Merge branch 'release-0.6'

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+## [0.6] - 2019-02-11
+### Changed
+- remove index from record tuple
+
 ## [0.5] - 2019-02-5
 ### Added
 - `func` argument to `parse` function.

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2016, Simone Marsili
+Copyright (c) 2019, Simone Marsili
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

lilbio/__init__.py

@@ -1,8 +1,6 @@
 # -*- coding: utf-8 -*-
-# Copyright (C) 2019, Simone Marsili
-# All rights reserved.
+# Author: Simone Marsili <[email protected]>
 # License: BSD 3 clause
-# Author: Simone Marsili ([email protected])
 """A little parser for alignments of biological sequences."""
 
 import time

lilbio/funcs.py

@@ -1,3 +1,6 @@
+# -*- coding: utf-8 -*-
+# Author: Simone Marsili <[email protected]>
+# License: BSD 3 clause
 """
 Functions of sequences. If a transformed version of the sequence is
 returned, it should be a list of symbols (not a string).

lilbio/parser.py

@@ -1,3 +1,6 @@
+# -*- coding: utf-8 -*-
+# Author: Simone Marsili <[email protected]>
+# License: BSD 3 clause
 """alignment parser"""
 import sys
 import logging
@@ -24,8 +27,8 @@ def parse(source, fmt, func=None):
 
     Yields
     ------
-    (index, header, seq) : tuple (int, str, str)
-        For each record, a tuple containing index, header and sequence.
+    (header, seq) : tuple (str, str)
+        For each record, a tuple containing header and sequence.
 
     """
     from collections import Iterable
@@ -48,12 +51,10 @@ def func(x):
     if not callable(func):
         raise TypeError('%s object is not callable' % type(func))
 
-    index = 0
     data = gopen.gread(source)
     parsed_data = bioparser(data)
     for title, seq in parsed_data:
-        yield index, title, func(seq)
-        index += 1
+        yield title, func(seq)
 
 
 def write(a, f=sys.stdout):
@@ -74,8 +75,8 @@ def main():
     fmt = args.format
 
     parsed_records = parse(filename, fmt)
-    for index, title, seq in parsed_records:
-        print('%s %s\n%s' % (title, index, seq))
+    for title, seq in parsed_records:
+        print('%s\n%s' % (title, seq))
 
 
 if __name__ == '__main__':

lilbio/utils.py

@@ -1,3 +1,6 @@
+# -*- coding: utf-8 -*-
+# Author: Simone Marsili <[email protected]>
+# License: BSD 3 clause
 """Utility functions."""
 
 import logging

tests/test_template.py

@@ -1,7 +1,7 @@
 import os
 import lilbio
 
-RECORDS = "[(0, 'VP54_CPSVP/90-227', '........LGTLKSITDKLRKLGGESSQPFIQFYKVQCMYIPLFSRVDGDNG......EITVSLIDDGKEAAGQDPIIQSITFDASQMAMVELSMNFFVEKKDMDFIGIHVSAENVPVQDRAYGSINLAFFTNEQSVPMMQEEKKSSYLMID..'), (1, 'Q6E6Y4_9VIRU/93-231', 'ttkvkitt-------MDKVTSLIKFEKFPFYRVDRLKILYIPLFSGENSEGK......NITFSIQDRSMVVAGKPKKISSATAPINKMSMIELSATYFVQSKDLSKIEFGYKAKGIPVSGRSFAAVYLAFYIHGDHFPATMRPKDPIVLLID..'), (2, 'A0A075IE34_9VIRU/105-247', '.iatmgrv-------VNLFKKATG-NEMPFVKFEKVQVMYIPLFQKTNEEDDpdkkipSMTVALVDKGQEEAGGDGIIQSITFRADEMALMELSMNFFVTRKDIEKIVVDACVDEIPVEGRAYGAMTIAFFVHEDYVPLRTELKPSTLMY--it')]"
+RECORDS = "[('VP54_CPSVP/90-227', '........LGTLKSITDKLRKLGGESSQPFIQFYKVQCMYIPLFSRVDGDNG......EITVSLIDDGKEAAGQDPIIQSITFDASQMAMVELSMNFFVEKKDMDFIGIHVSAENVPVQDRAYGSINLAFFTNEQSVPMMQEEKKSSYLMID..'), ('Q6E6Y4_9VIRU/93-231', 'ttkvkitt-------MDKVTSLIKFEKFPFYRVDRLKILYIPLFSGENSEGK......NITFSIQDRSMVVAGKPKKISSATAPINKMSMIELSATYFVQSKDLSKIEFGYKAKGIPVSGRSFAAVYLAFYIHGDHFPATMRPKDPIVLLID..'), ('A0A075IE34_9VIRU/105-247', '.iatmgrv-------VNLFKKATG-NEMPFVKFEKVQVMYIPLFQKTNEEDDpdkkipSMTVALVDKGQEEAGGDGIIQSITFRADEMALMELSMNFFVTRKDIEKIVVDACVDEIPVEGRAYGAMTIAFFVHEDYVPLRTELKPSTLMY--it')]"
 
 
 def tests_dir():

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py{27,35}
+envlist = py{35}
 
 [testenv]
 deps = -r{toxinidir}/requirements.txt

version.json

@@ -1,3 +1,3 @@
 {
-    "version": "0.5"
+    "version": "0.6"
 }