What is the easiest/simplest way to iterate through a large CSV file in Python 2.7, comparing 3 columns?
I am a total beginner and have only completed a few online courses, I have managed to use CSV reader to do some basic stats on the CSV file, but nothing comparing groups within each other.
The data is roughly set up as follows:
Group sub-group processed
1 a y
1 a y
1 a y
1 b
1 b
1 b
1 c y
1 c y
1 c
2 d y
2 d y
2 d y
2 e y
2 e
2 e
2 f y
2 f y
2 f y
3 g
3 g
3 g
3 h y
3 h
3 h
Everything belongs to a group, but within each group are sub-groups of 3 rows (replicates). As we are working through samples, we will adding to the processed column, but we don't always do the full complement, so sometimes there will only be 1 or 2 processed out of the potential 3.
I'm trying to work towards a statistic showing % completeness of each group, with a sub group being "complete" if it has at least 1 row processed (doesn't have to have all 3).
I've managed to get halfway there, by using the following:
for row in reader:
all_groups[group] = all_groups.get(group,0)+1
if not processed == "":
processed_groups[group] = processed_groups.get(group,0)+1
result = {}
for family in (processed_groups.viewkeys() | all_groups.keys()):
if group in processed_groups: result.setdefault(group, []).append(processed_groups[group])
if group in processed_groups: result.setdefault(group, []).append(all_groups[group])
for group,v1 in result.items():
todo = float(v1[0])
done = float(v1[1])
progress = round((100 / done * todo),2)
print group,"--", progress,"%"
The problem with the above code is it doesn't take into account the fact that some sub-groups may not be totally processed. As a result, the statistic will never read as 100% unless the processed column is always complete.
What I get:
Group 1 -- 55.56%
Group 2 -- 77.78%
Group 3 -- 16.67%
What I want:
Group 1 -- 66.67%%
Group 2 -- 100%
Group 3 -- 50%
How would you make it so that it just looks to see if the first row for each sub column is complete, and just use that, before continuing on to the next sub group?
One way to do this is with a couple of defaultdict of sets. The first keeps track of all of the subgroups seen, the second keeps track of those subgroups that have been processed. Using a set simplifies the code somewhat, as does using a defaultdict when compared to using a standard dictionary (although it's still possible).
import csv
from collections import defaultdict
subgroups = defaultdict(set)
processed_subgroups = defaultdict(set)
with open('data.csv') as csvfile:
for group, subgroup, processed in csv.reader(csvfile):
subgroups[group].add(subgroup)
if processed == 'y':
processed_subgroups[group].add(subgroup)
for group in sorted(processed_subgroups):
print("Group {} -- {:.2f}%".format(group, (len(processed_subgroups[group]) / float(len(subgroups[group])) * 100)))
Output
Group 1 -- 66.67%
Group 2 -- 100.00%
Group 3 -- 50.00%
Related
I have the following code which reads a csv file and then analyzes it. One patient has more than one illness and I need to find how many times an illness is seen on all patients. But the query given here
raw_data[(raw_data['Finding Labels'].str.contains(ctr)) & (raw_data['Patient ID'] == i)].size
is so slow that it takes more than 15 mins. Is there a way to make the query faster?
raw_data = pd.read_csv(r'C:\Users\omer.kurular\Desktop\Data_Entry_2017.csv')
data = ["Cardiomegaly", "Emphysema", "Effusion", "No Finding", "Hernia", "Infiltration", "Mass", "Nodule", "Atelectasis", "Pneumothorax", "Pleural_Thickening", "Pneumonia", "Fibrosis", "Edema", "Consolidation"]
illnesses = pd.DataFrame({"Finding_Label":[],
"Count_of_Patientes_Having":[],
"Count_of_Times_Being_Shown_In_An_Image":[]})
ids = raw_data["Patient ID"].drop_duplicates()
index = 0
for ctr in data[:1]:
illnesses.at[index, "Finding_Label"] = ctr
illnesses.at[index, "Count_of_Times_Being_Shown_In_An_Image"] = raw_data[raw_data["Finding Labels"].str.contains(ctr)].size / 12
for i in ids:
illnesses.at[index, "Count_of_Patientes_Having"] = raw_data[(raw_data['Finding Labels'].str.contains(ctr)) & (raw_data['Patient ID'] == i)].size
index = index + 1
Part of dataframes:
Raw_data
Finding Labels - Patient ID
IllnessA|IllnessB - 1
Illness A - 2
From what I read I understand that ctr stands for the name of a disease.
