Monday, July 13, 2020

gffutils, big macbook pro


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']

>>> 

No comments:

Post a Comment