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Old 09-07-2011, 12:55 PM   #1
shilez
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Default DEXSeq python script error message

When I try to run dexseq_prepare_annotation.py, I got a python error at line 29:
exons[f.iv] += ( f.attr['gene_id'], f.attr['transcript_id'] )
TypeError: unsupported operand type(s) for +=: 'StepVector' and 'tuple'
Anyone has any idea how to fix it?
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Old 09-07-2011, 11:18 PM   #2
Jane M
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I have no idea, but I managed to run this script, so there is no error in it. Nevertheless, if I remeber well, a certain version of python is needed...
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Old 09-08-2011, 05:27 AM   #3
Simon Anders
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Could it be that you have an outdated version of HTSeq installed?
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Old 09-08-2011, 10:42 AM   #4
shilez
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Thank you, guys.
Once I update the HTSeq, it works fine.
However, I do got the error message "Same name found on two chromosomes".
Does it mean we need to remove the duplicated genes from the annotation gtf file first before running dexseq_prepare_annotation.py?

*and also an error from HTSeq
ValueError: start is larger than end

Last edited by shilez; 09-08-2011 at 10:57 AM.
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Old 09-08-2011, 10:55 PM   #5
areyes
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The first error can be solved by adding an additional ID tag to these genes. (e.g. if the gene is called A, you could write A_dup1 and A_dup2 foreach one so that the gene names become unique). They are usually not to many in the annotation files. (I have done it manually for the ensembl mouse gtf annotation).

The second I have also seen it, for some genes, the start value is higher to the end value. I guess this is a mistake in the gtf files. Can be corrected just by shifting the columns in this cases. Also, there are usually not to many.
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