When you are doing this query:
raw_data[(raw_data['Finding Labels'].str.contains(ctr)) & (raw_data['Patient ID'] == i)].size
You are not only filtering the rows which have the disease, but also which have a specific patient id. If you have a lot of patients, you will need to do this query a lot of times. A simpler way to do it would be to not filter on the patient id and then take the count of all the rows which have the disease.
This would be:
raw_data[raw_data['Finding Labels'].str.contains(ctr)].size
And in this case since you want the number of rows, len is what you are looking for instead of size (size will be the number of cells in the dataframe).
Finally another source of error in your current code was the fact that you were not keeping the count for every patient id. You needed to increment illnesses.at[index, "Count_of_Patientes_Having"] not set it to a new value each time.
The code would be something like (for the last few lines), assuming you want to keep the disease name and the index separate:
for index, ctr in enumerate(data[:1]):
illnesses.at[index, "Finding_Label"] = ctr
illnesses.at[index, "Count_of_Times_Being_Shown_In_An_Image"] = len(raw_data[raw_data["Finding Labels"].str.contains(ctr)]) / 12
illnesses.at[index, "Count_of_Patientes_Having"] = len(raw_data[raw_data['Finding Labels'].str.contains(ctr)])
I took the liberty of using enumerate for a more pythonic way of handling indexes. I also don't really know what "Count_of_Times_Being_Shown_In_An_Image" is, but I assumed you had had the same confusion between size and len.
Likely the reason your code is slow is that you are growing a data frame row-by-row inside a loop which can involve multiple in-memory copying. Usually this is reminiscent of general purpose Python and not Pandas programming which ideally handles data in blockwise, vectorized processing.
Consider a cross join of your data (assuming a reasonable data size) to the list of illnesses to line up Finding Labels to each illness in same row to be filtered if longer string contains shorter item. Then, run a couple of groupby() to return the count and distinct count by patient.
# CROSS JOIN LIST WITH MAIN DATA FRAME (ALL ROWS MATCHED)
raw_data = (raw_data.assign(key=1)
.merge(pd.DataFrame({'ills':ills, 'key':1}), on='key')
.drop(columns=['key'])
)
# SUBSET BY ILLNESS CONTAINED IN LONGER STRING
raw_data = raw_data[raw_data.apply(lambda x: x['ills'] in x['Finding Labels'], axis=1)]
# CALCULATE GROUP BY count AND distinct count
def count_distinct(grp):
return (grp.groupby('Patient ID').size()).size
illnesses = pd.DataFrame({'Count_of_Times_Being_Shown_In_An_Image': raw_data.groupby('ills').size(),
'Count_of_Patients_Having': raw_data.groupby('ills').apply(count_distinct)})
To demonstrate, consider below with random, seeded input data and output.
Input Data (attempting to mirror original data)
import numpy as np
import pandas as pd
alpha = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789'
data_tools = ['sas', 'stata', 'spss', 'python', 'r', 'julia']
ills = ["Cardiomegaly", "Emphysema", "Effusion", "No Finding", "Hernia",
"Infiltration", "Mass", "Nodule", "Atelectasis", "Pneumothorax",
"Pleural_Thickening", "Pneumonia", "Fibrosis", "Edema", "Consolidation"]
np.random.seed(542019)
raw_data = pd.DataFrame({'Patient ID': np.random.choice(data_tools, 25),
'Finding Labels': np.core.defchararray.add(
np.core.defchararray.add(np.array([''.join(np.random.choice(list(alpha), 3)) for _ in range(25)]),
np.random.choice(ills, 25).astype('str')),
np.array([''.join(np.random.choice(list(alpha), 3)) for _ in range(25)]))
})
print(raw_data.head(10))
# Patient ID Finding Labels
# 0 r xPNPneumothoraxXYm
# 1 python ScSInfiltration9Ud
# 2 stata tJhInfiltrationJtG
# 3 r thLPneumoniaWdr
# 4 stata thYAtelectasis6iW
# 5 sas 2WLPneumonia1if
# 6 julia OPEConsolidationKq0
# 7 sas UFFCardiomegaly7wZ
# 8 stata 9NQHerniaMl4
# 9 python NB8HerniapWK
Output (after running above process)
print(illnesses)
# Count_of_Times_Being_Shown_In_An_Image Count_of_Patients_Having
# ills
# Atelectasis 3 1
# Cardiomegaly 2 1
# Consolidation 1 1
# Effusion 1 1
# Emphysema 1 1
# Fibrosis 2 2
# Hernia 4 3
# Infiltration 2 2
# Mass 1 1
# Nodule 2 2
# Pleural_Thickening 1 1
# Pneumonia 3 3
# Pneumothorax 2 2
I have a data frame with 384 rows (and an additional dummy one in the bigining).
