Merge pull request #12 from klavinslab/release-v1.0.0

Release v1.0.0

.gitignore

@@ -1,9 +1,17 @@
 # Created by .ignore support plugin (hsz.mobi)
-### Example user template template
-### Example user template
+# Example user template template
+# Example user template
 
-# IntelliJ project files
-.idea
-.idea/workspace.xml
+## IntelliJ project files
+**/.idea
+**/.idea/workspace.xml
 .cache
-tests/secrets/config.json
+tests/secrets/config.json
+.DS_Store
+**/tests/secrets/config.json
+**/tests/example_outputs
+**/__pycache__/*
+**/*.pyc
+.coverage
+*.pyc
+*.xml

.travis.yml

@@ -0,0 +1,31 @@
+language: python
+python:
+- '3.4'
+- '3.5'
+- '3.5-dev'
+- '3.6'
+- '3.6-dev'
+- '3.7-dev'
+- 'nightly'
+install:
+- pip install .
+before_install:
+- openssl aes-256-cbc -K $encrypted_1b322a262dd5_key -iv $encrypted_1b322a262dd5_iv -in tests/secrets/config.json.enc -out tests/secrets/config.json -d
+- pip install lxml
+- pip install pyandoc
+- pip install pytest pytest-cov
+- pip install coveralls
+after_install:
+- pandoc --from=markdown --to=rst --output=README README.md
+script:
+- py.test --cov benchlingapi --cov-report term-missing
+after_success:
+- coveralls
+deploy:
+  provider: pypi
+  user: jvrana
+  password:
+    secure: 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
+  on:
+    tags: true
+    branch: master

LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Justin Dane Vrana
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1 @@
+include README LICENSE.txt *.md

