Finally! A release of ProtGraph, fixing some problems, having slight improvements and reducing the number of essential dependencies by introducing optional dependencies (mostly for exports).
**Changes**
* Refactoring of many functions, reducing duplicated code. (ProtGraph also seems more responsive, due to removing the delay in TQDM)
* Added more customization for the generated statistics file, you can now select which columns you are interested in!
* This refactoring also led to add multiple execution scripts into protgraph, there are now more cli-commands which can be used for automation
* New easy scripts to generate decoys as well as to replace (extract) header information from fasta files! There is now also a script available which allows to easily sum up columns in generated statistic files!
* Also added support to parse ProPeptide and Peptide FeatureTables (FT) from the SP-EMBL-Format
* Added support for simple PTMs in graphs by adding an additional Attribute `delta_mass`. Currently only the mass shift is supported on aminoacids and NOT on the terminis... (this most probably will be added in the next release!)
* New Exporter: Graphs can be now exported into a **C**ompressed **S**parse **R**ow-Representation (Protein-CSR --> PCSR, Binary-PCSR -> BPCSR)
* New Trie Exporter abusing the filesystem. A slower peptide exporter with an interesting concept!
* New (fast) exporter from graphs into peptides! Using SQLite (with an additionally added script) allows a quick generation of a Fasta-file even for complete UniProt!
* Added new option in peptide traversal, you can now filter by weight instead of only peptide length! (or filter by both)
The changlist got a bit lengthy, so was this release, which took almost 5 months!