About ImportError: No module named vcf.parser

[JeonHyungJin]

Hello, i cloned this project and want to use. when i run this program the result became like this

Traceback (most recent call last):
File "gtc_to_vcf.py", line 10, in <module>
from vcf.parser import Writer, Reader
ImportError: No module named vcf.parser

I used python 2.7, anaconda, pycharm and i installed

conda install -c anaconda numpy=1.11.2
conda install -c bioconda pyvcf=0.6.8
conda install -c bioconda pysam=0.9.0

all these things.

and when i just run 'gtc_to_vcf.py' at pycharm the result came like this

usage: gtc_to_vcf.py [-h] [--gtc-paths GTC_PATHS [GTC_PATHS ...]]
                     --manifest-file MANIFEST_FILE --genome-fasta-file
                     GENOME_FASTA_FILE [--output-vcf-path OUTPUT_VCF_PATH]
                     [--skip-indels] [--log-file LOG_FILE]
                     [--expand-identifiers] [--unsquash-duplicates]
                     [--auxiliary-loci AUXILIARY_LOCI]
                     [--filter-loci FILTER_LOCI] [--disable-genome-cache]
                     [--version]
gtc_to_vcf.py: error: argument --manifest-file is required

So i thought that VCF module has installed well. but when i run such as

python gtc_to_vcf.py args~~~~~~

the error came out. Can i get some help?

[hhg7]

I have this issue too, how did you solve this problem?

[jjzieve]

@hhg7 Did you get this error: ImportError: No module named vcf.parser or the gtc_to_vcf.py: error: argument --manifest-file is required error?

[hhg7]

@jjzieve I got the ImportError problem

[jjzieve]

@hhg7 You followed the conda install recommendations? i.e. as outlined here: https://github.com/Illumina/GTCtoVCF#requirements

[hhg7]

@jjzieve the environment setup on the server that I'm using is extremely complex, a coworker of mine fixed the problem. Thanks for your help though