sh: -c: line 1: syntax error near unexpected token `;'
<p>I'm testing on my python script:</p>

<pre><code>#!/usr/bin/python

import os,sys
import glob
import commands
import gzip
from itertools import islice

f1=gzip.open("/home/xug/scratch/test_trim.fastq","w")
LIST=[]
N = 4
with open("/home/xug/scratch/test.fastq", "r") as f:
    while True:
        line_group = list(islice(f, N))
        if not line_group:
            break
        l3=line_group[3].rstrip()
        l3_trim=commands.getoutput("sed 's/\(.\)B*$/\1/g'" + l3)
        #l3_to = subprocess.Popen(["sed 's/\(.\)B*$/\1/g'",l3],
                                  #stdout=subprocess.PIPE,bufsize=1)
        #l3_trim=l3_to.stdout
        if ( float(len(l3_trim))/float(len(l3)) &gt; 0.70 ):
               LIST.append(line_group[0])
               LIST.append(line_group[1][:int(len(l3_trim))])
               LIST.append(line_group[2])
               LIST.append(l3_trim)

    output=f1.writelines(LIST)
</code></pre>

<p>However I got errors like:</p>

<pre><code>sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
</code></pre>

<p>Eventually to put an end to the while loop....</p>
