TO DO list
Created by: rlapar
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indices fix -
offset out of sequence -
rewrite sketcher:
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nl -> segmented nl
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to_fasta
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to_gff
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to_png
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to_pdf
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include different output types to cli
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offset na output elementy (+- nukleotidy vlavo vpravo) -
2 fasta subory pre kazdy element (s vystrihnutymi vnoreniami aj bez nich) -
expand ltr's for gff -
prepisat help -
spatne domeny -
pridat target site duplication z LTR finderu do hodnotenia + gff + sketch -
dokumentovat -
logs and results directory for each run /YYYYmmdd_HHmmss -
config do /usr/local/share -
add logs - global logging module -
nested config as a cli parameter -
modify generator to find LTR's and domains for given element -
remove tmp fasta entry after done processing -
complete text output about an element -
delete gt import and call gt sketch externally only -
sketch ltr's, pbs, ppt -
if not cropped, do not add sequence to tmp.fa -
process genes one by one -
improve scoring:
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repetitive scoring (external file to compare with BLAST)
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score LTR by itself
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interal part of TE by itself
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include score from LTR_finder
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crop threshold based on score -
create external file to look at repetitivity -
process input file in batches -
check for LTR "sharp" ends -
option to write sequence to GFF -
verbose flag for complete GFF3 -
compare script to TEnest, RepeatMasker and others -
clear code (reengineer to OOP) -
install package -
documentation -
from gff - create python script to crop fasta (https://daler.github.io/pybedtools/)