I have a CSV file whose columns are frequency counts of words, and whose rows are time periods. I want to sum for each column the total frequencies. Then I want to write to a CSV file for sums greater than or equal to 30, the column and row values, thus dropping columns whose sums are less than 30.
Just learning python and pandas. I know it is a simple question, but my knowledge is at that level. Your help is most appreciated.
I can read in the CSV file and compute the column sums.
df = pd.read_csv('data.csv')
Except of data file containing 3,874 columns and 100 rows
df.sum(axis = 0, skipna = True)
Excerpt of sums for columns
I am stuck on how to create the output file so that it looks like the original file but no longer has columns whose sums were less than 30.
I am stuck on how to write to a CSV file each row for each column whose sums are greater than or equal to 30. The layout of the output file would be the same as for the input file. The sums would not be included in the output.
Thanks very much for your help.
So, here is a link showing an excerpt of a file containing 100 rows and 3,857 columns:
It's easiest to do this in two steps:
1. Filter the DataFrame to just the columns you want to save
df_to_save = df.loc[:, (df.sum(axis=0, skipna=True) >= 30)]
.loc is for picking rows/columns based either on labels or conditions; the syntax is .loc[rows, columns], so : means "take all the rows", and then the second part is the condition on our columns - I've taken the sum you'd given in your question and set it greater than or equal to 30.
2. Save the filtered DataFrame to CSV
df_to_save.to_csv('path/to/write_file.csv', header=True, index=False)
Just put your filepath in as the first argument. header=True means the header labels from the table will be written back out to the file, and index=False means the numbered row labels Pandas automatically created when you read in the CSV won't be included in the export.
See this answer here: How to delete a column in pandas dataframe based on a condition? . Note, the solution for your question doesn't need isnull() before the sum(), as that is specific to their question for counting NaN values.
Related
I have two Dataframes, one containing my data read in from a CSV file and another that has the data grouped by all of the columns but the last and reindexed to contain a column for the count of the size of the groups.
df_k1 = pd.read_csv(filename, sep=';')
columns_for_groups = list(df_k1.columns)[:-1]
k1_grouped = df_k1.groupby(columns_for_groups).size().reset_index(name="Count")
I need to create a series such that every row(i) in the series corresponds to row(i) in my original Dataframe but the contents of the series need to be the size of the group that the row belongs to in the grouped Dataframe. I currently have this, and it works for my purposes, but I was wondering if anyone knew of a faster or more elegant solution.
size_by_row = []
for row in df_k1.itertuples():
for group in k1_grouped.itertuples():
if row[1:-1] == group[1:-1]:
size_by_row.append(group[-1])
break
group_size = pd.Series(size_by_row)
I'm using read_csv to make a df, but the csv includes some garbage rows before the actual columns, the actual columns are located say in the 5th rows in the csv.
Here's the thing, I don't know how many garbage rows are there in advance and I can only read_csv once, so I can't use "head" or "skiprows" in read_csv.
So my question is how to select a different row as the columns in the df or just delete the first n rows including the columns? If I were to use "df.iloc[3:0]" the columns are still there.
Thanks for your help.
EDIT: Updated so that it also resets the index and does not include an index name:
df.columns = df.iloc[4].values
df = df.iloc[5:].reset_index(drop=True)
If you know your column names start in row 5 as in your example, you can do:
df.columns = df.iloc[4]
df = df.iloc[5:]
If the number of garbage rows is determined, then you can use 'iloc', example the number of garbage rows is 3 firs rows (index 0,1,2), then you can use the following code to get all remaining actual data rows:
df=df.iloc[3:]
If the number of garbage rows is not determined, then you must search the index of first actual data rows from the garbage rows. so you can find the first index of actual data rows and can be used to get all remaining data rows.
df=df.iloc[n:]
n=fisrt index of actual data
I initially had 100k rows in my dataset. I read the csv using pandas into a dataframe called data. I tried to do a subset selection of 51 rows using .loc. My index labels are numeric values 0, 1, 2, 3 etc. I tried using this command -
data = data.loc['0':'50']
But the results were weird, it took all the rows from 0 to 49999, looks like it is taking rows till the index value starts with 50.
Similarly, I tried with this command - new_data = data.loc['0':'19']
and the result was all the rows, starting from 0 till 18999.
Could this be a bug in pandas?
You want to use .iloc in place of .loc, since you are selecting data from the dataframe via numeric indices.
For example:
data.iloc[:50,:]
Keep in mind that your indices are of numeric-type, not string-type, so querying with a string (as you have done in your OP) attempts to match string-wise comparisons.
I am working with pandas / python /numpy / datalab/bigQuery to generate an input table for machine learning processing. The data is genomic - and right now, I am working with small subset of
174 rows
12430 columns
The column names are extracted from bigQuery (df_pik3ca_features = bq.Query(std_sql_features).to_dataframe(dialect='standard',use_cache=True))
at the same way, the row names are extracted: samples_rows = bq.Query('SELECT sample_id FROMspeedy-emissary-167213.pgp_orielresearch.pgp_PIK3CA_all_features_values_step_3GROUP BY sample_id')
what would be the easiest way to create a dataframe / matrix with named rows and columns that were extracted.
I explored the dataframes in pandas and could not find the way to pass the names as parameter.
for empty array, I was able to find the following (numpy) with no names:
a = np.full([num_of_rows, num_of_columns], np.nan)
a.columns
I know R very well (if there is no other way - I hope that I can use it with datalab)
any idea?
Many thanks!
If you have your column names and row names stored in lists then you can just use .loc to select the exact rows and columns you desire. Just make sure that the row names are in the index. You might need to do df.set_index('sample_id') to put the correct row name in the index.
Assuming the rows and columns are in variables row_names and col_names, do this.
df.loc[row_names, col_names]
I was experimenting with HDF and it seems pretty great because my data is not normalized and it contains a lot of text. I love being able to query when I read data into pandas.
loc2 = r'C:\\Users\Documents\\'
(my dataframe with data is called 'export')
hdf = HDFStore(loc2+'consolidated.h5')
hdf.put('raw', export, format= 'table', complib= 'blosc', complevel=9, data_columns = True, append = True)
21 columns and about 12 million rows so far and I will add about 1 million rows per month.
1 Date column [I convert this to datetime64]
2 Datetime columns (one of them for each row and the other one is null about 70% of the time) [I convert this to datetime64]
9 text columns [I convert these to categorical which saves a ton of room]
1 float column
8 integer columns, 3 of these can reach a max of maybe a couple of hundred and the other 5 can only be 1 or 0 values
I made a nice small h5 table and it was perfect until I tried to append more data to it (literally just one day of data since I am receiving daily raw .csv files). I received errors which showed that the dtypes were not matching up for each column although I used the same exact ipython notebook.
Is my hdf.put code correct? If I have append = True does that mean it will create the file if it does not exist, but append the data if it does exist? I will be appending to this file everyday basically.
For columns which only contain 1 or 0, should I specify a dtype like int8 or int16 - will this save space or should I keep it at int64? It looks like some of my columns are randomly float64 (although no decimals) and int64. I guess I need to specify the dtype for each column individually. Any tips?
I have no idea what blosc compression is. Is that the most efficient one to use? Any recommendations here? This file is mainly used to quickly read data into a dataframe to join to other .csv files which Tableau is connected to