Personal python package for bioinformatics.
python3 -m pi
6E41
p install git+https://github.com/ymat2/bithon
bithon --help ## show helpSee detail: 日本語版, English ver.
usage: bithon gls [-h] [-i INDIR] [-o OUTDIR] [-p PREFIX] [--keep_identity] [--header {original,gene}] [--report REPORT]
options:
-h, --help show this help message and exit
-i INDIR, --indir INDIR
PATH to directory that contains `cds_from_genomic.fna` and `protein.faa`.
-o OUTDIR, --outdir OUTDIR
PATH to output directory.
-p PREFIX, --prefix PREFIX
default=longest: Prefix of files. `longest.cds.fa` and `longest.pep.fa` will be generated by default.
--keep_identity Whether keep only seqs that has no mismatches between Protein and translated CDS.
--header {original,gene}
'original' or 'gene'. Type of fasta header. Original sequence ID will be used by default (`original`).
Gene_symbol+species_name will be used when `gene`.
--report REPORT Path to report file (.tsv). Ungenerated by default.bithon ensgls -i infile -o outfile --header str-i/--infile: input fasta file name-o/--outfile: output fasta file name--header: one of "transcript", "id", or "symbol". Chosen one is written as header of fasta.
Help function to use prank
bithon prank -i file_path -o file_name --prank_exe prank_path-i/--infile: Fasta file to align-o/--outfile: Path and file name. file_name.best.fas are genarated.--prank_exe: Path forprankexecutable file. Defaut isprank.