Reputation: 105
Loops are Hard [Python]
Not a programmer by vocation, please excuse if this is obvious. I cannot loop :/ ...
I have 3 lists:
gene_concepts[0] = ['+0|+77|CFTR', '+12|+77|CYP2C19']
genes = ['CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR',
'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CYP2C19', 'CYP2C19',
'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19']
haplotypes = ['CFTR F508del(CTT)', 'CFTR F508del(TCT)', 'CFTR G1244E',
'CFTR G1349D', 'CFTR G178R', 'CFTR G551D', 'CFTR G551S', 'CFTR S1251N',
'CFTR S1255P', 'CFTR S549N', 'CFTR S549R(A>C)', 'CFTR S549R(T>G)',
'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19
*10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10']
Note that the haplotypes and genes match (i.e., the first term of the string in the haplotype list is "CFTR", and matches the first element of the list in genes list...so these are ordered)
I want to build a new list or just output a set of strings, such that the haplotypes that have the same gene (so the genes may match each other, or the substring of the first part of the haplotype string, whichever) are assigned a particular code, which is found in the gene_concepts list, and corresponds to the first term before the "|" delimiter in the list of strings.
Output desired is:
+21|+0|CFTR F508del(CTT)
+22|+0|CFTR F508del(TCT)
+23|+0|CFTR G1244E
+24|+0|CFTR G1349D
+25|+0|CFTR G178R
+26|+0|CFTR G551D
+27|+0|CFTR G551S
+28|+0|CFTR S1251N
+29|+0|CFTR S1255P
+30|+0|CFTR S549N
+31|+0|CFTR S549R(A>C)
+32|+0|CFTR S549R(T>G)
+33|+12|CYP2C19 *10
+34|+12|CYP2C19 *10
+35|+12|CYP2C19 *10
+36|+12|CYP2C19 *10
+37|+12|CYP2C19 *10
+38|+12|CYP2C19 *10
+39|+12|CYP2C19 *10
+40|+12|CYP2C19 *10
So the first part of the text above is "+21...+39 is the temp_code_2"...this is just an arbitrary id I've assigned it to keep track. The part between the delimiters is the code I'm trying to assign the matching genes. The last part after the 2nd delimiter is the haplotype.
Here's my code so far...
def generate_haplotype_concepts(gene_concepts[0], haplotypes):
temp_code_2 = 20
index = 0
for batch_line in gene_concepts[0]:
gene_parent_code = batch_line.split("|")[0]
gene_parent_medcodes.append(gene_parent_code)
index_gene = 0
index_parent_code = 0
for gene in genes:
if (index_gene == 0):
print("+" + str(temp_code_2) + "|"
+ gene_parent_medcodes[index_parent_code] + "|"
+ haplotypes[index_gene])
index_gene += 1
elif (genes[index_gene] == genes[index_gene-1]):
print("+" + str(temp_code_2) + "|"
+ gene_parent_medcodes[index_parent_code] + "|"
+ haplotypes[index_gene-1])
else:
index_parent_code += 1
print("+" + str(temp_code_2) + "|"
+ gene_parent_medcodes[index_parent_code] + "|"
+ haplotypes[index_gene])
index_gene += 1
temp_code_2 += 1
generate_haplotype_concepts(gene_concepts[0], haplotypes)
My output is this:
+21|+0|CFTR F508del(CTT)
+22|+0|CFTR F508del(TCT)
+23|+0|CFTR G1244E
+24|+0|CFTR G1349D
+25|+0|CFTR G178R
+26|+0|CFTR G551D
+27|+0|CFTR G551S
+28|+0|CFTR S1251N
+29|+0|CFTR S1255P
+30|+0|CFTR S549N
+31|+0|CFTR S549R(A>C)
+32|+12|CYP2C19 *10
+33|+12|CYP2C19 *10
+34|+12|CYP2C19 *10
+35|+12|CYP2C19 *10
+36|+12|CYP2C19 *10
+37|+12|CYP2C19 *10
+38|+12|CYP2C19 *10
+39|+12|CYP2C19 *10
2 problems I see...I'm missing the last CFTR haplotype (+32|+0|CFTR S549R(T>G) should be there instead) and I'm getting a "list index out of range" error.
