pandas DataFrame.to_string() truncating strings from columns

Question

When I try to use to_string to output a column from a dataframe, it truncates the output of the column.

print gtf_df.ix[:1][['transcript_id','attributes']].to_string(header=False,index=False)

Out: ' CUFF.1.1  gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM '

print gtf_df.ix[:1]['attributes'][0]

Out: 'gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "1670303.8168650887"; frac "1.000000"; conf_lo "0.000000"; conf_hi "5010911.450595"; cov "9658.694354";'

Any ideas as to how to resolve this problem? Thanks!

What is the type of attributes -- i.e. what do you get back from type(gtf_df['attributes'][0]) -- If it is a string, can you tell us whether removing the quotes and semicolons solves the problem -- i.e. gtf_df.attributes = gtf_df.attributes.replace('\"','').replace(';','') — DanB, Aug 17 '12 at 04:54
It is a string column. However, your recommended fix did not change anything. The answer presented below works. — Kunal B., Aug 17 '12 at 17:08

score 13 · Accepted Answer · edited Aug 17 '16 at 23:33

13

Using __repr__ or to_string columns are by default truncated at 50 chars. In versions of Pandas older than 0.13.1, this can be controlled using pandas.set_printoptions():

In [64]: df
Out[64]:
                                                   A    B
a  this is a very long string, longer than the defau  bar
b                                                foo  baz

In [65]: pandas.set_printoptions(max_colwidth=100)

In [66]: df
Out[66]:
                                                                      A    B
a  this is a very long string, longer than the default max_column width  bar
b                                                                   foo  baz

In more recent versions of Pandas, use this instead:

pd.options.display.max_colwidth = 100

edited Aug 17 '16 at 23:33

Brandon Rhodes

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answered Aug 17 '12 at 06:54

Wouter Overmeire

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Thanks. That was definitely the problem. – Kunal B. Aug 17 '12 at 17:09
14

As of now, Pandas version 0.13.1, the setting is of the form `pd.options.display.max_colwidth = 100`. – Luis E. May 05 '14 at 17:43

score 1 · Answer 2 · answered Sep 22 '18 at 03:48

1

Pandas changed how to set this option. Here is the current documentation

pd.set_option('display.max_colwidth', 100)

See the docs for other nice ones like:

pd.set_option('display.max_rows', 999)

answered Sep 22 '18 at 03:48

neves

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pandas DataFrame.to_string() truncating strings from columns

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