Question: find_circ - test data error
0
gravatar for harry
6 weeks ago by
harry0
harry0 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 • 167 views
ADD COMMENTlink modified 6 weeks ago by ATpoint21k • written 6 weeks ago by harry0

plz tell anyone about this as soon as possible. thanks

ADD REPLYlink written 6 weeks ago by harry0

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 6 weeks ago • written 6 weeks ago by Sej Modha4.3k
0
gravatar for ATpoint
6 weeks ago by
ATpoint21k
Germany
ATpoint21k wrote:

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

ADD COMMENTlink written 6 weeks ago by ATpoint21k

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by harry0

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 6 weeks ago • written 6 weeks ago by ATpoint21k

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 6 weeks ago by harry0

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

ADD REPLYlink written 6 weeks ago by harry0

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

ADD REPLYlink written 6 weeks ago by ATpoint21k
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