search

aineniamh / snipit

snipit: summarise snps relative to your reference sequence
GNU General Public License v3.0
141 stars 28 forks source link

pip install snipit missing latest parameters displayed on github repo #10

Closed rebeelouise closed 2 years ago

rebeelouise commented 3 years ago

Love this tool - thank you so much for sharing it!

I installed this last week and noticed the latest parameters (e.g. below) aren't available or recognised when used!

  --flip-vertical       Flip the orientation of the plot so sequences are below the reference rather than above it.
  --include-positions INCLUDED_POSITIONS [INCLUDED_POSITIONS ...]
                        One or more range (closed, inclusive; one-indexed) or specific position only included in the output. Ex. '100-150' or Ex. '100 101' Considered before '--exclude-positions'.
  --exclude-positions EXCLUDED_POSITIONS [EXCLUDED_POSITIONS ...]
                        One or more range (closed, inclusive; one-indexed) or specific position to exclude in the output. Ex. '100-150' or Ex. '100 101' Considered after '--include-positions'.
  --exclude-ambig-pos   Exclude positions with ambig base in any sequences. Considered after '--include-positions'
  --sort-by-mutation-number
                        Render the graph with sequences sorted by the number of SNPs relative to the reference (fewest to most). Default: False
  --high-to-low         If sorted by mutation number is selected, show the sequences with the fewest SNPs closest to the reference. Default: False
matt-sd-watson commented 3 years ago

Hey Rebee,

You should be able to install it from source with the following commands: git clone https://github.com/aineniamh/snipit.git cd snipit pip install .

And get the latest changes to the repo in this way.

rebeelouise commented 3 years ago

Hi Matt :)

Just tried this and got the below error:

`Processing /home/hlrpenri/tools/snipit
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
Requirement already satisfied: biopython>=1.70 in /home/hlrpenri/miniconda3/lib/python3.9/site-packages (from snipit==1.0.3) (1.79)
Requirement already satisfied: matplotlib>=3.2.1 in /home/hlrpenri/miniconda3/lib/python3.9/site-packages (from snipit==1.0.3) (3.4.3)
ERROR: Could not install packages due to an OSError: [Errno 2] No such file or directory: '/home/hlrpenri/miniconda3/lib/python3.9/site-packages/biopython-1.79.dist-info/METADATA'`

Will look at these errors later myself when I get a chance - but dropping them here first just incase you know how to solve :)

corneliusroemer commented 2 years ago

Had the same issue. Would be nice if the version on pypa was identical with the one here on Github

aineniamh commented 2 years ago

Pypi release has been updated now!