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POGzip problem,traceback and IOError: [Errno 2] No such file or directory
 

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  1. POGzip problem,traceback and IOError: [Errno 2] No such file or directory
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    <p>I'm new to python and bioinformatics field. I'm using python-2.6. Now I'm trying to select all fastq.gz files, then gzip.open(just a few lines because it's too huge and time-wasting), then count 'J' , then pick out those files with 'J' count NOT equal to 0.</p> <p>The following is my code:</p> <pre><code>#!/usr/bin/python import os,sys,re,gzip path = "/home/XXX/nearline" for file in os.listdir(path): if re.match('.*\.recal.fastq.gz', file): text = gzip.open(file,'r').readlines()[:10] word_list = text.split() number = word_list.count('J') + 1 if number !== 0: print file </code></pre> <p>But I got some errors:</p> <pre><code>Traceback (most recent call last): File "fastqfilter.py", line 9, in &lt;module&gt; text = gzip.open(file,'r').readlines()[:10] File "/share/lib/python2.6/gzip.py", line 33, in open return GzipFile(filename, mode, compresslevel) File "/share/lib/python2.6/gzip.py", line 79, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: 'ERR001268_1.recal.fastq.gz' </code></pre> <p>What's this traceback: File...... Is there anything wrong with gzip here? And why can't it find ERR001268_1.recal.fastq.gz? It's the first fastq file in the list, and DOES exist there.</p> <p>Hope give me some clues, and any point out any other errors in the script.</p> <p>THanks a lot.</p> <p>Edit: thx everyone. I followed Dan's suggestion. And I tried on ONE fastq file first. My script goes like:</p> <pre><code>#!/usr/bin/python import os,sys import gzip import itertools file = gzip.open('/home/xug/nearline/ERR001274_1.recal.fastq.gz','r') list(itertools.islice(file.xreadlines(),10)) word_list = list.split() number = word_list.count('J') + 1 if number != 0: print 'ERR001274_1.recal.fastq.gz' </code></pre> <p>Then errors are:</p> <pre><code>Traceback (most recent call last): File "try2.py", line 8, in &lt;module&gt; list(itertools.islice(text.xreadlines(),10)) AttributeError: GzipFiles instance has no attribute 'xreadlines' </code></pre> <p>Edit again: Thx Dan, I've solved the problem yesterday. Seems GzipFiles don't support xreadlines. So I tried the similar way as you suggested later. And it works. See below:</p> <pre><code>#!/usr/bin/python import os,sys,re import gzip from itertools import islice path = "/home/XXXX/nearline" for file in os.listdir(path): if re.match('.*\.recal.fastq.gz', file): fullpath = os.path.join(path, file) myfile = gzip.open(fullpath,'r') head = list(islice(myfile,1000)) word_str = ";".join(str(x) for x in head) number = word_str.count('J') if number != 0: print file </code></pre>
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    1. US有些吃饱了没事干的外国人对我们的事情指手画脚
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    1. COYou should either change cwd to path or pass path+filename to the function
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