Description
Original report by Rian Stockbower (Bitbucket: rianjs, GitHub: rianjs).
I feel like I'm missing something simple and obvious, but I can't get the Jiang2013 example to work. I'm not a Python developer, but I do have about a decade of professional experience as a software developer in other ecosystems, so I'm not totally ignorant.
This is what I did, starting from a fresh install of macOS:
- Install the xcode CLI tools (which gets you gcc without needing all 10GB of the xcode IDE): xcode-select --install
- Downloaded python 3.9.4 from https://www.python.org/downloads/mac-osx/ and installed it (This gets you pip3, too)
- I then installed presto: pip3 install presto --user which also grabbed the associated dependencies -- everything installed without errors.
I launched the python3 REPL, and quickly tested biopython, and had no problems. My test was fairly simple:
from Bio.Seq import Seq
my_seq = Seq("AGTACACTGGT")
print(my_seq)- After that, I imported presto, just to see if python3 could find it: import presto -- no problems. (Wasn't sure how to test it, though.)
- From there, I downloaded the Jiang sample, and tried to run the bash script, which errored out:
% ./ExamplePipeline_Jiang2013.sh
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
DIRECTORY: output
START
1: FilterSeq length 11:21 04/19/21
./ExamplePipeline_Jiang2013.sh: line 30: FilterSeq.py: command not found
2: FilterSeq quality 11:21 04/19/21
./ExamplePipeline_Jiang2013.sh: line 35: FilterSeq.py: command not found
3: MaskPrimers score 11:21 04/19/21
...etc...
Weird. MacOS did recently switch to zsh as the default shell, but it still has bash, not that it should matter given the script header. Nonethless, I launched bash, and tried running it again: same result.
So I went looking for FilterSeq.py, and the other files that are associated with pRESTO:
% ls /Users/rianjs/Library/Python/3.9/lib/python/site-packages/presto
total 344
-rw-r--r--@ 1 rianjs staff 24189 Jun 22 2020 Annotation.py
-rw-r--r--@ 1 rianjs staff 16014 Jul 15 2020 Applications.py
-rw-r--r--@ 1 rianjs staff 14310 Jun 22 2020 Commandline.py
-rw-r--r--@ 1 rianjs staff 1814 Jun 22 2020 Defaults.py
-rw-r--r--@ 1 rianjs staff 12264 Sep 27 2020 IO.py
-rw-r--r--@ 1 rianjs staff 23864 Jun 22 2020 Multiprocessing.py
-rw-r--r--@ 1 rianjs staff 66028 Sep 27 2020 Sequence.py
-rw-r--r--@ 1 rianjs staff 293 Oct 13 2020 Version.py
-rw-r--r-- 1 rianjs staff 259 Jun 22 2020 __init__.py
drwxr-xr-x 11 rianjs staff 352 Apr 19 10:21 __pycache__
I explored some of the subdirectories, and there was nothing that looked promising. (ls -la didn't show anything else.)
So I downloaded the raw tarball from pypi, and decompressed it. Poking around, I DO see FilterSeq.py, et al in the bin folder, which looks like the meat of pRESTO:
% ls ~/Downloads/presto-0.6.2/bin
total 600
-rwxr-xr-x@ 1 rianjs staff 20725 Sep 27 2020 AlignSets.py
-rwxr-xr-x@ 1 rianjs staff 24308 Jun 22 2020 AssemblePairs.py
-rwxr-xr-x@ 1 rianjs staff 24122 Jun 22 2020 BuildConsensus.py
-rwxr-xr-x@ 1 rianjs staff 28429 Jun 22 2020 ClusterSets.py
-rwxr-xr-x@ 1 rianjs staff 20407 Jun 22 2020 CollapseSeq.py
-rwxr-xr-x@ 1 rianjs staff 11328 Jun 22 2020 ConvertHeaders.py
-rwxr-xr-x@ 1 rianjs staff 36792 Jun 22 2020 EstimateError.py
-rwxr-xr-x@ 1 rianjs staff 12126 Jun 22 2020 FilterSeq.py
-rwxr-xr-x@ 1 rianjs staff 28060 Jun 22 2020 MaskPrimers.py
-rwxr-xr-x@ 1 rianjs staff 12157 Jun 22 2020 PairSeq.py
-rwxr-xr-x@ 1 rianjs staff 21913 Jun 22 2020 ParseHeaders.py
-rwxr-xr-x@ 1 rianjs staff 5419 Jun 22 2020 ParseLog.py
-rwxr-xr-x@ 1 rianjs staff 38028 Jun 22 2020 SplitSeq.py
-rwxr-xr-x@ 1 rianjs staff 7129 Jun 22 2020 UnifyHeaders.py
I went back to /Users/rianjs/Library/Python/3.9/lib/python/site-packages/presto, and there is NOTHING like that in there. I did a find, just to see, and nothing showed up:
rianjs@Galadriel: ~/Library/Python/3.9/lib/python
% find . -name "Filter*"
rianjs@Galadriel: ~/Library/Python/3.9/lib/python
% find . -name "Command*"
./site-packages/presto/Commandline.py
./site-packages/presto/__pycache__/Commandline.cpython-39.pyc
Is the macOS package broken in some way?