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smshuai / U1-snRNA

GNU General Public License v3.0
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pysam package version #3

Closed Gray-Tu closed 4 years ago

Gray-Tu commented 4 years ago

Hi smshuai,

I tried to run the mutation_call/analyze_multi_map.sh, but I get an error of pysam:

Traceback (most recent call last):
  File ".//bam2fq_for_realign.py", line 27, in <module>
    fq = pysam.fastq('-O', bam_tmp).split('\n')
AttributeError: module 'pysam' has no attribute 'fastq'

My python is 3.6.8 and the pysam version is 0.8.3. Could you tell me the version of pysam you used ?

smshuai commented 4 years ago

Hi Gary,

I think you need to upgrade the pysam. For example, version "0.15.3" has the function. Since this function is the same as samtools fastq, you may also need a compatible htslib library.

Best, Shimin

Gray-Tu commented 4 years ago

Hi smshuai, It work after updating the pysam package. Thank you for your rapid response.