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possible problem in DataWriter #9

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diekhans opened this issue Jun 11, 2022 · 0 comments
Open

possible problem in DataWriter #9

diekhans opened this issue Jun 11, 2022 · 0 comments
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@diekhans
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In [/primersjuju/genome_data.py}(https://github.com/diekhans/PrimerS-JuJu/blob/main/lib/primersjuju/genome_data.py
)

DataWriter in the below code work on MacOS but not Linux

# FIXME:
 # stdin=pipettor.DataWriter('\n'.join(names) + '\n')
 # for some reason work on MacOS, but not Linux
 transcript_beds = {}

 tmpNamesFile = fileOps.tmpFileGet()
 fileOps.writeLines(tmpNamesFile, names)
 with pipettor.Popen(['bigBedNamedItems', '-nameFile', bigbed, tmpNamesFile, '/dev/stdout'],
                     stdin=tmpNamesFile) as fh:
     for b in BedReader(fh):
         transcript_beds[b.name] = b
 os.unlink(tmpNamesFile)

@diekhans diekhans added the bug label Oct 12, 2023
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