I'm new to Python/Biopython programming. I'd like to install Biopython into my PyCharm IDE but I've tried all instructions on this, but it's not confirming it. I have the available biopython file already extracted. There's a SyntaxError for 'install' in: pip install biopython What's the proper way of installing and importing biopython? And how does one confirm the installation.
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1$\begingroup$ You probably should mention your operating system. $\endgroup$– Wouter De CosterJul 15, 2020 at 18:48
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$\begingroup$ Could you please show the complete error text? Which python version do you use? $\endgroup$– Mr_ZJul 15, 2020 at 20:11
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1$\begingroup$ A SyntaxError is an exception raised by python, so I guess you ran pip within the python interpreter rather than from your shell/terminal $\endgroup$– Chris_RandsJul 15, 2020 at 21:48
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$\begingroup$ @WouterDeCoster It's Windows 10 Pro, 64-bit OS, 4gb RAM $\endgroup$– BioIsaacJul 15, 2020 at 23:03
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$\begingroup$ @Mr_Z Python 3.8, PyCharm 2020.1.2. Here: pip install biopython File "<stdin>", line 1 pip install biopython ^ SyntaxError: invalid syntax $\endgroup$– BioIsaacJul 15, 2020 at 23:20
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1 Answer
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Install Anaconda3 the instructions are here. Then making sure you are connected to the internet type
conda install -c anaconda biopython
Once Anaconda is installed don't attempt to use pip, if you do then you need to set an 'environment' in Anaconda and work from that environment.
I suspect you used pip or pip3 via
pip install biopython