README

@@ -0,0 +1,212 @@
+Description
+===========
+
+Benchling provides a convenient way to store DNA sequences (plasmids,
+primers, pcr fragments, etc.) for an entire lab. This repo provides a
+convinient wrapper for making Benchling API requests.
+
+Features:
+
+.. raw:: html
+
+   <ul>
+
+.. raw:: html
+
+   <li>
+
+Accessing Benchling sequences and folders
+
+.. raw:: html
+
+   </li>
+
+.. raw:: html
+
+   <li>
+
+Creating new sequences and folders
+
+.. raw:: html
+
+   </li>
+
+.. raw:: html
+
+   <li>
+
+Searching through sequences and folders using regular expressions
+
+.. raw:: html
+
+   </li>
+
+.. raw:: html
+
+   <li>
+
+Converting Benchling sequence JSON to genbank or FASTA files
+
+.. raw:: html
+
+   </li>
+
+.. raw:: html
+
+   <li>
+
+Opening and accessing sequences in a Benchling Share links
+
+.. raw:: html
+
+   </li>
+
+.. raw:: html
+
+   </ul>
+
+Installation
+============
+
+::
+
+    cd directory/that/contains/benchling-api
+    pip install .
+
+Usage
+=====
+
+Initializing the API object
+---------------------------
+
+The BenchlingAPI object provides an interface for accessing Benchling
+sequences. It requires a benchling API-key, which can be requested from
+Benchling. More information on the Benchling API can be accessed here:
+https://api.benchling.com/docs/.
+
+::
+
+    from benchlingapi import BenchlingAPI
+
+    bench_api_key = 'sk_g7fo2vxskNUYffNPkShOFIsOmtY9ejIXX'
+    benchlingapi = BenchlingAPI(bench_api_key)
+
+The first argument is the Benchling API key, which can be requested
+through benchling and accessed by scrolling to the bottom of you account
+information on Benchling.
+
+Find
+^^^^
+
+getting folders
+
+.. code:: json
+
+    {'count': 59, 'created_at': '2013-10-01T20:07:18+00:00', 'description': '', 'id': 'lib_pP6d50rJn1', 'modified_at': '2017-01-20T21:57:55.991758+00:00', 'name': 'Plasmids', 'owner': 'ent_A7BlnCcJTU', 'permissions': {'admin': True, 'appendable': True, 'owner': False, 'readable': True, 'writable': True}, 'sequences': [{'id': 'seq_wHiaXdFM', 'name': 'pGPT4-pGAL1-G(m)AVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_WQ0wqb9f', 'name': 'pMODU6-pGALZ4-iaaH', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_okitCPyx', 'name': 'pGPT4-pGAL1-GAVNY(VP64)', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_bw3XWuZU', 'name': 'pMODT4-pGALZ4-AVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_K5hwGNwg', 'name': 'pMODU6-pGAL1-BleoMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_AyQ7ToIn', 'name': 'pBR322 (Sample Sequence)', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_t77GYXRB', 'name': 'pGPT4-pGAL1-EGFP', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_5bmPzcKN', 'name': 'pMODU6-pGALZ4-NatMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_Na2oNxzs', 'name': 'pMODU6-pGALZ4-FAR1-mut-87aa', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_0FmHFzJe', 'name': 'pMODT4-pGAL1-attB1-GAVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_m42PVReQ', 'name': 'pMODT4-pGALZ4-Z4AVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_mfMW58Dd', 'name': 'pGPL5G-pGALZ4-URA3', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_QteKmJdS', 'name': 'pGPT4-pGAL1-GAVNY_mutated_library', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_usn0K27s', 'name': 'pMODU6-pGALZ4-BleoMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_i0Yl6uzk', 'name': 'pMODH8-pGPD-TIR1_DM', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_TWAJLtvz', 'name': 'pMODU6-pGAL1-P1G1-HygMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_2rKmILGU', 'name': 'pMODU6-pGAL1-NatMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_5AXMlSvB', 'name': 'pYMOD2Kmx_pGAL1-HYG_pGAL1-iaah', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_qihkmlW4', 'name': 'pMODU6-pGAL1-AlphaFactor', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_k0MuYdIM', 'name': 'pMODU6-pGAL1-IAA17T2-FAR1', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_7yXay7Ep', 'name': 'pGP8G-TIR1-Y', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_GuqSGBXY', 'name': 'pGPT4-pGAL1-GAVNY(VP64) new design', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_fkFjzKkb', 'name': 'v63_pGP8zGAL-STE5(-)RING-SNC2 C-term', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_PKJNfuZA', 'name': 'pGPH8-pGAL1-GAVNY_v2', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_f4GgnFdY', 'name': 'pGPT4-pGAL1-GAVNY_seq_verified', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_SGfG2YeB', 'name': 'pMODU6-pGALZ4-HygMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_vA5dxrqd', 'name': 'pMODU6-pGALZ4-AlphaFactor', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_tMz0Xv3g', 'name': 'pMODU6-pGAL1-FAR1-L1-IAA17T2', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_2xGw2yCj', 'name': 