Question: find_circ - test data error
0
gravatar for harry
19 months ago by
harry10
harry10 wrote:

I use this command -------

/home/aclab/find_circ/unmapped2anchors.py /home/aclab/CircRNA/find_circ/unmapped/unmapped.bam | gzip >/home/aclab/CircRNA/find_circ/unmapped/anchors_unmapped.fastq.gz
I got this error-------
 File "/home/aclab/find_circ/unmapped2anchors.py", line 173
    print "@%s_A__%s" % (read.qname,seq)
                    ^
SyntaxError: invalid syntax

help me how to solve this problem

rna-seq • 571 views
ADD COMMENTlink modified 19 months ago by ATpoint44k • written 19 months ago by harry10

plz tell anyone about this as soon as possible. thanks

ADD REPLYlink written 19 months ago by harry10

Please read: Brief Reminder On How To Ask A Good Question and How To Ask Good Questions On Technical And Scientific Forums

ADD REPLYlink modified 19 months ago • written 19 months ago by Sej Modha4.7k
0
gravatar for ATpoint
19 months ago by
ATpoint44k
ATpoint44k wrote:

Do you have python2.7 running as default or python3? This tools need python2.7, see manual.

ADD COMMENTlink written 19 months ago by ATpoint44k

I convert it into 2.7 version but still same error occur. now i have 2.7.15+

ADD REPLYlink modified 19 months ago • written 19 months ago by harry10

I just checked on my machine. Using py3 it exactly produces that error while with py2 it doesn't. You have to remove the header line and put the your py2 executable like:

#!/path/to/your/py27/executable/python

ADD REPLYlink modified 19 months ago • written 19 months ago by ATpoint44k

I can convert default setting by alias python=python2.7 is it correct or not ,if not then you plz tell me how can i convert the python 3.7 to python2.7 version.

ADD REPLYlink written 19 months ago by harry10

If you have find_circ/unmapped2anchors.py script then please send me, if u change anything in that script. thanks

ADD REPLYlink written 19 months ago by harry10

Install python2. Please google for that. You can use anaconda to get an environment with python2.7

ADD REPLYlink written 19 months ago by ATpoint44k
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