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swarris / pyPaSWAS

Program for DNA/RNA/protein sequence alignment, read mapping and trimming. Extended python version of PaSWAS, supporting OpenCL and CUDA devices.
MIT License
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Error in script: 'Seq' object has no attribute 'alphabet' #11

Closed chan-98 closed 1 year ago

chan-98 commented 1 year ago

I ran this command after installing Biopython. Since the pypaswas.py was not executable, this is the command I ran:

python3 pyPaSWAS/pypaswas.py SO_11372_E13_NPC_UT_6_hr_070922_R1.fastq SO_11372_E13_NPC_UT_6_hr_070922_R2.fastq -1 fastq -2 fastq

Error:

Traceback (most recent call last): File "/home/ctprouser/aligner_tool/pyPaSWAS/pypaswas.py", line 11, in ppw.run() File "/home/ctprouser/aligner_tool/pyPaSWAS/pyPaSWAS/pypaswasall.py", line 207, in run query_sequences = self._get_query_sequences(self.arguments[0], start=query_start, end=query_end) File "/home/ctprouser/aligner_tool/pyPaSWAS/pyPaSWAS/pypaswasall.py", line 104, in _get_query_sequences reader.read_records(start,end) File "/home/ctprouser/aligner_tool/pyPaSWAS/pyPaSWAS/Core/Readers.py", line 105, in read_records self.records = [SWSeqRecord(Seq(str(record.seq), record.seq.alphabet), File "/home/ctprouser/aligner_tool/pyPaSWAS/pyPaSWAS/Core/Readers.py", line 105, in self.records = [SWSeqRecord(Seq(str(record.seq), record.seq.alphabet), AttributeError: 'Seq' object has no attribute 'alphabet'

I am not much of a programmer. Please debug and tell me what needs to be done to fix it?

nik875 commented 1 year ago

Should be fixed after the latest commit to master branch.

swarris commented 1 year ago

Indeed, should be fixed now