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POsh: -c: line 1: syntax error near unexpected token `;'
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copied!<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)) > 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>

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