Question: DEXSeq error: erro in dexseq_count.py
0
gravatar for as1023
2.6 years ago by
as10230
as10230 wrote:

Hi,

  I am using DEXSeq package and I encountered some problem. First I used this comand "python dexseq_prepare_annotation.py -r no GRCh38.79.gtf GRCh38.79_DEXSeq.gff". the gff file looks below:

head GRCh38.79_DEXSeq.gtf
1    dexseq_prepare_annotation.py    aggregate_gene    11869    14409    .    +    .    gene_id "ENSG00000223972"
1    dexseq_prepare_annotation.py    exonic_part    11869    12009    .    +    .    transcripts "ENST00000456328"; exonic_part_number "001"; gene_id "ENSG00000223972"
1    dexseq_prepare_annotation.py    exonic_part    12010    12057    .    +    .    transcripts "ENST00000456328+ENST00000450305"; exonic_part_number "002"; gene_id "ENSG00000223972"
1    dexseq_prepare_annotation.py    exonic_part    12058    12178    .    +    .    transcripts "ENST00000456328"; exonic_part_number "003"; gene_id "ENSG00000223972"
1    dexseq_prepare_annotation.py    exonic_part    12179    12227    .    +    .    transcripts "ENST00000456328+ENST00000450305"; exonic_part_number "004"; gene_id "ENSG00000223972"


then I used

/script_human/pythonScripts/dexseq_count.py -p yes -f bam Aligned.noS.bam -r pos -s reverse GRCh38.79_DEXSeq.gff dexseq.txt

it gave me follwoing error

Traceback (most recent call last):
  File "/script_human/pythonScripts/dexseq_count.py", line 94, in <module>
    for f in  HTSeq.GFF_Reader( gff_file ):
  File "/home/asingh/.local/lib/python2.7/site-packages/HTSeq-0.6.1p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py", line 207, in __iter__
    strand, frame, attributeStr ) = line.split( "\t", 8 )   
ValueError: need more than 1 value to unpack

I also tried  below script was posted some days ago  to check gff file and it did not give any error, but when i run dexseq_count.py it shows error. At the moment I am using HTSeq-0.6.1p1 version.

import HTSeq
gff_file="GRCh38.79_DEXSeq.gff"

features = HTSeq.GenomicArrayOfSets( "auto", stranded=True )     
for f in  HTSeq.GFF_Reader( gff_file ):
   if f.type == "exonic_part":
      f.name = f.attr['gene_id'] + ":" + f.attr['exonic_part_number']
features[f.iv] += f

I generated bam file from star with sorted by position. Kindly give some suggestion.

Thanks!

As

 

 

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by as10230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 153 users visited in the last hour