Improve similarity search

[bebatut]

• Add alignment class
• Improve similarity search (to fix #5)
  • Add possibility to have several alignment for a CDS
  • Change the approach to identify the correct sequence for a PYL CDS
    • Extract the CDS (current and possible alternative sequence) with the lowest evalue
    • Reset if the lowest evalue is too high and could be due to random alignment
    • Extract the CDS (current and possible alternative sequence) with the highest bitscore
• Extract 5 alignments per sequence
• Update documentation

[codecov[bot]]

Codecov Report

Merging #17 into master will decrease coverage by 0.13%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #17      +/-   ##
==========================================
- Coverage   99.75%   99.61%   -0.14%     
==========================================
  Files           5        6       +1     
  Lines         414      526     +112     
==========================================
+ Hits          413      524     +111     
- Misses          1        2       +1

Impacted Files	Coverage Δ
pylprotpredictor/alignment.py	100% <100%> (ø)
pylprotpredictor/check.py	100% <100%> (ø)	:arrow_up:
pylprotpredictor/cds.py	99.37% <100%> (-0.27%)	:arrow_down:

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