From 69255e061e6783e729d90026c2f65e458758a326 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Wed, 26 Apr 2017 10:38:10 +0200
Subject: [PATCH] MIN numpy and pandas are necessary too
Mention in README
Check before import
---
README.md | 4 ++--
metaSNV_post.py | 20 ++++++++++++++------
2 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index 0b0905a..dc76f79 100644
--- a/README.md
+++ b/README.md
@@ -40,14 +40,14 @@ universe repository before):
If you use [anaconda](https://www.continuum.io/downloads), you can create an
environment with all necessary dependencies using the following commands:
- conda create --name metaSNV boost htslib pkg-config
+ conda create --name metaSNV boost htslib pkg-config numpy pandas
source activate metaSNV
export CFLAGS=-I$CONDA_ENV_PATH/include
export LD_LIBRARY_PATH=$CONDA_ENV_PATH/lib:$LD_LIBRARY_PATH
If you do not have a C++ compiler, anaconda can also install G++:
- conda create --name metaSNV boost htslib pkg-config
+ conda create --name metaSNV boost htslib pkg-config numpy pandas
source activate metaSNV
# Add this command:
conda install gcc
diff --git a/metaSNV_post.py b/metaSNV_post.py
index 5317283..ccd1afc 100755
--- a/metaSNV_post.py
+++ b/metaSNV_post.py
@@ -1,12 +1,20 @@
#!/usr/bin/env python
-import os # interacting with operating system
-import sys # interact with system commandline
-import time # print current date/time
-import argparse # manage command line options and arguments
+import os
+import sys
+import time
+import argparse
import glob
-import numpy as np
-import pandas as pd
+try:
+ import numpy as np
+except ImportError:
+ sys.stderr.write("Numpy is necessary to run postfiltering.\n")
+ sys.exit(1)
+try:
+ import pandas as pd
+except ImportError:
+ sys.stderr.write("Pandas is necessary to run postfiltering.\n")
+ sys.exit(1)
basedir = os.path.dirname(os.path.abspath(__file__))
--
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