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NDBL / HECIL

Hybrid Error Correction of Long Reads using Iterative Learning
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Fix output crash when the LR file is located outside of the HECIL dir #5

Closed morispi closed 5 years ago

morispi commented 5 years ago

Hi,

I found out that if the file containing the long reads to correct is not located in the HECIL directory, it causes the program to crash at the very end, when outputting the corrected long reads.

Here's what it looks like from the terminal:

python HECIL.py --LR /mnt/nfs/NGSData/longReads/ADP1/MWE.fasta --SR /mnt/nfs/NGSData/shortReads/NaS/ADP1/ADP1.fasta --length 250 --output corADP1.fasta
Started running alignment
[samopen] SAM header is present: 1 sequences.
-e Finished running alignment

[...]

-e Finished running correction

-e Generating output file with all (corrected and uncorrected) reads

Traceback (most recent call last):
  File "Create_Corrected_AllLRReads.py", line 15, in <module>
    fout=open(out,'w')
IOError: [Errno 2] No such file or directory: 'Corrected_/mnt/nfs/NGSData/longReads/ADP1/MWE.fasta'
-e Finished running HECIL

Adding a "Corrected_" prefix indeed is a bad idea when the LR file is provided from another directory. Adding a suffix instead, like so, solves the problem.

Best, Pierre

ochoudhu commented 5 years ago

Thanks for pointing this out. I have updated the script to generate an output file ending with '_Corrected.fasta'.