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I am using selenium to retrieve text from a simple block of text on a website using the .text function in selenium webelements. The text in question is between <pre> HTML tags. The issue is that the function only returns text up to a certain length (about 56 lines of text). The amount of text on the website is closer to 1250 lines, but only the first 56 or so are returned. I am using the Firefox webdriver here.

The relevant function is as follows:

web_text = driver.find_element_by_xpath("//pre")
    output_text = web_text.text
    print(output_text)
    return(output_text)

So far I have tried using get_attribute() with its various text attributes. Any ideas?

2
  • Could you share the link to the website your trying to scrape? Commented Jul 29, 2020 at 17:04
  • link Basically I am just trying to get the text from the main body held by the pre tags. Commented Jul 29, 2020 at 17:07

1 Answer 1

1

I am able to get all of the text within the pre tags by using driver.find_element_by_xpath("/html/body/pre").

Code (Chrome):

from selenium import webdriver

driver = webdriver.Chrome()

driver.get(
    "http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5F21AC9A000078434DBE2580&wait=20")
pre_text = driver.find_element_by_xpath("/html/body/pre").text # gets the pre text


print(pre_text)

Code (Firefox):

from selenium import webdriver

driver = webdriver.Firefox()

driver.get(
    "http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5F21AC9A000078434DBE2580&wait=20")
pre_text = driver.find_element_by_xpath("/html/body/pre").text

print(pre_text)

Output:

# NetMHCpan version 4.1b

# Tmpdir made /usr/opt/www/webface/tmp/server/netmhcpan/5F21AC9A000078434DBE2580/netMHCpangwUDuR
# Input is in FSA format

# Peptide length 9

# Make EL predictions

HLA-A01:01 : Distance to training data  0.000 (using nearest neighbor HLA-A01:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-A*01:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0046960    7.476
   2 HLA-A*01:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0045910    7.581
   3 HLA-A*01:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0017130   13.642
   4 HLA-A*01:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0268270    2.868
   5 HLA-A*01:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0008990   19.889
   6 HLA-A*01:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0054000    6.931
   7 HLA-A*01:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0013350   15.772
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-A*01:01. Number of high binders 0. Number of weak binders 0. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-A01:01
-----------------------------------------------------------------------------------

HLA-A02:01 : Distance to training data  0.000 (using nearest neighbor HLA-A02:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-A*02:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000540   49.750
   2 HLA-A*02:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0000210   63.750
   3 HLA-A*02:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000230   62.500
   4 HLA-A*02:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.2437300    0.949 <= WB
   5 HLA-A*02:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0002100   32.111
   6 HLA-A*02:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0105610    6.565
   7 HLA-A*02:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0024300   12.546
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-A*02:01. Number of high binders 0. Number of weak binders 1. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-A02:01
-----------------------------------------------------------------------------------

HLA-A03:01 : Distance to training data  0.000 (using nearest neighbor HLA-A03:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-A*03:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0001350   30.273
   2 HLA-A*03:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0003670   20.630
   3 HLA-A*03:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0006280   16.760
   4 HLA-A*03:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0238070    3.854
   5 HLA-A*03:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0003990   19.947
   6 HLA-A*03:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0002880   22.657
   7 HLA-A*03:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0001470   29.308
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-A*03:01. Number of high binders 0. Number of weak binders 0. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-A03:01
-----------------------------------------------------------------------------------

HLA-A24:02 : Distance to training data  0.000 (using nearest neighbor HLA-A24:02)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-A*24:02      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000020   80.000
   2 HLA-A*24:02      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0000480   33.750
   3 HLA-A*24:02      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000200   44.000
   4 HLA-A*24:02      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0577830    1.703 <= WB
   5 HLA-A*24:02      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0965440    1.280 <= WB
   6 HLA-A*24:02      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0032610    6.706
   7 HLA-A*24:02      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0797820    1.431 <= WB
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-A*24:02. Number of high binders 0. Number of weak binders 3. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-A24:02
-----------------------------------------------------------------------------------

HLA-A26:01 : Distance to training data  0.000 (using nearest neighbor HLA-A26:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-A*26:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0001060   35.556
   2 HLA-A*26:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0002580   25.654
   3 HLA-A*26:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0081970    5.217
   4 HLA-A*26:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0976610    1.070 <= WB
   5 HLA-A*26:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0005860   18.306
   6 HLA-A*26:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0038720    7.729
   7 HLA-A*26:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0003450   22.842
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-A*26:01. Number of high binders 0. Number of weak binders 1. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-A26:01
-----------------------------------------------------------------------------------

HLA-B07:02 : Distance to training data  0.000 (using nearest neighbor HLA-B07:02)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*07:02      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000160   68.000
   2 HLA-B*07:02      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0000600   46.750
   3 HLA-B*07:02      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000250   60.714
   4 HLA-B*07:02      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0024230   10.079
   5 HLA-B*07:02      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0094630    5.272
   6 HLA-B*07:02      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0091830    5.348
   7 HLA-B*07:02      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0002790   26.192
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*07:02. Number of high binders 0. Number of weak binders 0. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B07:02
-----------------------------------------------------------------------------------

