biopython v1.71.0 Bio.Restriction.Restriction.Analysis
Provide methods for enhanced analysis and pretty printing.
Link to this section Summary
Functions
Initialize an Analysis with RestrictionBatch and sequence
Set boundaries to correct values
Filter result for keys which are in wanted
Test if site is between start and end
Test if site is between end and start (for circular sequences)
Return only results from enzymes that cut at least within borders
Return only cuts that have blunt ends
Change parameters of print output
Return only results from enzymes that produce defined overhangs
Return only results from enzymes that don’t cut between borders
Collect data and pass to PrintFormat
Perform analysis with all enzymes of batch and return all results
Return only results from enzymes that only cut within start, end
Return only results from enzymes that only cut outside start, end
Return only results from enzymes that at least cut outside borders
Return only cuts that have 3’ overhangs
Return only cuts that have 5’ overhangs
Print the output of the analysis
Return only results from within start, end
Return only results from enzymes that cut the sequence N times
Return only results from enzymes which names are listed
Return only results from enzymes that cut (x,y,z,…) times
Return only results form enzymes with a given site size
Return only results from enzyme with at least one cut
Return only results from enzymes that don’t cut the sequence
Link to this section Functions
Initialize an Analysis with RestrictionBatch and sequence.
Analysis([restrictionbatch [, sequence] linear=True]) -> New Analysis class.
For most of the methods of this class if a dictionary is given it will be used as the base to calculate the results. If no dictionary is given a new analysis using the RestrictionBatch which has been given when the Analysis class has been instantiated, will be carried out and used.
Set boundaries to correct values.
Format the boundaries for use with the methods that limit the search to only part of the sequence given to analyse.
Filter result for keys which are in wanted.
A._sub_set(other_set) -> dict.
Internal use only.
Screen the results through wanted set. Keep only the results for which the enzymes is in wanted set.
Test if site is between start and end.
Internal use only
Test if site is between end and start (for circular sequences).
Internal use only.
Return only results from enzymes that cut at least within borders.
Enzymes that cut the sequence at least in between start and end. They may cut outside as well.
Return only cuts that have blunt ends.
Change parameters of print output.
A.change(**attribute_name) -> Change attribute of Analysis.
It is possible to change the width of the shell by setting self.ConsoleWidth to what you want. self.NameWidth refer to the maximal length of the enzyme name.
Changing one of these parameters here might not give the results you expect. In which case, you can settle back to a 80 columns shell or try to change self.Cmodulo and self.PrefWidth in PrintFormat until you get it right.
Return only results from enzymes that produce defined overhangs.
Return only results from enzymes that don’t cut between borders.
Collect data and pass to PrintFormat.
A.format_output([dct[, title[, s1]]]) -> dct.
If dct is not given the full dictionary is used.
Perform analysis with all enzymes of batch and return all results.
A.full() -> dict.
Full Restriction Map of the sequence.
Return only results from enzymes that only cut within start, end.
Return only results from enzymes that only cut outside start, end.
Enzymes that cut the sequence outside of the region in between start and end but do not cut inside.
Return only results from enzymes that at least cut outside borders.
Enzymes that cut outside the region in between start and end. They may cut inside as well.
Return only cuts that have 3’ overhangs.
Return only cuts that have 5’ overhangs.
Print the output of the analysis.
A.printthat([dct[, title[, s1[,print]]]]) -> print the results from dct.
If dct is not given the full dictionary is used. s1: Title for non-cutting enzymes This method prints the output of A.format_output() and it is here for backwards compatibility.
Return only results from within start, end.
Enzymes must cut inside start/end and may also cut outside. However, only the cutting positions within start/end will be returned.
Return only results from enzymes that cut the sequence N times.
Return only results from enzymes which names are listed.
Return only results from enzymes that cut (x,y,z,…) times.
Return only results form enzymes with a given site size.
Return only results from enzyme with at least one cut.
Return only results from enzymes that don’t cut the sequence.