TypeError: ord() expected string of length 1, but int found

Dear Chris,

thank you for reporting this issue. The bug due to the use of an old pysam function has been fixed.
A novel version is now available, 1.2.1

Best,
Ernesto

Il giorno 8 apr 2019, alle ore 18:28, ChrisAI chria-ai@users.sourceforge.net ha scritto:

[tickets:#12] https://sourceforge.net/p/reditools/tickets/12/ TypeError: ord() expected string of length 1, but int found

Status: New
Created: Mon Apr 08, 2019 04:28 PM UTC by ChrisAI
Last Updated: Mon Apr 08, 2019 04:28 PM UTC
Owner: nobody

Dear Ernesto,

I am using REDItools 1.2 (Pysam 0.10). Once I start REDItools, I run in the following error:

Pysam version used: 0.10.0
Script time --> START: 08/04/2019 17:46:50
Analysis ID: 502560955
Sorting GFF file.
Indexing GFF file.
Analysis on 1 regions.
Started analysis on region: 22:1-51304566
Loading known splice sites for region 22
Loaded 62525 positions for 22
Process Process-2:
Traceback (most recent call last):
File "/b06x/cluster/42.2/x86_64/easybuild/software/Python/2.7.12-foss-2017a/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/b06x/cluster/42.2/x86_64/easybuild/software/Python/2.7.12-foss-2017a/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(self._args, self._kwargs)
File "/icgc/dkfzlsdf/analysis/B060/aichmueller_pan_cancer/software/REDItools-1.2/reditools/REDItoolDnaRna.py", line 1175, in do_work
exploreBAM(x)
File "/icgc/dkfzlsdf/analysis/B060/aichmueller_pan_cancer/software/REDItools-1.2/reditools/REDItoolDnaRna.py", line 1119, in exploreBAM
seq,qual,squal=normByStrand(seq,strand,squal,mystrand)
File "/icgc/dkfzlsdf/analysis/B060/aichmueller_pan_cancer/software/REDItools-1.2/reditools/REDItoolDnaRna.py", line 621, in normByStrand
qual+=ord(squal_[i])-QVAL
TypeError: ord() expected string of length 1, but int found*
REDItools is called with:

python ${REDITOOL}/REDItoolDnaRna.py \
-i $OUT_PATH/rna.bam \
-j $OUT_PATH/dna.bam \
-f hs37d5_chr_22.fa \
-t 1 \
-o $OUT_PATH \
-c 10,10 \
-q 30,30 \
-m 30,255 \
-s 2 \
-X \
-S \
-u \
-U \
-C 10000000 \
-T $OUT_PATH/gff_chr22_sorted.gff3 \
-v 5 \
-V \
-r 5 \
-w gencode.v28lift37_chr22_splice_sites.ss 2> $OUT_PATH/${CHROM}_log.txt
I checked the source code for REDItoolDnaRna.py, but from the documentation and code, the occurrence of the error does not make sense to me.
Could you please have a look at my problem?

Thanks for the tool and your help!!!!!

Best wishes,
Chris

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Dear Ernesto,
I am using REDItools 1.2.1 (Pysam 0.15.2). Once I start REDItoolDnaRna.py, I also have the above problem, described as follows. I want to know what caused this error and how to fix it. Could you please have a look at this problem and help me out.
Thank you very much!
Best wishes,
Sijia

python /home/binfo/RNAediting/software/installpath/bin/REDItoolDnaRna.py -i rna.bam -j dna.bam -f reference.fa -o /home/binfo/RNAediting/sampledata/output/ -c 10,1 -q 25,25 -m 20,20 -s 2 -g 1 -u -a 6-0 -v 2 -n0.0 -N0.0 -V
Pysam version used: 0.15.2
Script time --> START: 30/07/2019 09:57:30
Analysis ID: 267705323
Analysis on 1 regions.
Started analysis on region: chr21:1-48129895
Process Process-1:
Traceback (most recent call last):
File "/home/binfo/anaconda3/envs/py27/lib/python2.7/multiprocessing/process.py", line 267, in bootstrap
self.run()
File "/home/binfo/anaconda3/envs/py27/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(self._args, *self._kwargs)
File "/home/binfo/RNAediting/software/installpath/bin/REDItoolDnaRna.py", line 1179, in do_work
exploreBAM(x)
File "/home/binfo/RNAediting/software/installpath/bin/REDItoolDnaRna.py", line 1123, in exploreBAM
seq,qual,squal=normByStrand(seq,strand,squal,mystrand)
File "/home/binfo/RNAediting/software/installpath/bin/REDItoolDnaRna.py", line 623, in normByStrand
if type(i)==int: qual+=ord(squal[str(i)])-QVAL
TypeError: list indices must be integers, not str
Merging Tables.
Results saved on /home/binfo/RNAediting/sampledata/output/DnaRna_267705323/outTable_267705323
Script time --> END: 30/07/2019 09:57:37