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Author: Andreas Tille <tille@debian.org>
Bug-Debian: https://bugs.debian.org/931784
https://bugs.debian.org/937105
Bug-Upstream: https://github.com/jts/nanopolish/issues/626
Last-Update: Wed, 11 Dec 2019 15:02:32 +0100
Description: Fix some remaining interpreter names from python to python3
--- a/scripts/dropmodel.py
+++ b/scripts/dropmodel.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#! /usr/bin/python3
# Generate a new model with a lower k-mer size than the input model
import sys
--- a/scripts/import_ont_models_from_dir.sh
+++ b/scripts/import_ont_models_from_dir.sh
@@ -4,12 +4,12 @@
for i in `ls $DIR`; do
echo "Processing", $DIR/$i
- python scripts/import_ont_model.py -i $DIR/$i -o etc/r9-models/ > new_files.txt
+ python3 scripts/import_ont_model.py -i $DIR/$i -o etc/r9-models/ > new_files.txt
done
for i in `cat new_files.txt`; do
echo "Dropping", $i
- python scripts/dropmodel.py -i $i
+ python3 scripts/dropmodel.py -i $i
done
rm new_files.txt
--- a/scripts/polya_training/hmmplot.py
+++ b/scripts/polya_training/hmmplot.py
@@ -3,7 +3,7 @@
Plot a random segmentation from a dataset.
Usage:
- $ python polya.out.tsv reads.fastq.readdb.index
+ $ python3 polya.out.tsv reads.fastq.readdb.index
"""
import h5py
import pandas as pd
--- a/scripts/polya_training/workflow.md
+++ b/scripts/polya_training/workflow.md
@@ -57,7 +57,7 @@
* `retrain_emission.py`: take the arrays from a run of `dump_signal.py` and output the coefficients and parameters
of a gaussian mixture model for each segment.
-Run `python <SCRIPT> --help` for further usage instructions for each script.
+Run `python3 <SCRIPT> --help` for further usage instructions for each script.
The files above required a suite of numerical packages to be installed as dependencies. A full list of dependencies,
-in a conda-compatible environment file, is available at `hmmplot/environment.yml`.
\ No newline at end of file
+in a conda-compatible environment file, is available at `hmmplot/environment.yml`.
--- a/scripts/reestimate_polya_emissions.py
+++ b/scripts/reestimate_polya_emissions.py
@@ -5,7 +5,7 @@
infer the best new parameters for the HMM emissions.
Usage:
-$ python reestimate_polya_emissions.py samples.old.tsv seg.old.tsv samples.new.tsv
+$ python3 reestimate_polya_emissions.py samples.old.tsv seg.old.tsv samples.new.tsv
where:
* `samples.old.tsv` is the output of `nanopolish polya -vv [...] | grep 'polya-samples'`,
generated by the **old** kmer models;
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