each row has 4 variable I wrote manually. 3 calculated fields based on those 4 variables.
and 3 that are comparing each calculated variable to the row before. each field can have 1 of two values (basically True/False).
Final goal - I want to arrange the data frame in a way that the 64 possible combination of the 6 calculated fields (2^6), occur 6 times (2^6*6=384).
Each iteration does a frequency table (pivot) and if one of the fields differ from 6 it breaks and randomize the order.
The problem that there are 384!-12*6! possible combinations and my computer is running the following script for over 4 days without a solution.
import pandas as pd
from numpy import random
# a function that calculates if a row is congruent or in-congruent
def set_cong(df):
if df["left"] > df["right"] and df["left_size"] > df["right_size"] or df["left"] < df["right"] and df["left_size"] < df["right_size"]:
return "Cong"
else:
return "InC"
# open file and calculate the basic fields
DF = pd.read_csv("generator.csv")
DF["distance"] = abs(DF.right-DF.left)
DF["CR"] = DF.left > DF.right
DF["Cong"] = DF.apply(set_cong, axis=1)
again = 1
# main loop to try and find optimal order
while again == 1:
# make a copy of the DF to not have to load it each iteration
df = DF.copy()
again = 0
df["rand"] = [[random.randint(low=1, high=100000)] for i in range(df.shape[0])]
# as 3 of the fields are calculated based on the previous row the first one is a dummy and when sorted needs to stay first
df.rand.loc[0] = 0
Sorted = df.sort_values(['rand'])
Sorted["Cong_n1"] = Sorted.Cong.eq(Sorted.Cong.shift())
Sorted["Side_n1"] = Sorted.CR.eq(Sorted.CR.shift())
Sorted["Dist_n1"] = Sorted.distance.eq(Sorted.distance.shift())
# here the dummy is deleted
Sorted = Sorted.drop(0, axis=0)
grouped = Sorted.groupby(['distance', 'CR', 'Cong', 'Cong_n1', 'Dist_n1', "Side_n1"])
for name, group in grouped:
if group.shape[0] != 6:
again = 1
break
Sorted.to_csv("Edos.csv", sep="\t",index=False)
print ("bye")
the data frame looks like this:
left right size_left size_right distance cong CR distance_n1 cong_n1 side_n1
1 6 22 44 5 T F dummy dummy dummy
5 4 44 22 1 T T F T F
2 3 44 22 1 F F T F F
I am trying to calculate the difference between records by group and also include row number by group. This could be done using lag and row number functions in HIVE using windowing functions. Trying to recreate this using PIG and python UDFs.
In the following example, I need the row number to restart from 1 for each name and increment for a new month (new record). Also, I need the difference in balance from prior month for each name.
input data
name month balance
A 1 10
A 2 5
A 3 15
B 2 20
B 3 10
B 4 45
B 5 50
output data
name month balance row_number balance_diff
A 1 10 1 0
A 2 5 1 -5
A 3 15 3 10
B 2 20 1 0
B 3 10 2 -10
B 4 45 3 35
B 5 50 4 5
How can I do this using PIG and python UDF? Below is what I tried.
PIG
output = foreach (group input by (name)) {
sorted = order input BY month asc;
row_details= myudf.rownum_and_diff(sorted.(month, balance));
generate flatten (sorted), flatten (row_details));
};
Python UDF
def row_num(mth):
return [x+1 for x,y in enumerate (mth)]
def diff(bal, n=1):
return [x-y if (x is not None and y is not None) else 0.0 \
for x,y in zip(bal, [:n] + bal)]
#outputSchema('udfbag:bag{udftuple:tuple(row_number: int, balance_diff: int)}')
def row_metrics(mthbal):
mth, bal = zip(*mthbal)
row_number = row_num(mth)
balance_diff = diff(bal)
return zip(row_number, balance_diff)
My python functions work. However, I am having trouble combining the two bags (sorted and row_detail) once I bring the results into PIG. Any help is much appreciated.
