postoga v.0.4.0-devel

splited main functions in ordered modules following TogaDir class layout (filter_bed will be improved in v.0.5.0-devel)
improved logging (specifies some stats about annotation or filtered annotation [if user choose to filter it]) + connect() method to call it within a module (bed2gtf/bed2gff log info bothers the structure of postoga log -> will be fixed in v.0.5.0-devel)
included transcripts.quality.tsv in query_table() and calculates some stats about it (included in logging)
re-implemented TOGA_assemblyStats.py to estimate annotation completeness in single mode and haplotype-resolved assemblies -> --assembly_qual (to specify genes db -> tab-separated file [.txt,.tsv,.csv,...]; default ancestral); --haplotype_path (to specify path of both haplotypes) -> the equivalent of TOGA_assemblyStats.py -m stats && TOGA_assemblyStats.py -m stats -ances ./ances.txt is completed, TOGA_assemblyStats.py -m merge will be available in v.0.5.0-devel.
postoga now automates: 1) dependencies [v.0.5.0-devel], 2) filtering, 3) conversion, 4) assembly quality estimation (just 1/4 quality steps postoga will have)
shell is now utils.py (postoga base utility module)
added https://github.com/hillerlab/TOGA/blob/master/TOGAInput/human_hg38/Ancestral_placental.txt to ./supply/Ancestral_placental.txt

postoga v.0.5.0-devel

postoga fully works now on two modes postoga base & postoga haplotype
base/haplo branches initiate own logs (haplo branch chooses the first path of the list provided)
fixed filter_bed() module -> handles different filter combinations (--by_class, --by_rel, --threshold)
removed unnecessary imports in all modules
TOGA_assemblyStats.py -m merge is now fully functional in postoga under postoga haplotypes -hpath path1,path2,path3 --source [query, loss] --rule I>PI>UL>L>M>PM>PG>abs.
logger.py is automatically updated with the current version
postoga now automates installing requirements (python/rust) through ./configure sh
implemented test.sh to make an initial test with random data in ./supply/test

Fixed unnecessary imports and comments in all modules.
Added plotter.py, the plotter module of postoga.
postoga now reports findings automatically and save them under POSTOGA_REPORT.pdf
Modules have been updated to synchronize with plotter module.
Added plotter-dependent project-wide constants
Implemented get_stats_from_bed under filter_query_annotation, to quickly extract query stats

Now postoga evaluates all the non-overlapping exon lenghts of your annotation and outputs additional stats about it
Instead of implementing a way to perform BUSCO completeness from scratch, postoga uses a set of curated DBs to evaluate your assembly completeness
Introducing --source. Now you can choose which gene nomeclature background postoga should use: ensmebl IDs, gene names or Entrez IDs.
Introducing --phylo. Now you can choose the phylo group of your species to be use a set of BUSCO DBs. See arguments.
Some changes from the last PR where rolled back. This version of postoga is up to date with TOGA's output dir structure.
The quality of transcript is no longer considered in this release. postoga now uses orthology prediction scores as an implicit source for quality.

Adds --paralog, a new argument to preserve transcripts with paralog projections probabilities less or equal to a given threshold.
Implements --skip to only use postoga as a filtering tool, skipping additional post-processing steps.
Adds bed as an option to --to to avoid the conversion to gtf/gff.
Modifies logger.py to send logging information to stdout (this is also written to postoga.log)