HLA-B08:01 : Distance to training data  0.000 (using nearest neighbor HLA-B08:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*08:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000700   63.409
   2 HLA-B*08:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0002690   41.333
   3 HLA-B*08:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0001180   54.512
   4 HLA-B*08:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0082280    8.907
   5 HLA-B*08:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.1109260    1.478 <= WB
   6 HLA-B*08:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.2449270    0.644 <= WB
   7 HLA-B*08:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0830030    1.926 <= WB
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*08:01. Number of high binders 0. Number of weak binders 3. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B08:01
-----------------------------------------------------------------------------------

HLA-B27:05 : Distance to training data  0.000 (using nearest neighbor HLA-B27:05)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*27:05      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000140   65.000
   2 HLA-B*27:05      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0001850   27.278
   3 HLA-B*27:05      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000510   44.000
   4 HLA-B*27:05      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0106230    5.231
   5 HLA-B*27:05      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0005460   17.557
   6 HLA-B*27:05      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0059040    6.668
   7 HLA-B*27:05      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0008280   14.816
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*27:05. Number of high binders 0. Number of weak binders 0. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B27:05
-----------------------------------------------------------------------------------

HLA-B39:01 : Distance to training data  0.000 (using nearest neighbor HLA-B39:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*39:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000030   80.000
   2 HLA-B*39:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0000830   37.000
   3 HLA-B*39:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000500   43.250
   4 HLA-B*39:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0078790    6.031
   5 HLA-B*39:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0138640    4.423
   6 HLA-B*39:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0922070    1.394 <= WB
   7 HLA-B*39:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0007930   16.756
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*39:01. Number of high binders 0. Number of weak binders 1. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B39:01
-----------------------------------------------------------------------------------

HLA-B40:01 : Distance to training data  0.000 (using nearest neighbor HLA-B40:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*40:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000010   85.000
   2 HLA-B*40:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0003270   15.064
   3 HLA-B*40:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000050   62.500
   4 HLA-B*40:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0040450    5.141
   5 HLA-B*40:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0007510   10.653
   6 HLA-B*40:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0130780    3.155
   7 HLA-B*40:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0000240   40.500
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*40:01. Number of high binders 0. Number of weak binders 0. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B40:01
-----------------------------------------------------------------------------------

HLA-B58:01 : Distance to training data  0.000 (using nearest neighbor HLA-B58:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*58:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000180   74.286
   2 HLA-B*58:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0010330   18.059
   3 HLA-B*58:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0002550   32.950
   4 HLA-B*58:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.3524310    0.756 <= WB
   5 HLA-B*58:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0011160   17.476
   6 HLA-B*58:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0055600    8.227
   7 HLA-B*58:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0001540   40.000
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*58:01. Number of high binders 0. Number of weak binders 1. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B58:01
-----------------------------------------------------------------------------------

HLA-B15:01 : Distance to training data  0.000 (using nearest neighbor HLA-B15:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
---------------------------------------------------------------------------------------------------------------------------
 Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
---------------------------------------------------------------------------------------------------------------------------
   1 HLA-B*15:01      CIDSTFNWQ CIDSTFNWQ  0  0  0  0  0    CIDSTFNWQ        Sequence 0.0000250   62.500
   2 HLA-B*15:01      IDSTFNWQH IDSTFNWQH  0  0  0  0  0    IDSTFNWQH        Sequence 0.0002870   29.593
   3 HLA-B*15:01      DSTFNWQHR DSTFNWQHR  0  0  0  0  0    DSTFNWQHR        Sequence 0.0000110   74.000
   4 HLA-B*15:01      STFNWQHRI STFNWQHRI  0  0  0  0  0    STFNWQHRI        Sequence 0.0065120    8.706
   5 HLA-B*15:01      TFNWQHRIL TFNWQHRIL  0  0  0  0  0    TFNWQHRIL        Sequence 0.0009100   19.116
   6 HLA-B*15:01      FNWQHRILL FNWQHRILL  0  0  0  0  0    FNWQHRILL        Sequence 0.0028310   12.227
   7 HLA-B*15:01      NWQHRILLV NWQHRILLV  0  0  0  0  0    NWQHRILLV        Sequence 0.0001040   42.000
---------------------------------------------------------------------------------------------------------------------------

Protein Sequence. Allele HLA-B*15:01. Number of high binders 0. Number of weak binders 0. Number of peptides 7

Link to Allele Frequencies in Worldwide Populations HLA-B15:01
-----------------------------------------------------------------------------------

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8 Comments

Hey thanks for your quick reply. I tried your code and got the same error. The only big difference I see is that you're using Chrome and I'm using firefox. Could that be the issue here?
It could be, It could also be that maybe other code is breaking it. I will try on Firefox
@TomaszTabernacki I tested code with Firefox and it also gives full code. The only idea is that you replaced print() with own function print() which crops text. Or you run is tool which crops all strings on screen. OR maybe you return it to function which crops text and displays only 56 cahrs. Did you run only this code using python script.py ?
@TomaszTabernacki See my edit it works on firefox too! Could you maybe put ur full code in a github gist or pastebin so we can see what's going on
Strange. I'm running it in the PyCharm IDE with default settings.
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