I have also seen the enumerate function in PIG doing what I want with the row number. As part of learning PIG, however, I am looking for a solution using python UDFs.
Try this.
Python UDF:
def row_num(mth):
return [x+1 for x,y in enumerate (mth)]
def diff(bal, n=1):
return [0]+[x-y for x,y in zip(bal[n:],bal[:-n])]
#outputSchema('udfbag:bag{udftuple:tuple(name: chararray, mth: int, row_number: int, balance_diff: int)}')
def row_metrics(mthbal):
name, mth, bal = zip(*mthbal)
row_number = row_num(mth)
balance_diff = diff(bal)
return zip(name,mth,row_number, balance_diff)
Pig Script:
register 'myudf.py' using jython as myudf;
inpdat = load 'input.dat' using PigStorage(',') as (name:chararray, month:int, balance:int);
outdat = foreach (group inpdat by name) {
sorted = order inpdat BY month asc;
row_details = myudf.row_metrics(sorted);
generate flatten (row_details);
};
dump outdat;
Using the stitch function from piggybank worked in my case. Would be interested to learn any other ways to do this.
REGISTER /mypath/piggybank.jar;
define Stitch org.apache.pig.piggybank.evaluation.Stitch;
input = load 'input.dat' using PigStorage(',') as (name:chararray, month:int, balance:int);
output = FOREACH (group input by name) {
sorted = ORDER input by month asc;
udf_fields = myudf.row_metrics(sorted.(month, balance));
generate flatten(Stitch(sorted,udf_fields)) as (name, month, balance, row_number, balance_diff);
};
Firstly, sorry if this is a bit lengthy, but I wanted to fully describe what I have having problems with and what I have tried already.
I am trying to join (merge) together two dataframe objects on multiple conditions. I know how to do this if the conditions to be met are all 'equals' operators, however, I need to make use of LESS THAN and MORE THAN.
The dataframes represent genetic information: one is a list of mutations in the genome (referred to as SNPs) and the other provides information on the locations of the genes on the human genome. Performing df.head() on these returns the following:
SNP DataFrame (snp_df):
chromosome SNP BP
0 1 rs3094315 752566
1 1 rs3131972 752721
2 1 rs2073814 753474
3 1 rs3115859 754503
4 1 rs3131956 758144
This shows the SNP reference ID and their locations. 'BP' stands for the 'Base-Pair' position.
Gene DataFrame (gene_df):
chromosome chr_start chr_stop feature_id
0 1 10954 11507 GeneID:100506145
1 1 12190 13639 GeneID:100652771
2 1 14362 29370 GeneID:653635
3 1 30366 30503 GeneID:100302278
4 1 34611 36081 GeneID:645520
This dataframe shows the locations of all the genes of interest.
What I want to find out is all of the SNPs which fall within the gene regions in the genome, and discard those that are outside of these regions.
If I wanted to merge together two dataframes based on multiple (equals) conditions, I would do something like the following:
merged_df = pd.merge(snp_df, gene_df, on=['chromosome', 'other_columns'])
However, in this instance - I need to find the SNPs where the chromosome values match those in the Gene dataframe, and the BP value falls between 'chr_start' and 'chr_stop'. What makes this challenging is that these dataframes are quite large. In this current dataset the snp_df has 6795021 rows, and the gene_df has 34362.
I have tried to tackle this by either looking at chromosomes or genes seperately. There are 22 different chromosome values (ints 1-22) as the sex chromosomes are not used. Both methods are taking an extremely long time. One uses the pandasql module, while the other approach is to loop through the separate genes.
