Ref https://daler.github.io/gffutils/installation.html
(base) CS313BQin:aln2snps hqin$ conda create -n gff python=3.7 anaconda
Accept 'y', many things are added.
(base) CS313BQin:aln2snps hqin$ conda activate gff
(gff) CS313BQin:aln2snps hqin$
(gff) CS313BQin:aln2snps hqin$ conda install --channel bioconda pybedtools bedtools biopython
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/anaconda3/envs/gff
added / updated specs:
- bedtools
- biopython
- pybedtools
The following packages will be downloaded:
package | build
---------------------------|-----------------
bedtools-2.29.2 | h37cfd92_0 868 KB bioconda
biopython-1.77 | py37haf1e3a3_0 2.1 MB
libdeflate-1.0 | h1de35cc_1 45 KB bioconda
pybedtools-0.8.1 | py37h2dec4b4_0 12.1 MB bioconda
pysam-0.15.3 | py37h726f235_1 2.1 MB bioconda
------------------------------------------------------------
Total: 17.1 MB
The following NEW packages will be INSTALLED:
bedtools bioconda/osx-64::bedtools-2.29.2-h37cfd92_0
biopython pkgs/main/osx-64::biopython-1.77-py37haf1e3a3_0
libdeflate bioconda/osx-64::libdeflate-1.0-h1de35cc_1
pybedtools bioconda/osx-64::pybedtools-0.8.1-py37h2dec4b4_0
pysam bioconda/osx-64::pysam-0.15.3-py37h726f235_1
(gff) CS313BQin:aln2snps hqin$ conda install --channel bioconda gffutils
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/anaconda3/envs/gff
added / updated specs:
- gffutils
The following packages will be downloaded:
package | build
---------------------------|-----------------
argcomplete-1.11.1 | py_1 36 KB
gffutils-0.10.1 | py_0 1.2 MB bioconda
pyfaidx-0.5.9 | pyh4c3bd37_0 28 KB bioconda
simplejson-3.17.0 | py37h1de35cc_0 98 KB
------------------------------------------------------------
Total: 1.3 MB
The following NEW packages will be INSTALLED:
argcomplete pkgs/main/noarch::argcomplete-1.11.1-py_1
gffutils bioconda/noarch::gffutils-0.10.1-py_0
pyfaidx bioconda/noarch::pyfaidx-0.5.9-pyh4c3bd37_0
simplejson pkgs/main/osx-64::simplejson-3.17.0-py37h1de35cc_0
Proceed ([y]/n)?
In shell python, it worked using in-memory database.
(gff) CS313BQin:aln2snps hqin$ python
Python 3.7.7 (default, Mar 26 2020, 10:32:53)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gffutils
>>> fn = gffutils.example_filename('mouse_extra_comma.gff3')
>>> db = gffutils.create_db(fn, ':memory:')
>>> db
<gffutils.interface.FeatureDB object at 0x7f9568158b90>
>>>
Package path
>> import sys
>>> sys.path
['', '/opt/anaconda3/envs/gff/lib/python37.zip', '/opt/anaconda3/envs/gff/lib/python3.7', '/opt/anaconda3/envs/gff/lib/python3.7/lib-dynload', '/opt/anaconda3/envs/gff/lib/python3.7/site-packages', '/opt/anaconda3/envs/gff/lib/python3.7/site-packages/aeosa']
>>>
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