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newgenome throws ValueError: invalid literal for int() with base 10 #11

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fog-bank opened this issue Jan 5, 2021 · 2 comments
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@fog-bank
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fog-bank commented Jan 5, 2021

Hello,

Thank you for developing GALA. I have a problem with newgenome as follows.

$ /media/Users/src/GALA/newgenome drafts.txt gathering
Traceback (most recent call last):
  File "/media/Users/src/GALA/newgenome", line 28, in <module>
    genomes(genomes=draft,gathering=gathering,gathering_name=name,outpath=output)
  File "/media/Users/src/GALA/src/new_genome.py", line 82, in genomes
    b=new_genome(cut_file=gathering+gathering_name+'_'+a+'_cuts.txt',old_genome=aa,out_path=outpath,name='new_'+a)
  File "/media/Users/src/GALA/src/new_genome.py", line 48, in new_genome
    i[base+'_'+str(h)+'_'+'awad']=e[base][int(g[j]):int(g[j+1])]
ValueError: invalid literal for int() with base 10: '6067162.0'

Single command mode throws a similar error.
The content of gathering/gathering_draft_01_cuts.txt:

scaffold0003	6067162.0	4	3	0
...
scaffold0016	1397294.3333333333	3	2	0

I edited the *_cuts.txt files as all float values were trucated to integer values:

scaffold0003	6067162	4	3	0
...
scaffold0016	1397294	3	2	0

Then newgenome exited successfully. However, will the final result be expected?

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@fog-bank
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fog-bank commented Jan 6, 2021

Sorry, I should use python2.
python2 newgenome
Thanks.

@fog-bank fog-bank closed this as completed Jan 6, 2021
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