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On Thu, Nov 6, 2014 12:57 AM CET Cameron Simpson wrote:
>On 05Nov2014 14:05, jarod...@libero.it <jarod...@libero.it> wrote:
>> I need to use external program from my scirpt.
>> code = "intersectBed -a %s -b /database/Refseq_Gene2.bed -wa -wb|cut -f
>> 4,8|uniq > tmp.tmp1"%("gene5.tmp.bed")
>> code2 = "intersectBed -a %s -b /database/Refseq_Gene2.bed -wa -wb|cut -f
>> 4,8|uniq > tmp.tmp2"%("gene3.tmp.bed")
>> proc = []
>> p = subprocess.Popen(code,shell=True)
>> proc.append(p)
>> time.sleep(1) # seconds
>> p = subprocess.Popen(code2,shell=True)
>> proc.append(p)
>> time.sleep(1)
>> print
>> >sys.stderr,'-------------------------------------------------------------------------'
>> print >sys.stderr,"Waiting for Star Fusion Annotate to finish running..."
>> for p in proc:
>> p.communicate()
>
>First remark: as written above, your shell pipelines do not read any input and
>all their output goes to your temp files. Therefore using p.communicate() is a
>waste of time. Just use p.wait(); there is no I/O to do from the point of view
>of your Python code.
>
>Second remark: it is generally a bad idea to use Python's % operator to embed
>strings in shell commands (or other "parsed by someone else" text, such as
>SQL) because unless you are always very careful about the inserted string (eg
>"gene5.tmp.bed") you may insert punctuation, leading to bad behaviour. In your
>example code above you are sort of ok, and we can address this as a separate
>issue after you have things working.
>
>> What append I don't habve any error however the file are truncated.
>
>You need to find out why.
>
>The shell code _will_ truncate "tmp.tmp1", but then we expect the output of
>"uniq" to appear there.
>
>Start by stripping back the shell pipeline.
>
>If you remove the "|uniq", is there anything in "tmp.tmp1"?
>
>If there is not, strip off the "|cut -f 4,8" as well and check again. At that
>point we're asking: does intersectBed actually emit any output?
>
>You can test that on the command line directly, and then build up the shell
>pipeline to what you have above by hand. When working, _then_ put it into your
>Python program.
>
>> So I try to use subprocess.call
>>
>> p = subprocess.call(shlex.split(code),stdout = subprocess.PIPE, stderr =
>> subprocess.STDOUT, shell = False)
>> but with p.comunicate I have this error:
>>
>> ('\n***** ERROR: Unrecognized parameter: -wb|cut *****\n***** ERROR:
>> Unrecognized parameter: >
>[...]
>
>This is a standard mistake. shlex is _not_ a full shell syntax parser. It is
>a simple parser that understands basic shell string syntax (quotes etc) but
>NOT redirections. It is really a tool for using with your own minilanguages,
>as you might if you were writing an interactive program that accepts user
>commands.
>
>You can't use shlex for shell pipelines or shell redirections.
>
>What is happening above is that all the "words" are being gathered up and
>passed to the "intersectBed" command as arguments; no pipelines! And
>"intersectBed" complains bitterly as you show.
>
>You can see this in the example you post below:
>
>> shlex.split(code)
>> Out[102]:
>> ['intersectBed',
>> '-a',
>> 'gene5.tmp.bed',
>> '-b',
>> '/home/maurizio/database/Refseq_Gene2.bed',
>> '-wa',
>> '-wb|cut',
>> '-f',
>> '4,8|uniq',
>> '>',
>> 'tmp.tmp1']
>>
>> So what can I do? which system do you suggest to my Problem?
>
>First, forget about shlex. It does not do what you want.
>
>Then there are three approaches:
>
>1: Fix up your shell pipeline. You original code should essentially work:
>there is just something wrong with your pipeline. Strip it back until you can
>see the error.
>
>2: Construct the pipeline using Popen. This is complicated for someone new to
>Popen and subprocess. Essentially you would make each pipeline as 3 distinct
>Popen calls, using stdout=PIPE and attached that to the stdin of the next
>Popen.
Look for "connecting segments" on
http://pymotw.com/2/subprocess/
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