SQL method
import pandas as pd
import pandasql as psql
pysqldf = lambda q: psql.sqldf(q, globals())
q = """
SELECT s.SNP, g.feature_id
FROM this_snp s INNER JOIN this_genes g
WHERE s.BP >= g.chr_start
AND s.BP <= g.chr_stop;
"""
all_dfs = []
for chromosome in snp_df['chromosome'].unique():
this_snp = snp_df.loc[snp_df['chromosome'] == chromosome]
this_genes = gene_df.loc[gene_df['chromosome'] == chromosome]
genic_snps = pysqldf(q)
all_dfs.append(genic_snps)
all_genic_snps = pd.concat(all_dfs)
Gene iteration method
all_dfs = []
for line in gene_df.iterrows():
info = line[1] # Getting the Series object
this_snp = snp_df.loc[(snp_df['chromosome'] == info['chromosome']) &
(snp_df['BP'] >= info['chr_start']) & (snp_df['BP'] <= info['chr_stop'])]
if this_snp.shape[0] != 0:
this_snp = this_snp[['SNP']]
this_snp.insert(len(this_snp.columns), 'feature_id', info['feature_id'])
all_dfs.append(this_snp)
all_genic_snps = pd.concat(all_dfs)
Can anyone give any suggestions of a more effective way of doing this?
I've just thought of a way to solve this - by combining my two methods:
First, focus on the individual chromosomes, and then loop through the genes in these smaller dataframes. This also doesn't have to make use of any SQL queries either. I've also included a section to immediately identify any redundant genes that don't have any SNPs that fall within their range. This makes use of a double for-loop which I normally try to avoid - but in this case it works quite well.
all_dfs = []
for chromosome in snp_df['chromosome'].unique():
this_chr_snp = snp_df.loc[snp_df['chromosome'] == chromosome]
this_genes = gene_df.loc[gene_df['chromosome'] == chromosome]
# Getting rid of redundant genes
min_bp = this_chr_snp['BP'].min()
max_bp = this_chr_snp['BP'].max()
this_genes = this_genes.loc[~(this_genes['chr_start'] >= max_bp) &
~(this_genes['chr_stop'] <= min_bp)]
for line in this_genes.iterrows():
info = line[1]
this_snp = this_chr_snp.loc[(this_chr_snp['BP'] >= info['chr_start']) &
(this_chr_snp['BP'] <= info['chr_stop'])]
if this_snp.shape[0] != 0:
this_snp = this_snp[['SNP']]
this_snp.insert(1, 'feature_id', info['feature_id'])
all_dfs.append(this_snp)
all_genic_snps = pd.concat(all_dfs)
While this doesn't run spectacularly quickly - it does run so that I can actually get some answers. I'd still like to know if anyone has any tips to make it run more efficiently though.
You can use the following to accomplish what you're looking for:
merged_df=snp_df.merge(gene_df,on=['chromosome'],how='inner')
merged_df=merged_df[(merged_df.BP>=merged_df.chr_start) & (merged_df.BP<=merged_df.chr_stop)][['SNP','feature_id']]
Note: your example dataframes do not meet your join criteria. Here is an example using modified dataframes:
snp_df
Out[193]:
chromosome SNP BP
0 1 rs3094315 752566
1 1 rs3131972 30400
2 1 rs2073814 753474
3 1 rs3115859 754503
4 1 rs3131956 758144
gene_df
Out[194]:
chromosome chr_start chr_stop feature_id
0 1 10954 11507 GeneID:100506145
1 1 12190 13639 GeneID:100652771
2 1 14362 29370 GeneID:653635
3 1 30366 30503 GeneID:100302278
4 1 34611 36081 GeneID:645520
merged_df
Out[195]:
SNP feature_id
8 rs3131972 GeneID:100302278
I'm trying to make a simple spreadsheet:
I input some details, and it gets saved into the spreadsheet.
So, I input the details into 2 lists, and 1 normal variable:
Dates = ['01/01/14', '01/02/14', '01/03/14']
Amount = ['1', '2', '3']
Cost = 12 (because it is always the same)
I'm trying to insert these into a spreadsheet like this:
for i in range(len(Dates)):
insertThese.extend([Dates[i], Amount[i], Cost])
ws.append(insertThese)
but this adds the 3 things side-by-side like:
A B C D E F G H I
01/01/14 1 12 01/02/14 2 12 01/03/14 3 12
but I want it to be like, basically adding a new row at the end of insertThese.expand...
A B C
01/01/14 1 12
01/02/14 2 12
01/03/14 3 12
I don't understand how to do this without removing by headers at the top of the file.
I tried using iter_rows() but that removes the header.
So how do I get the details to be added row-by-row?
I'm new to openpyxl, so if anything's obvious - sorry!
You can use zip/ itertools.izip to loop over your lists in parallel. Something like the following:
for d, a in zip(Dates, Amount):
ws.append([d, a, 12])