep EXPRESSION_P, --expression_p EXPRESSION_P The reqular expression applying on positive strand. Example:'ATCGAA{2,3}A' -en EXPRESSION_N, --expression_n EXPRESSION_N The reqular expression applying on negative strand. Example:'ATCGAA{2,3}A'
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