Rnajena-sugar

* core: deprecate filter methods, use select instead

* core:
- add tolists, topandas and frompandas methods to FeaturList
- add tobiopython and frombiopython methods to BioSeq and BioBasket classes to convert to or convert from biopython objects
- add tobiotite and frombiotite methods to BioSeq and BioBasket classes to convert to or convert from biotite objects
- remove the toobj and fromobj methods from BioSeq and BioBasket classes instead
- add BioBasket.merge method to merge sequences of the same id into a single sequence
- add BioBasket.plot_alignment method
- add BioSeq.slindex method
- add update_fts option to translate
- switch default value of inplace option to False for filter methods
* io:
- writers: allow to pass None as fname, in this case a string will be returned
- add GTF IO support for features
- add TSV/CSV IO support for features
- add SJSON IO support for features (custom lossless file format), add private option to write private metadata
- add the possibility to read GFF files for old format versions
- allow to write compressed files just by specifying the filename extension
- add a sugar header comment for some writers (stockholm, gff, gtf)
- glob expressions in file names are now evaluated in sorted order
- remove the tool option for reading and writing, use the new to/from methods instead
* scripts:
- rename convert and convertf commands to cat and catf, respectively, also accept multiple files as input
- add merge command to merge sequence files
* index: rename get method to get_basket, add get_seq method
* add imaging module with plot_alignment function
* substantially improve the documentation

* core:
- add sort, filter and groupby methods to FeatureList and BioBasket
- BioSeq.match: rename orf option to rf, allow tuple-like arguments
- consequently rename BioSeq.meta.features to BioSeq.meta.fts
- add BioBasket.fts attribute, add add_fts method for BioSeq and BioBasket
- move all str methods to BioSeq.str and BioBasket.str namespace
- new class LocationTuple used internally for Feature.locs
- introduce BioSeq.sl and BioBasket.sl methods and options for slices
(gap, inplace, update_fts)
- refactor Defect code
* cane:
- add sugar.core.cane module with seq and ft tools
- add ORF finding functions and methods
- add final_stop parameter in translate
* io:
- add option to store comments in most readers
- refactor and update read support for BLAST files (outfmt 6, 7 and 10)
- add read support for MMseqs2 files (fmtmode 0 and 4)
- add read support for Infernal tblout files
- stockholm: add support for multiline files
* more minor and major changes ;)

* io.fasta: robust parsing of seq ids from header line, ignore comment lines
* io.stockholm: add row2fts and fts2row functions to parse, write GC and similar lines

* translate: add check_start option

* io: add option to write files automatically into an archive
* io.gff: allow to store comment lines while reading
* scripts: add translate and feature commands