boscoh / inmembrane Goto Github PK

The TMHMM web service at CBS seems somewhat unreliable.
Consider adding the Phobius transmembrane prediction service as the (default?) option. See: https://www.ebi.ac.uk/Tools/webservices/services/pfa/phobius_rest

Hi Boscoh
I am interested to identify surface exposed protein in Lactobacillus by using inmembrane tool.
I have appox 7000 sequences and for this i need locally install TMHMM, SignalP, LipoP. Which have done.
I don't know where to change path in the inmembrane files so that all the web services TMHMM, SignalP, LipoP will be use locally through inmembrane programs

Thanks Dimple

For a particular protocol (gram_neg or gram_pos). This way we can quickly check if everything is working for our particular protocol without needing to interpret the test output.

Currently when running ALL tests, many frequently fail depending on the state of external servers and optional local dependencies - we'd rather avoid testing the ones we don't need.

Dear Andrew,
Hi had installed inmembrane via github with given below command.
$ git clone http://github.com/boscoh/inmembrane.git

Later while given below command were executed but found issues. I have pasted log file. KINDLY GUIDE ME.
cd inmembrane
$ sudo python setup.py install

Error as given below :-

1. byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/init.py to init.cpython-38.pyc
   File "/usr/local/lib/python3.8/dist-packages/inmembrane/init.py", line 115
   def process(params):
   ^
   SyntaxError: import * only allowed at module level

2. File "/usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmhmm_web.py", line 75
   newseqid = seqcount + re.sub(r'[^\w]', "", seqid)
   ^
   SyntaxError: invalid syntax

3. File "/usr/local/lib/python3.8/dist-packages/inmembrane/helpers.py", line 89
   print s
   ^
   SyntaxError: Missing parentheses in call to 'print'. Did you mean print(s)?

