Question

having trouble with dexseq_prepare_annotation.py

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vakul.mohanty ▴ 10

@vakulmohanty-8232

Last seen 6.8 years ago

United States

I'm running dexseq_prepare_annotation.py on ENSEMBL GTF (I have tried gtf files from a couple of releases) files and have the following error.

File "dexseq_prepare_annotation.p", line 129

raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) )

SyntaxError: invalid syntax

<font face="monospace">I'm not particularly familiar with python and will be grateful for any pointers on how to deal with this problem.</font>

Thanking You,

Vakul

dexseq gtf • 2.2k views

ADD COMMENT • link updated 8.4 years ago by Alejandro Reyes ★ 1.9k • written 8.4 years ago by vakul.mohanty ▴ 10

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Hi,

I changed the script to:

raise ValueError ("Same name found on two chromosomes: %s, %s") % ( str(l[i]), str(l[i+1]) )

and it did the trick in my case (at least for this particular syntax error). I would guess that this is a python 2/python 3 issue. I hope that I made a good choice :D

ADD REPLY • link 6.2 years ago swiatowid2002 ▴ 10

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worked for me too, thx & dzięki! To adapt to python3, you need also replace xrange with range around those lines.

ADD REPLY • link 5.2 years ago michal.okoniewski ▴ 10

score 1 · Answer 1 · 2015-11-12

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Alejandro Reyes ★ 1.9k

@alejandro-reyes-5124

Last seen 20 hours ago

Novartis Institutes for BioMedical Rese…

Hi Vakul,

The error message is indicating that the same gene id was found in two different chromosomes. Did you check if this was the case in your gtf file?

Alejandro

ADD COMMENT • link 8.4 years ago Alejandro Reyes ★ 1.9k

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Hi Alejandro,

I look up the GTF file it had no repeats. I however got the script to work when I switched platforms from windows to linux. Thanks you for the help.

Vakul

ADD REPLY • link 8.4 years ago vakul.mohanty ▴ 10