DEXSeq error: erro in dexseq_count.py
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as1023 • 0
@as1023-11442
Last seen 7.5 years ago

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

 

 

dexseq_count dexseq htseqcounts • 1.0k views
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