-----------------------------------------------------------------------
----
IndexError Traceback (most recent call
last)
<ipython-input-16-1410b2513457> in <module>()
55
56
---> 57 generate_haplotype_concepts(gene_concepts[0], haplotypes)
<ipython-input-16-1410b2513457> in
generate_haplotype_concepts(temp_code_2, haplotypes)
30 # + "\n" )
31 index_gene += 1
---> 32 elif (genes[index_gene] == genes[index_gene-1]):
33 print("+" + str(temp_code_2) + "|"
34 + gene_parent_medcodes[index_parent_code] +
"|"
IndexError: list index out of range
Apologies for any typos I've made...I've tried posting simpler code than what I'm actually doing but the issue is the same...any help is appreciated!
Upvotes: 4
Views: 207
Answers (4)
Reputation: 8561
I think you want something like this:
gene_concepts = {} # just initializes an empty dictionary to fill on the next line
gene_concepts[0] = ['+0|+77|CFTR', '+12|+77|CYP2C19']
# we don't actually end up using the genes list, since we can get the same info from the first part of each haplotype
genes = ['CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR',
'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CYP2C19', 'CYP2C19',
'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19']
haplotypes = ['CFTR F508del(CTT)', 'CFTR F508del(TCT)', 'CFTR G1244E',
'CFTR G1349D', 'CFTR G178R', 'CFTR G551D', 'CFTR G551S', 'CFTR S1251N',
'CFTR S1255P', 'CFTR S549N', 'CFTR S549R(A>C)', 'CFTR S549R(T>G)',
'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10',
'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10']
# split the gene_concepts strings into usable pieces
gene_concept_codes = {} # create a dictionary for looking up gene_concepts by gene name
for gene_concept in gene_concepts[0]:
pieces = gene_concept.split('|') # this turns a string like "+0|+77|CFTR" into a list like ["+0", "+77", "CFTR"]
gene_concept_codes[pieces[2]] = pieces # add the list to the dictionary, with the gene name as key
temp_id = 20 # arbitrary to match your values, change it however you need
# for each haplotype, match it up with the right gene_concept info
for haplotype in haplotypes:
temp_id += 1
gene = haplotype.split()[0] # pull out the name of the gene
print("+{}|{}|{}".format(temp_id, gene_concept_codes[gene][0], haplotype)) # gene_concept_codes[gene] will be the list like ["+0", "+77", "CFTR"], so [0] gives us the first element of that list
That gives the desired output:
+21|+0|CFTR F508del(CTT)
+22|+0|CFTR F508del(TCT)
+23|+0|CFTR G1244E
+24|+0|CFTR G1349D
+25|+0|CFTR G178R
+26|+0|CFTR G551D
+27|+0|CFTR G551S
+28|+0|CFTR S1251N
+29|+0|CFTR S1255P
+30|+0|CFTR S549N
+31|+0|CFTR S549R(A>C)
+32|+0|CFTR S549R(T>G)
+33|+12|CYP2C19 *10
+34|+12|CYP2C19 *10
+35|+12|CYP2C19 *10
+36|+12|CYP2C19 *10
+37|+12|CYP2C19 *10
+38|+12|CYP2C19 *10
+39|+12|CYP2C19 *10
+40|+12|CYP2C19 *10
Upvotes: 1
Reputation: 15310
I'm not sure if you have control over it, but your gene_concepts should be a dictionary. If you convert (as I do below), then the matching operation becomes a straightforward lookup:
gene_concepts = [None]
gene_concepts[0] = ['+0|+77|CFTR', '+12|+77|CYP2C19']
genes = ['CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR',
'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CFTR', 'CYP2C19', 'CYP2C19',
'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19', 'CYP2C19']
haplotypes = ['CFTR F508del(CTT)', 'CFTR F508del(TCT)', 'CFTR G1244E',
'CFTR G1349D', 'CFTR G178R', 'CFTR G551D', 'CFTR G551S', 'CFTR S1251N',
'CFTR S1255P', 'CFTR S549N', 'CFTR S549R(A>C)', 'CFTR S549R(T>G)',
'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10',
'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10']
def generate_haplotype_concepts(gene_concepts, genes, haplotypes):
"""Match gene id's in (genes+haplotypes) with genes in concepts list."""
