class AddThree(IrisCommand):
title = "add three numbers {x} {y} {z}"
examples = ["add three"]
argument_types = {"x":t.Int("first int"),"y":t.Int("second int"),"z":t.Int("third int")}
def command(self, x, y, z):
return x + y + z
def explanation(self, result):
return result
class Equals(IrisCommand):
title = "{x} equals {y}"
examples = ["eq {x} {y}", "equal {x} {y}"]
argument_types = {
"x": t.Int("What is the first number?"),
"y": t.Int("What is the second number?")
}
def command(self, x, y):
return x == y
def explanation(self, result):
return result
class GotermEnrichment(IrisCommand):
title = "compute GO term enrichment on {gene_list}"
examples = [ "compute GO term enrichment on a list of gene symbols" , "describe the function of a list of genes"]
help_text = [
"Gene Ontology (GO) Consortium contains functional and structure annotations for genes. Given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented using annotations for a list of genes. \nCurrenlty, Iris takes in Gene Symbols (e.g. CTSK) and corrects p-values with FDR"
]
argument_types = {
"gene_list": t.List("What is the list of gene symbols (e.g. CTSK) you want to analyze?"),
"n_top": t.Int("How many top results you want to see?")
}
argument_help = {
"gene_list": "A list of gene symbols of interest",
"n_top": "Number of the top enrichment GO terms you want to see",
}
def command(self, gene_list, n_top):
from gprofiler import GProfiler
import numpy as np
gp = GProfiler("")
r0 = gp.gprofile(gene_list,correction_method=GProfiler.THR_FDR,ordered=True)
r0 = np.array(r0)
r0 = r0[r0[:,9]=='MF']
name_out = r0[0:n_top,-3]
p_out = r0[0:n_top,2]
data = np.array([x for x in zip(name_out, p_out)])
dataframe = pd.DataFrame(data=data, columns=["Name", "p-values"])
return dataframe
def explanation(self, results):
iris_df = iris_objects.IrisDataframe(data=results)
return [ "These are the enriched molecular function GO terms with corrected p-values", iris_df]
class Identity(IrisCommand):
title = "identity function {x}"
examples = []
argument_types = {"x":t.Int("What value?")}
def command(self, x):
return x
def explanation(self, result):
return result
class AddTwo(IrisCommand):
title = "add two to {x}"
examples = []
argument_types = {"x": t.Int("Add two?")}
def command(self, x):
return x + 2
def explanation(self, result):
return result
class GenerateArray(IrisCommand):
title = "generate a random array of {n} numbers"
examples = ["generate numpy array of size {n}"]
argument_types = {"n": t.Int("Please enter size of array:")}
def command(self, n):
import numpy
return numpy.random.randint(100, size=n)
def explanation(self, result):
return ["Here are the numbers", result]
class Take_A_Break(IrisCommand):
title = "take {x} second break"
examples = [
"pause for {x} seconds", "rest for {x} seconds",
"wait for {x} seconds", "nap for {x} seconds"
]
argument_types = {
"x": t.Int("How long of a break you want to take (in second)?")
}
def command(self, x):
#pause for x second
import time
time.sleep(x)
return str(x)
def explanation(self, result):
return 'Iris just took {} seconds nap'.format(result)