Log file

sudo python setup.py install
[sudo] password for dimple:
/usr/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
/usr/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'zip_safe'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib
creating build/lib/inmembrane
copying inmembrane/init.py -> build/lib/inmembrane
copying inmembrane/helpers.py -> build/lib/inmembrane
creating build/lib/inmembrane/plugins
copying inmembrane/plugins/bomp_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/hmmsearch3.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/tmbetadisc_rbf_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/lipop_scrape_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/init.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/tmbhunt_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/tmhmm_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/memsat3.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/tmhmm.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/lipop1.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/tmhmm_scrape_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/lipop_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/signalp4.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/signalp_scrape_web.py -> build/lib/inmembrane/plugins
copying inmembrane/plugins/tatfind_web.py -> build/lib/inmembrane/plugins
creating build/lib/inmembrane/protocols
copying inmembrane/protocols/gram_pos.py -> build/lib/inmembrane/protocols
copying inmembrane/protocols/init.py -> build/lib/inmembrane/protocols
copying inmembrane/protocols/gram_neg.py -> build/lib/inmembrane/protocols
creating build/lib/inmembrane/tests
copying inmembrane/tests/test_misc.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_bomp_web.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_signalp_scrape_web.py -> build/lib/inmembrane/tests
copying inmembrane/tests/init.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_signalp4.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_tatfind_web.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_hmmsearch3.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_tmbetadisc_rbf_web.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_tmhmm_scrape_web.py -> build/lib/inmembrane/tests
copying inmembrane/tests/PluginTestBase.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_lipop_scrape_web.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_tmhmm.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_lipop1.py -> build/lib/inmembrane/tests
copying inmembrane/tests/test_memsat3.py -> build/lib/inmembrane/tests
creating build/lib/inmembrane/protocols/gram_neg_profiles
copying inmembrane/protocols/gram_neg_profiles/Tat_PS51318.hmm -> build/lib/inmembrane/protocols/gram_neg_profiles
creating build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/SLH.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/LPxTG_PS50847.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/NLPC_P60.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/GW2.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/GW3.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/Gram_pos_anchor.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/LPxTG.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/PG_binding_2.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/GW1.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/PG_binding_3.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/CW_binding_2.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/LysM.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/PG_binding_1.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
copying inmembrane/protocols/gram_pos_profiles/CW_binding_1.hmm -> build/lib/inmembrane/protocols/gram_pos_profiles
creating build/lib/inmembrane/tests/signalp_scrape_web
copying inmembrane/tests/signalp_scrape_web/input.fasta -> build/lib/inmembrane/tests/signalp_scrape_web
creating build/lib/inmembrane/tests/tmhmm_scrape_web
copying inmembrane/tests/tmhmm_scrape_web/input.fasta -> build/lib/inmembrane/tests/tmhmm_scrape_web
creating build/lib/inmembrane/tests/memsat3
copying inmembrane/tests/memsat3/input.fasta -> build/lib/inmembrane/tests/memsat3
creating build/lib/inmembrane/tests/tatfind_web
copying inmembrane/tests/tatfind_web/input.fasta -> build/lib/inmembrane/tests/tatfind_web
creating build/lib/inmembrane/tests/signalp4
copying inmembrane/tests/signalp4/input.fasta -> build/lib/inmembrane/tests/signalp4
creating build/lib/inmembrane/tests/lipop_scrape_web
copying inmembrane/tests/lipop_scrape_web/input.fasta -> build/lib/inmembrane/tests/lipop_scrape_web
creating build/lib/inmembrane/tests/lipop1
copying inmembrane/tests/lipop1/input.fasta -> build/lib/inmembrane/tests/lipop1
creating build/lib/inmembrane/tests/tmhmm
copying inmembrane/tests/tmhmm/input.fasta -> build/lib/inmembrane/tests/tmhmm
creating build/lib/inmembrane/tests/hmmsearch3
copying inmembrane/tests/hmmsearch3/input.fasta -> build/lib/inmembrane/tests/hmmsearch3
creating build/lib/inmembrane/tests/tmbetadisc_rbf_web
copying inmembrane/tests/tmbetadisc_rbf_web/input.fasta -> build/lib/inmembrane/tests/tmbetadisc_rbf_web
creating build/lib/inmembrane/tests/bomp_web
copying inmembrane/tests/bomp_web/input.fasta -> build/lib/inmembrane/tests/bomp_web
running build_scripts
creating build/scripts-3.8
copying and adjusting inmembrane_scan -> build/scripts-3.8
changing mode of build/scripts-3.8/inmembrane_scan from 644 to 755
running install_lib
copying build/lib/inmembrane/protocols/gram_pos.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols
copying build/lib/inmembrane/protocols/init.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols
copying build/lib/inmembrane/protocols/gram_neg.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols
copying build/lib/inmembrane/protocols/gram_neg_profiles/Tat_PS51318.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_neg_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/SLH.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/LPxTG_PS50847.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/NLPC_P60.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/GW2.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/GW3.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/Gram_pos_anchor.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/LPxTG.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/PG_binding_2.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/GW1.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/PG_binding_3.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/CW_binding_2.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/LysM.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/PG_binding_1.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/protocols/gram_pos_profiles/CW_binding_1.hmm -> /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos_profiles
copying build/lib/inmembrane/tests/test_misc.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/signalp_scrape_web/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/signalp_scrape_web
copying build/lib/inmembrane/tests/test_bomp_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_signalp_scrape_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/tmhmm_scrape_web/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/tmhmm_scrape_web
copying build/lib/inmembrane/tests/init.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_signalp4.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/memsat3/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/memsat3
copying build/lib/inmembrane/tests/test_tatfind_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_hmmsearch3.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/tatfind_web/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/tatfind_web
copying build/lib/inmembrane/tests/signalp4/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/signalp4
copying build/lib/inmembrane/tests/test_tmbetadisc_rbf_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_tmhmm_scrape_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/PluginTestBase.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_lipop_scrape_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_tmhmm.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/test_lipop1.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/lipop_scrape_web/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/lipop_scrape_web
copying build/lib/inmembrane/tests/lipop1/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/lipop1
copying build/lib/inmembrane/tests/test_memsat3.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests
copying build/lib/inmembrane/tests/tmhmm/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/tmhmm
copying build/lib/inmembrane/tests/hmmsearch3/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/hmmsearch3
copying build/lib/inmembrane/tests/tmbetadisc_rbf_web/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/tmbetadisc_rbf_web
copying build/lib/inmembrane/tests/bomp_web/input.fasta -> /usr/local/lib/python3.8/dist-packages/inmembrane/tests/bomp_web
copying build/lib/inmembrane/init.py -> /usr/local/lib/python3.8/dist-packages/inmembrane
copying build/lib/inmembrane/plugins/bomp_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/hmmsearch3.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/tmbetadisc_rbf_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/lipop_scrape_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/init.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/tmbhunt_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/tmhmm_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/memsat3.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/tmhmm.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/lipop1.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/tmhmm_scrape_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/lipop_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/signalp4.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/signalp_scrape_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/plugins/tatfind_web.py -> /usr/local/lib/python3.8/dist-packages/inmembrane/plugins
copying build/lib/inmembrane/helpers.py -> /usr/local/lib/python3.8/dist-packages/inmembrane
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_pos.py to gram_pos.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/init.py to init.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/protocols/gram_neg.py to gram_neg.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_misc.py to test_misc.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_bomp_web.py to test_bomp_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_signalp_scrape_web.py to test_signalp_scrape_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/init.py to init.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_signalp4.py to test_signalp4.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_tatfind_web.py to test_tatfind_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_hmmsearch3.py to test_hmmsearch3.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_tmbetadisc_rbf_web.py to test_tmbetadisc_rbf_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_tmhmm_scrape_web.py to test_tmhmm_scrape_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/PluginTestBase.py to PluginTestBase.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_lipop_scrape_web.py to test_lipop_scrape_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_tmhmm.py to test_tmhmm.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_lipop1.py to test_lipop1.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/tests/test_memsat3.py to test_memsat3.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/init.py to init.cpython-38.pyc
File "/usr/local/lib/python3.8/dist-packages/inmembrane/init.py", line 115
def process(params):
^
SyntaxError: import * only allowed at module level

byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/bomp_web.py to bomp_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/hmmsearch3.py to hmmsearch3.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmbetadisc_rbf_web.py to tmbetadisc_rbf_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/lipop_scrape_web.py to lipop_scrape_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/init.py to init.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmbhunt_web.py to tmbhunt_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmhmm_web.py to tmhmm_web.cpython-38.pyc
File "/usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmhmm_web.py", line 75
newseqid = seqcount + re.sub(r'[^\w]', "", seqid)
^
SyntaxError: invalid syntax

byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/memsat3.py to memsat3.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmhmm.py to tmhmm.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/lipop1.py to lipop1.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tmhmm_scrape_web.py to tmhmm_scrape_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/lipop_web.py to lipop_web.cpython-38.pyc
File "/usr/local/lib/python3.8/dist-packages/inmembrane/plugins/lipop_web.py", line 88
newseqid = seqcount + re.sub(r'[^\w]', "", seqid)
^
SyntaxError: invalid syntax

byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/signalp4.py to signalp4.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/signalp_scrape_web.py to signalp_scrape_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/plugins/tatfind_web.py to tatfind_web.cpython-38.pyc
byte-compiling /usr/local/lib/python3.8/dist-packages/inmembrane/helpers.py to helpers.cpython-38.pyc
File "/usr/local/lib/python3.8/dist-packages/inmembrane/helpers.py", line 89
print s
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(s)?

running install_scripts
copying build/scripts-3.8/inmembrane_scan -> /usr/local/bin
changing mode of /usr/local/bin/inmembrane_scan to 755
running install_egg_info
Removing /usr/local/lib/python3.8/dist-packages/inmembrane-0.95.0.egg-info
Writing /usr/local/lib/python3.8/dist-packages/inmembrane-0.95.0.egg-info

The test for MEMSAT3 almost always returns 'failed' even if it's working correctly since the results are dependant on a BLAST search and the locally installed BLAST database is unlikely to match the one used to derive the test results. If the numbers in the test output look similar it should be okay. There is now a note about this to the test output, but it's confusing and we should consider finding a way to make this test more robust in the future, such that is can detect a broken MEMSAT3 installation, but passes if vaguely sensible (close) predictions are output.