# Convert concepts into dictionary:
gc = { t3[2]:t3[0] for t3 in map(lambda s: s.split('|'), gene_concepts)}
# Look up gene/haplotype prefix in gc dictionary for concept
for gene, hap in zip(genes, haplotypes):
concept = gc.get(gene)
if concept is None:
hprefix = hap.split()[0]
concept = gc.get(hprefix)
if concept is None:
raise ValueError("Missing gene/prefix: {}/{} in hap {}".format(
gene, hprefix, hap))
yield concept, hap
print("##### Concept|Haplotype, no ID #####")
for concept, haplotype in generate_haplotype_concepts(gene_concepts[0], genes, haplotypes):
print("{}|{}".format(concept, haplotype))
print("\n\n##### ID|Concept|Haplotype #####")
for iden, (cept, hapl) in enumerate(generate_haplotype_concepts(gene_concepts[0], genes, haplotypes), start=21):
print("+{}|{}|{}".format(iden, cept, hapl))
Upvotes: 1
Reputation: 61289
The following may be helpful (note the importance of checking for unexpected conditions):
haplotypes = ['CFTR F508del(CTT)', 'CFTR F508del(TCT)', 'CFTR G1244E', 'CFTR G1349D', 'CFTR G178R', 'CFTR G551D', 'CFTR G551S', 'CFTR S1251N', 'CFTR S1255P', 'CFTR S549N', 'CFTR S549R(A>C)', 'CFTR S549R(T>G)', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10', 'CYP2C19 *10']
gene_concepts = {'CFTR':0, 'CYP2C19':12} #Dictionaries are useful
for x in haplotypes:
prefix = x.split()[0] #Get prefix by splitting on spaces and looking at substring before first space
if prefix in gene_concepts: #Do we recognize this gene concept?
print("{0}|{1}".format(gene_concepts[prefix],x))
else: #If not, inform the user
print('Gene with unknown concept: "{0}"'.format(x))
Gives output:
0|CFTR F508del(CTT)
0|CFTR F508del(TCT)
0|CFTR G1244E
0|CFTR G1349D
0|CFTR G178R
0|CFTR G551D
0|CFTR G551S
0|CFTR S1251N
0|CFTR S1255P
0|CFTR S549N
0|CFTR S549R(A>C)
0|CFTR S549R(T>G)
12|CYP2C19 *10
12|CYP2C19 *10
12|CYP2C19 *10
12|CYP2C19 *10
12|CYP2C19 *10
12|CYP2C19 *10
12|CYP2C19 *10
12|CYP2C19 *10
Which may not be exactly what you are looking for but is, I think, closer. By changing the values in the dictionary you should be able to achieve what you want.
Upvotes: 2
Reputation: 26570
To help you along with the main problem you seem to be facing in your loop, we should look at what you are looping over. Instead of looping over the genes, loop over your haplotypes instead, and then in each iteration take the part of interest and compare with the list of genes. The following example will help illustrate this.
for haplotype in haplotypes:
if haplotype.split()[0] in genes:
print(haplotype)
So, what is happening here, is for each haplotype, we are going to be dealing with a string. We see that based on the example data you provided, that we can split this string on spaces so we can only look at the first part of this split. What split does in Python, is actually take a string and convert it to a list based on some "separator". In this case a space. Then, the [0] part will simply take the first index of this list, which is the exact portion we are interested in.
From here, you will see we are using the in keyword. This will simply lookup against genes to see if the string of interest is in that genes list. Now you have your condition set for each haplotype you are interested in. From there, I believe you can just prefix that code as something like:
for haplotype in haplotypes:
if haplotype.split()[0] in genes:
print("your code {}".format(haplotype))
Upvotes: 0