Annotates genes based on sequence coverage, takes start position as input and gives annotated files (dna, protein, gff).
Introns are searched for by coverage differences and the GT...AG pattern.
With the less stringent option ("--gt") the G+...+T pattern is defining the intron.
Use option "-h" or "--help" to get further instructions.
anotomat.py
--genome <genome.fasta>
--pos <start_positions.txt> *exact format see below*
--cov <coverage> *file with '#chr bp coverage' from "samtools depth -a -Q 0 <file.bam>"*
--mincov <int> minimal coverage of the START pos for a reannotation*default=0*
--mincov_exon <int> minimal coverage for annotation of exon after intron*default=0*
--gt use less stringency in defining introns *G._.G defines intron*(default=GT_AG)
--cores <int> number of cores used *default=(cpu_count-1)*
--name <gene name> *default='genes' + <int>[0000-9999]*
--out <name for output files> *default='genes'*
EXAMPLE for start_positions.txt:
Bgt_chr-01 39472
Bgt_chr-01 47323 ~ #
Bgt_chr-01 49207 ~BgtAcSP-31373 #make a comment
Bgt_chr-01 85828 #only comment
Bgt_chr-01 284818 ~BgtE-20066 #tab separated???
Bgt_chr-01 300256 ~BgtE-20114 #special sign "~ "before gene-name!!!