I was looking at this script from https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc297 and wanted to use it to determine outliers for tentative Horizontal gene transfer.
The data set is provided in the example, under the section 20.2.2 Plot of sequence GC%.
I want to yield a identifier for the x axis instead of just an arbitrary number of genes or cds' so I can actually determine which sequences have the outlying values, as I can not with the current graph.
I am not great at python or understanding list comprehensions, so if anyone could augment the code provided in the example to do so, it would be appreciated.
I provided the code below also.
#from : https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc297, data set under #section 20.2.2 Plot of sequence GC%, ls_orchid.fasta from Bio import SeqIO from Bio.SeqUtils import GC gc_values = sorted(GC(rec.seq) for rec in SeqIO.parse("ls_orchid.fasta", "fasta")) import pylab pylab.plot(gc_values) pylab.title("%i orchid sequences\nGC%% %0.1f to %0.1f" \ % (len(gc_values),min(gc_values),max(gc_values))) pylab.xlabel("Genes") pylab.ylabel("GC%") pylab.show()