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GRAMMy Manual
Commandline Tools
- grammy_gdt -- to include reference sequences needed by grammy
- grammy_rdt -- to generate read data needed by grammy
- grammy_pre -- to parse the alignment results and get the probability matrix needed by grammy
- grammy_em -- to calculate the estimation(not normalized), the extra bootstrap estimations and the final log likelihood
- grammy_post -- to normalize the result and get the genome length and relative abundance estimates
grammy_gdt Input
- o_prefix --output prefix, o_prefix.gdt will be the output filename
- taxids --taxids to include, taxids: t1,t2,...,tm, each tid is a INTEGER and must be found in grefs/gid_tid.dmp
grammy_gdt Options
usage: grammy_gdt [-h] [-d DMP] [-r REF] [-p PER] o_prefix taxids optional arguments: -h, --help show this help message and exit -d DMP, --dmp DMP gid to tid dump file, default=grefs/gid_tid.dmp -r REF, --ref REF reference genome dir, default=grefs -p PER, --per PER number of genomes per file, default=20
grammy_gdt Output
- o_prefix.gdt --genome data file needed by grammy
- o_prefix.fna.1,...o_prefix.fna.n --including reference sequences needed by grammy
grammy_rdt Input
- i_prefix --itput dir prefix, a dir where reads files reside
- o_prefix --output dir prefix, the output will be o_prefix/xxx.rdt, use '.' for current dir
grammy_rdt Options
usage: grammy_rdt [-h] [-s SUF] [-t TEC] [-c CHG] i_prefix o_prefix optional arguments: -h, --help show this help message and exit -s SUF, --suf SUF read files suffix, default=fa.gz -t TEC, --tec TEC sequencing tech, default=sanger -c CHG, --chg CHG name change set 'o1:n1,o2:n2', default=
grammy_rdt Output
- o_prefix.rdt --the read data file need by grammy
- o_prefix.fasta.gz --the zipped reads fasta file
grammy_pre Input
- read_dat --will use read_dat.rdt as read data file
- gen_dat --will use gen_dat.gdt as genome data file
grammy_pre Options
usage: grammy_pre [-h] [-m {tbl,bam}] [-p PAR1] [-q PAR2] read_dat gen_dat optional arguments: -h, --help show this help message and exit -m {tbl,bam}, --mtd {tbl,bam} method for read assignment, tbl -- tabular blast format -p PAR1, --par1 PAR1 first parameter for read assignment method, tbl filename or k -q PAR2, --par2 PAR2 second parameter for read assignment method, al,id,ev or bg
grammy_pre Output
- read_dat.mtx --the probability matrix file needed by grammy
grammy_em Input
- read_prob_file --input read probability matrix file from grammy-pre
grammy_gdt Options
usage: grammy_em [-h] [-b BTP] [-t TOL] [-c {U,L}] [-n MIT] [-i {M,R}] read_prob_file optional arguments: -h, --help show this help message and exit -b BTP, --btp BTP bootstrap number, default=10 -t TOL, --tol TOL tolerance for stopping, default=10e-6 -c {U,L}, --mtd {U,L} convergenece method, (U)niform, (L)ikelihood, default=U -n MIT, --mit MIT maximum number of iteration, default=1000 -i {M,R}, --ini {M,R} initilization method, (M)oment, (R)andom, default=M
grammy_em Output
- read_prob_file.est --where the estimation is, not normalized
- read_prob_file.btp --where the extra bootstrap estimations are
- read_prob_file.lld --where final log likelihood is
grammy_post Input
- mix_par --untransformed mixing parameter estimates, from grammy-em
- gen_dat --gen_dat.gdt genome data file, from grammy-gdt
- btp --bootstrap file, from grammy-em
grammy_post Options
usage: grammy_post [-h] mix_par gen_dat btp optional arguments: -h, --help show this help message if exit
grammy_post Output
- read_prob_file.avl --average genome length estimates"
- read_prob_file.gra --genome relative abundance, first line is taxon id, second line is relative abundance, last line is error bound"
Have fun!
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