[Biopython-dev] [Biopython] SeqIO.index improvement suggestions

[Peter]

On Wed, Feb 24, 2010 at 4:07 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
>
> After this I also looked into python3 (3.1.1) just in case they fixed it
> already and apparently they did. See for yourself:

You seem to be right, I tried this on Windows using Python 3.0.1 and 3.1.1,

C:\repositories\biopython_pjc\Tests>c:\python30\python
Python 3.0.1 (r301:69561, Feb 13 2009, 20:04:18) [MSC v.1500 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import gzip
>>> gzip.open("Quality\example.fastq.gz", "r").read()
b'@EAS54_6_R1_2_1_413_324\nCCCTTCTTGTCTTCAGCGTTTCTCC\n+\n;;3;;;;;;;;;;;;7;;;;;;;
88\n at EAS54_6_R1_2_1_540_792\nTTGGCAGGCCAAGGCCGATGGATCA\n+\n;;;;;;;;;;;7;;;;;-;;;
3;83\n at EAS54_6_R1_2_1_443_348\nGTTGCTTCTGGCGTGGGTGGGGGGG\n+\n;;;;;;;;;;;9;7;;.7;
393333\n'
>>> gzip.open("Quality\example.fastq.gz", "rb").read()
b'@EAS54_6_R1_2_1_413_324\nCCCTTCTTGTCTTCAGCGTTTCTCC\n+\n;;3;;;;;;;;;;;;7;;;;;;;
88\n at EAS54_6_R1_2_1_540_792\nTTGGCAGGCCAAGGCCGATGGATCA\n+\n;;;;;;;;;;;7;;;;;-;;;
3;83\n at EAS54_6_R1_2_1_443_348\nGTTGCTTCTGGCGTGGGTGGGGGGG\n+\n;;;;;;;;;;;9;7;;.7;
393333\n'
>>> gzip.open("Quality\example.fastq.gz", "rU").read()
b'@EAS54_6_R1_2_1_413_324\nCCCTTCTTGTCTTCAGCGTTTCTCC\n+\n;;3;;;;;;;;;;;;7;;;;;;;
88\n at EAS54_6_R1_2_1_540_792\nTTGGCAGGCCAAGGCCGATGGATCA\n+\n;;;;;;;;;;;7;;;;;-;;;
3;83\n at EAS54_6_R1_2_1_443_348\nGTTGCTTCTGGCGTGGGTGGGGGGG\n+\n;;;;;;;;;;;9;7;;.7;
393333\n'


C:\repositories\biopython_pjc\Tests>c:\python31\python
Python 3.1.1 (r311:74483, Aug 17 2009, 17:02:12) [MSC v.1500 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import gzip
>>> gzip.open("Quality\example.fastq.gz", "r").read()
b'@EAS54_6_R1_2_1_413_324\nCCCTTCTTGTCTTCAGCGTTTCTCC\n+\n;;3;;;;;;;;;;;;7;;;;;;;
88\n at EAS54_6_R1_2_1_540_792\nTTGGCAGGCCAAGGCCGATGGATCA\n+\n;;;;;;;;;;;7;;;;;-;;;
3;83\n at EAS54_6_R1_2_1_443_348\nGTTGCTTCTGGCGTGGGTGGGGGGG\n+\n;;;;;;;;;;;9;7;;.7;
393333\n'
>>> gzip.open("Quality\example.fastq.gz", "rb").read()
b'@EAS54_6_R1_2_1_413_324\nCCCTTCTTGTCTTCAGCGTTTCTCC\n+\n;;3;;;;;;;;;;;;7;;;;;;;
88\n at EAS54_6_R1_2_1_540_792\nTTGGCAGGCCAAGGCCGATGGATCA\n+\n;;;;;;;;;;;7;;;;;-;;;
3;83\n at EAS54_6_R1_2_1_443_348\nGTTGCTTCTGGCGTGGGTGGGGGGG\n+\n;;;;;;;;;;;9;7;;.7;
393333\n'
>>> gzip.open("Quality\example.fastq.gz", "rU").read()
b'@EAS54_6_R1_2_1_413_324\nCCCTTCTTGTCTTCAGCGTTTCTCC\n+\n;;3;;;;;;;;;;;;7;;;;;;;
88\n at EAS54_6_R1_2_1_540_792\nTTGGCAGGCCAAGGCCGATGGATCA\n+\n;;;;;;;;;;;7;;;;;-;;;
3;83\n at EAS54_6_R1_2_1_443_348\nGTTGCTTCTGGCGTGGGTGGGGGGG\n+\n;;;;;;;;;;;9;7;;.7;
393333\n'

So this does look like a Python 2.x bug which has been fixed in Python
3.x, and we should probably report this (after searching to see if it
is a known issue).

However, even if it is fixed in Python 2.6.x and 2.7.x, it won't get
fixed in older versions like Python 2.4 or 2.5.

Peter