errors while using python dexseq_prepare_annotation.py

[greener]

Hi there, I am trying to use the dexseq_prepare_annotation.py tool in DEXseq and have tried several different gtf files but they all seem to get the same error. Not sure what could be causing this (below). Python version maybe? Any suggestions folks have are appreciated. Thanks -Rich

python dexseq_prepare_annotation.py test.gtf

Traceback (most recent call last):
File "dexseq_prepare_annotation.py", line 25, in ?
for f in HTSeq.GFF_Reader( gtf_file ):
File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.3p3-py2.4-linux-x86_64.egg/HTSeq/__init__.py", line 204, in __iter__
for line in FileOrSequence.__iter__( self ):
File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.3p3-py2.4-linux-x86_64.egg/HTSeq/__init__.py", line 42, in __iter__
if self.fos.lower().endswith( ( ".gz" , ".gzip" ) ):
TypeError: expected a character buffer object

[areyes]

Hi greener,

I am not sure, but I think the problem is that you did not specify an output file:

Usage: python dexseq_prepare_annotation.py <in.gtf> <out.gff>

Alejandro

[greener]

Thanks areyes, Yes I did try it with an out file. still get the same error

[areyes]

hmm strange. could you show the first lines of your gtf file?

[greener]

here is one

[greener@kojak bowtie]$ head -n 10 /vol01/genome/mouse/ucsc/annotation/mm9_ucsc_refGene.txt.gtf2.2
chr1 ucsc exon 134212701 134213049 . + 0 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134221529 134221650 . + 0 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134224273 134224425 . + 1 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134224707 134224773 . + 0 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134226534 134226654 . + 0 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134227135 134227268 . + 0 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134227897 134230065 . + 1 gene_id "NM_028778:134212701"; transcript_id "NM_028778:134212701";
chr1 ucsc exon 134212701 134213049 . + 0 gene_id "NM_001195025:134212701"; transcript_id "NM_001195025:134212701";
chr1 ucsc exon 134221529 134221650 . + 0 gene_id "NM_001195025:134212701"; transcript_id "NM_001195025:134212701";
chr1 ucsc exon 134222782 134222806 . + 1 gene_id "NM_001195025:134212701"; transcript_id "NM_001195025:134212701";

[fadista]

I got the same error message here. Did you find any solutions?

Thanks.

[areyes]

I just noticed we never answer this message, an apology for that.

Could you try to update python (to at least 2.5 ) and HTSeq to the most recent?
I was unable to reproduce the error, I think this might solve it. Let me know if not.

Alejandro

[senkewiczs]

Hi areyes,

I'm also getting an error message when trying to use the dexseq_prepare_annotation.py. I'm trying to use it on the gtf file for drosophila from http://useast.ensembl.org/info/data/ftp/index.html.

$python dexseq_prepare_annotation.py Drosophila_melanogaster.BDGP5.67.gtf Drosophila_melanogaster.BDGP5.67.gff

The error message I receive is:
Traceback (most recent call last):
File "dexseq_prepare_annotation.py", line 89, in <module>
assert l[i].iv.end <= l[i+1].iv.start, str(l[i+1]) + " starts too early"
AssertionError: <GenomicFeature: exonic_part 'FBgn0261841+FBgn0261840+FBgn0261837+FBgn0261843+FBgn0261845+FBgn0261844+FBgn0261838+FBgn0261839+FBgn0002781+FBgn0261842' at 3R: 17178958 -> 17178091 (strand '-')> starts too early

We've used dexseq_prepare_annotation.py on gtf files from other species and it has always worked great. Seems strange since the pasilla package in R uses drosophila as the example dataset.

Here is the head of the drosophila gtf file:

3R protein_coding exon 380 509 . + . gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "1"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB";
3R protein_coding exon 578 1913 . + . gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "2"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB";
3R protein_coding CDS 1115 1913 . + 0 gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "2"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB"; protein_id "FBpp0078601";
3R protein_coding start_codon 1115 1117 . + 0 gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "2"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB";
3R protein_coding exon 7784 8649 . + . gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "3"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB";
3R protein_coding CDS 7784 8649 . + 2 gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "3"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB"; protein_id "FBpp0078601";
3R protein_coding exon 9439 10200 . + . gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "4"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB";
3R protein_coding CDS 9439 9768 . + 0 gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "4"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB"; protein_id "FBpp0078601";
3R protein_coding stop_codon 9769 9771 . + 0 gene_id "FBgn0037213"; transcript_id "FBtr0078961"; exon_number "4"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RB";
3R protein_coding exon 380 1913 . + . gene_id "FBgn0037213"; transcript_id "FBtr0078962"; exon_number "1"; gene_name "CG12581"; gene_biotype "protein_coding"; transcript_name "CG12581-RA";


Any thoughts? Thanks in advance

[areyes]

I give a look into that annotation file, the annotation of the gene mod(mdg4) seems to have some problems, I just removed it:

grep -v "mod(mdg4)" Drosophila_melanogaster.BDGP5.67.gtf > Drosophila_melanogaster.BDGP5.67.filtered.gtf

And the DEXSeq error goes away!

[senkewiczs]

Thanks areyes! Helpful as always!

[Ajayi Oyeyemi]

Hi everyone,
I've been trying to use the dexseq_prepare_annotation.py script but I kept on getting error. Please see the code below.

imumorin@ansci253135199:~/myrnaseqexp$ python dexseq_prepare_annotation.py Drosophila_melanogaster.BDGP5.70.gtf Drosophila_melanogaster.BDGP5.70.gff
File "dexseq_prepare_annotation.py", line 4
<!DOCTYPE html>
^
SyntaxError: invalid syntax

I got the script from this page https://github.com/olgabot/rna-seq-d..._annotation.py and I used the wget command. Can someone please help me?

[Ajayi Oyeyemi]

I was suspecting that it was incorrectly installed since I searched the package but couldn't get the script out. See a part of my ls -al for the script:

-rw-rw-r-- 1 imumorin imumorin 55209 2013-02-22 15:24 dexseq_prepare_annotation.py

Any clue?

[Simon Anders]

Well, a Python file is not supposed to contain a Doctype tag. You downloaded the HTML source of the page displaying the code of the Python script, not the script itself.

Why did you download it separately from the DEXSeq package at all?

Use the R command system.file( package="DEXSeq" ) to see which directory R has installed DEXSeq in. There you will find a sub-directory python-scripts containing the correct file.

[Ajayi Oyeyemi]

Well, a Python file is not supposed to contain a Doctype tag. You downloaded the HTML source of the page displaying the code of the Python script, not the script itself.

Why did you download it separately from the DEXSeq package at all?

Use the R command system.file( package="DEXSeq" ) to see which directory R has installed DEXSeq in. There you will find a sub-directory python-scripts containing the correct file.

Thanks Simon. I followed your que and it worked for version 2.15. I'm using ubuntu linux and I tried to upgrade it to version 2.15.2 but it appears I couldn't figure it out. Is there anyone that knows how I can upgrade the R version 2.13 in ubuntu linux to 2.15.2?
Any help will be greatly appreciated.

Thanks Simon once again...

[Simon Anders]

The R version included in Canonical's official Ubuntu package repository is always a bit old. If you add the package repository from CRAN to your package sources, you can always get the newest version.

See here for details: http://cran.r-project.org/bin/linux/ubuntu/README