fixed tar/gtar problem with MacOS, added OS detection

Author: Psy-Fer

Diff for: README.md

@@ -6,7 +6,6 @@
 
 **fast5_fetcher** is a tool for fetching nanopore fast5 files to save time and simplify downstream analysis.
 
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1413903.svg)](https://doi.org/10.5281/zenodo.1413903)
 
 ## Contents
@@ -21,9 +20,11 @@ Reducing the number of fast5 files per folder in a single experiment was a welco
 
 Following a self imposed guideline, most things written to handle nanopore data or bioinformatics in general, will use as little 3rd party libraries as possible, aiming for only core libraries, or have all included files in the package.
 
-In the case of `fast5_fetcher.py` and `batch_tater.py`, only core python libraries are used. So as long as **Python 2.7+** is present, everything should work with no extra steps. (Python 3 compatibility is coming in the next update)
+In the case of `fast5_fetcher.py` and `batch_tater.py`, only core python libraries are used. So as long as **Python 2.7+** is present, everything should work with no extra steps. (Python 3 compatibility is coming in the next big update)
+
+##### Operating system:
 
-There is one catch. Everything is written primarily for use with **Linux**. Due to **MacOS** running on Unix, so long as the GNU tools are installed, there should be minimal issues running it. **Windows 10** however may require more massaging to work with the new Linux integration.
+There is one catch. Everything is written primarily for use with **Linux**. Due to **MacOS** running on Unix, so long as the GNU tools are installed (see below), there should be minimal issues running it. **Windows 10** however may require more massaging to work with the new Linux integration.
 
 # Getting Started
 
@@ -187,6 +188,14 @@ Download the repository:
 
     git clone https://github.com/Psy-Fer/fast5_fetcher.git
 
+If using MacOS, and NOT using homebrew, install it here:
+
+    https://brew.sh/
+
+then install gnu-tar with:
+
+    brew install gnu-tar
+
 ### Quick start
 
 Basic use on a local computer
@@ -355,13 +364,13 @@ echo $CMD && $CMD
 
 ## Acknowledgements
 
-I would like to thank the rest of my lab (Shaun Carswell, Kirston Barton) in Genomic Technologies team from the [Garvan Institute](https://www.garvan.org.au/) for their feedback on the development of this tool.
+I would like to thank the rest of my lab (Shaun Carswell, Kirston Barton, Kai Martin) in Genomic Technologies team from the [Garvan Institute](https://www.garvan.org.au/) for their feedback on the development of this tool.
 
 ## Cite
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1413903.svg)](https://doi.org/10.5281/zenodo.1413903)
 
-James M. Ferguson, & Martin A. Smith. (2018, September 12). Psy-Fer/fast5_fetcher: Initial release of fast5_fetcher (Version v1.0). Zenodo. http://doi.org/10.5281/zenodo.1413903
+James M. Ferguson, & Martin A. Smith. (2018, September 12). Psy-Fer/fast5_fetcher: Initial release of fast5_fetcher (Version v1.0). Zenodo. <http://doi.org/10.5281/zenodo.1413903>
 
 ## License
 

Diff for: fast5_fetcher.py

@@ -5,6 +5,7 @@
 import subprocess
 import traceback
 import argparse
+import platform
 from functools import partial
 '''
 
@@ -17,17 +18,17 @@
     It takes 3 files as input: fastq/paf/flat, sequencing_summary, index
 
     --------------------------------------------------------------------------------------
-    version 0.0 - initial
-    version 0.2 - added argparser and buffered gz streams
-    version 0.3 - added paf input
-    version 0.4 - added read id flat file input
-    version 0.5 - pppp print output instead of extracting
-    version 0.6 - did a dumb. changed x in s to set/dic entries O(n) vs O(1)
-    version 0.7 - cleaned up a bit to share and removed some hot and steamy features
-    version 0.8 - Added functionality for un-tarred file structures and seq_sum only
-    version 1.0 - First release
-    version 1.1 - refactor with dicswitch and batch_tater updates
-
+    version 0.0   - initial
+    version 0.2   - added argparser and buffered gz streams
+    version 0.3   - added paf input
+    version 0.4   - added read id flat file input
+    version 0.5   - pppp print output instead of extracting
+    version 0.6   - did a dumb. changed x in s to set/dic entries O(n) vs O(1)
+    version 0.7   - cleaned up a bit to share and removed some hot and steamy features
+    version 0.8   - Added functionality for un-tarred file structures and seq_sum only
+    version 1.0   - First release
+    version 1.1   - refactor with dicswitch and batch_tater updates
+    version 1.1.1 - Bug fix on --transform method, added OS detection
 
     TODO:
         - Python 3 compatibility
@@ -82,8 +83,8 @@ def main():
                        help="paf alignment file for read ids")
     group.add_argument("-f", "--flat",
                        help="flat file of read ids")
-    # parser.add_argument("-b", "--fast5",
-    #                    help="fast5.tar path to extract from - individual")
+    parser.add_argument("--OSystem", default=platform.system(),
+                        help="running operating system - leave default unless doing odd stuff")
     parser.add_argument("-s", "--seq_sum",
                         help="sequencing_summary.txt.gz file")
     parser.add_argument("-i", "--index",
@@ -128,7 +129,7 @@ def main():
             continue
         else:
             try:
-                extract_file(p, f, args.output)
+                extract_file(args, p, f)
             except:
                 traceback.print_exc()
                 print >> sys.stderr, "Failed to extract:", p, f
@@ -312,17 +313,32 @@ def get_paths(index_file, filenames, f5=None):
     return paths
 
 
-def extract_file(path, filename, save_path):
+def extract_file(args, path, filename):
     '''
     Do the extraction.
     I was using the tarfile python lib, but honestly, it sucks and was too volatile.
     if you have a better suggestion, let me know :)
-    That --transform hack is awesome btw. Blows away all the leading folders. use it
+    That --transform hack is awesome btw. Blows away all the leading folders. use
     cp for when using untarred structures. Not recommended, but here for completeness.
+
+    --transform not working on MacOS. Need to use gtar
+    Thanks to Kai Martin for picking that one up!
+
     '''
+    OSystem = ""
+    OSystem = args.OSystem
+    save_path = args.output
     if path.endswith('.tar'):
-        cmd = "tar -xf {} --transform='s/.*\///' -C {} {}".format(
-            path, save_path, filename)
+        if OSystem in ["Linux", "Windows"]:
+            cmd = "tar -xf {} --transform='s/.*\///' -C {} {}".format(
+                path, save_path, filename)
+        elif OSystem == "Darwin":
+            cmd = "gtar -xf {} --transform='s/.*\///' -C {} {}".format(
+                path, save_path, filename)
+        else:
+            print >> sys.stderr, "Unsupported OSystem, trying Tar anyway, OS:", OSystem
+            cmd = "tar -xf {} --transform='s/.*\///' -C {} {}".format(
+                path, save_path, filename)
     else:
         cmd = "cp {} {}".format(filename, os.path.join(
             save_path, filename.split('/')[-1]))