'pGPH8-pGAL1-GAVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_rwDoRd9Q', 'name': 'pMODU6-pGALZ4-FAR1', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_ri07UntS', 'name': 'pMODU6-pGPD-EYFP', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_TsTM0B8q', 'name': 'pMOD4-pGAL1Z3(P3)-MF(AL', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_QGfqobtP', 'name': 'pGPT4-pGAL1-AVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_9ph0SnJV', 'name': 'AmpR-T4-pGAL1-GAL4DBD-L1', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_F4tEc0XU', 'name': 'pMODU6-pGALZ4-STE5(-)RING', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_iGdjEEx4', 'name': 'pGPT4-pGAL1-P1G1-GEV', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_hhI5TTbO', 'name': 'pMODU6-pGAL1-FAR1-IAA17T2', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_AgQ1w9ak', 'name': 'pLAB2', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_y9xdtVx7', 'name': 'pMODKan-HO-pACT1GEV', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_D1iAdKMz', 'name': 'pGPL5G-pGAL1-URA3', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_etTsAfD4', 'name': 'pGPU6-pGALZ4-eYFP', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_5HcRWKi8', 'name': 'pMODU6-pGALZ4-P1G1-HygMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_Qc6f2Kii', 'name': 'pMOD4G-NLS_dCas9_VP64', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_VazadBJw', 'name': 'pGPT4-pGAL1-GAVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_ztl4dnOW', 'name': 'pLAB1', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_kKtPZ1Rs', 'name': 'pMODT4-pGAL1-P1G1-GAVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_4ccBmI1j', 'name': 'pGPU6-pGAL1-AFB2', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_tFGIIL0C', 'name': 'pMODU6-pGAL1-FAR1', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_7O7ThYSI', 'name': 'pMODU6-pGALZ4-Z4AVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_w2IZPFzd', 'name': 'pMODOK-pACT1-GAVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_UbsucV1t', 'name': 'pMODU6-pGAL1-HygMX', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_Nv6wYspV', 'name': 'FAR1-mut-87aa-TP', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_rzQGBzv2', 'name': 'pGP5G-ccdB', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_QuWMpfRK', 'name': 'pMODT4-pGAL1-attB1-GVNY', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_l5VHTc8Z', 'name': 'pGPU6-pGAL1-TIR1_DM', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_6VN5FDpP', 'name': 'pMODOK-pACT1-GAVN', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_2MFFshfl', 'name': 'pYMOD2Kmx_pGAL1-HYG_ZEV4-cassette', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_IyZI9bEh', 'name': 'pMODU6-pGAL1-FAR1-L1-IAA17T1_opt', 'folder': 'lib_pP6d50rJn1'}, {'id': 'seq_beOWphBv', 'name': 'pMODKan-HO-pACT1-ZEV4', 'folder': 'lib_pP6d50rJn1'}], 'type': 'ALL'}
+
+e.g. find all sequences that contain the word "CRY2" in the name
+
+::
+
+    benchlingapi.findSequence('CRY2', query='name', regex=True)
+
+e.g. find all sequences that with regular expression pattern
+
+::
+
+    benchlingapi.findSequence('\wcas9.+', query='name', regex=True)
+
+e.g. find all sequence with id 'seq\_aupKOZRb'
+
+::
+
+    benchlingapi.findSequence('seq_aupKOZRb', query='id', regex=False)
+
+e.g. find all folders that contain the word "CRY2" in the name
+
+::
+
+    benchlingapi.findFolder('CRY2', query='name', regex=True)
+
+e.g. get all folders
+
+::
+
+    benchlingapi.getFolderList()
+
+e.g. get all sequences
+
+::
+
+    benchlingapi.getSequenceList()
+
+e.g. get sequence from a share link
+
+::
+
+    benchlingapi.getSequenceFromShareLink('share_link')
+
+Create
+^^^^^^
+
+e.g. create a folder
+
+::
+
+    benchlingapi.createFolder('new_folder', description='this is a new folder', owner='ent_OMJXXX')
+
+e.g. create a sequence
+
+::
+
+    benchlingapi.createSequence(
+        'sequence name', #name
+        'agggggggtctgtagctgacttatcgtatgtgcgcga', #bases
+        True, #circular or not
+        'lib_0g4T1FJV', #folder_id
+        description='sequence description',
+        #annotations=[], #annotations are not currently supported in Benchling's api
+        )
+
+
+e.g. create a folder
+
+::
+
+    benchlingapi.createFolder('folder_Name', description='folder_description', 'owner'='ent_OMJXXX')
+
+Delete
+^^^^^^
+
+e.g. delete a folder
+
+::
+
+    benchlingapi.deleteFolder(folder_id)
+
+e.g. delete a sequence
+
+::
+
+    benchlingapi.deleteSequence(folder_id)
+
+Edit
+^^^^
+
+e.g. edit a folder
+
+::
+
+    benchlingapi.patchFolder(name=None, description=None, owner=None)
+
+e.g. edit a sequence
+
+::
+
+    benchlingapi.patchsequence(name=None, bases=None, circular=None,
+                      folder=None, description=None, color=None)
+
+BenchlingPortal
+---------------
+
+Not supported for non-aquarium users