wdecoster / fastqmetrics Goto Github PK
View Code? Open in Web Editor NEWExtract metrics from a fastq file, streaming
License: MIT License
Extract metrics from a fastq file, streaming
License: MIT License
On Python 3.6
, OS X 10.12.3
after running
pip3 install fastqmetrics
Collecting fastqmetrics
Downloading fastqmetrics-0.1.0.tar.gz
Collecting nanoget>=0.14.0 (from fastqmetrics)
Downloading nanoget-0.14.0.tar.gz
Requirement already satisfied: pandas in /usr/local/lib/python3.6/site-packages (from nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: numpy in /usr/local/lib/python3.6/site-packages (from nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: biopython in /usr/local/lib/python3.6/site-packages (from nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: pysam>0.10.0.0 in /usr/local/lib/python3.6/site-packages (from nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: nanomath in /usr/local/lib/python3.6/site-packages (from nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: pytz>=2011k in /usr/local/lib/python3.6/site-packages (from pandas->nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: python-dateutil>=2 in /usr/local/lib/python3.6/site-packages (from pandas->nanoget>=0.14.0->fastqmetrics)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.6/site-packages (from python-dateutil>=2->pandas->nanoget>=0.14.0->fastqmetrics)
Building wheels for collected packages: fastqmetrics, nanoget
Running setup.py bdist_wheel for fastqmetrics ... done
Stored in directory: /Users/username/Library/Caches/pip/wheels/5f/dc/83/88496d60b9a41ff9735641f32abe35bb4959f62a15fb292001
Running setup.py bdist_wheel for nanoget ... done
Stored in directory: /Users/username/Library/Caches/pip/wheels/fa/83/3a/68d4da094ce7e51c7fab77f87becd310f79b9f63a55627cf04
Successfully built fastqmetrics nanoget
Installing collected packages: nanoget, fastqmetrics
Found existing installation: nanoget 0.13.1
Uninstalling nanoget-0.13.1:
Successfully uninstalled nanoget-0.13.1
Successfully installed fastqmetrics-0.1.0 nanoget-0.14.0
The attempting to run the tool, with
fastqmetrics --threads 2 ../demultiplexed_run1/data/BC10.fastq
Traceback (most recent call last):
File "/usr/local/bin/fastqmetrics", line 7, in <module>
from fastqmetrics.fastqmetrics import main
File "/usr/local/lib/python3.6/site-packages/fastqmetrics/fastqmetrics.py", line 1, in <module>
from nanoget import stream_fastq_full
ImportError: cannot import name 'stream_fastq_full'
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