To extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013
extract_fasta_seq is a tool to extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013/extract_fasta_seq
pip install extract_fasta_seq
There will be a command
extract_fasta_seq created under the same directory as your
$ extract_fasta_seq usage: extract_fasta_seq.py [-h] [-q <str> [<str> ...]] [-f <query file>] [-s [<subject file>]] [-s1 <pattern>] [-s2 <pattern>] [-d1 [<int>]] [-d2 [<int>]] [-o [<outfile>]] [-v] [-V] [--lazy] [--version] To extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013 optional arguments: -h, --help show this help message and exit -q <str> [<str> ...] query list. "-s1" and "-d1" have no effect on this option. -f <query file> query list file, one line should contain only one queryid! (but can be mixed with others, and we can use "-s1" and "-d1" option to extract the queryid) -s [<subject file>] subject file [stdin] -s1 <pattern> query file sep_pattern [\s+] -s2 <pattern> subject file sep_pattern [\s+] -d1 [<int>] which field in the query_file is to used?  -d2 [<int>] which field in the subject_file is to used? useful for finding out all sequences in the subject_file whose seqids equal to the queryids  -o [<outfile>] outfile [stdout] -v invert the output [False] -V verbose output --lazy Stop searching once each required seqid has at least one sequence found, which can be problems if some required seqids have more than sequences! Works only for non-invert mode. [False] --version show program's version number and exit
Currently I have no plan to publish
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