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Zhenlisme/SeqFindpy
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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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This script can be used for searching a sequence in a fasta-format file.
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