Commit e9a77fea authored by Laros's avatar Laros
Browse files

Setup fix retry 4.

parent 549cc411
...@@ -31,17 +31,17 @@ To get substitutions in a readable format, we can use the following: ...@@ -31,17 +31,17 @@ To get substitutions in a readable format, we can use the following:
variants = subst_to_cds(substitutions, 12) variants = subst_to_cds(substitutions, 12)
## Command line interface ## Command line interface
Use the command `back_translate` to find substitutions that explain an amino Use the command `backtranslate` to find substitutions that explain an amino
acid change: acid change:
$ back_translate with_dna -o 210 data/mhv.fa - 1 Leu $ backtranslate with_dna -o 210 data/mhv.fa - 1 Leu
1 A C 1 A C
1 A T 1 A T
If no reference is available, use the `without_dna` subcommand: If no reference is available, use the `without_dna` subcommand:
$ back_translate without_dna - Asp 92 Tyr $ backtranslate without_dna - Asp 92 Tyr
274 G T 274 G T
...@@ -50,7 +50,7 @@ to stop codons. This list of destructive substitutions are useful when ...@@ -50,7 +50,7 @@ to stop codons. This list of destructive substitutions are useful when
analysing a pool of viral transcripts. Counting the appropriate nucleotides at analysing a pool of viral transcripts. Counting the appropriate nucleotides at
the given positions gives insight into how many transcripts are active. the given positions gives insight into how many transcripts are active.
$ back_translate find_stops -o 210 data/mhv.fa - $ backtranslate find_stops -o 210 data/mhv.fa -
216 A T 216 A T
225 A T 225 A T
230 C A 230 C A
......
...@@ -71,8 +71,8 @@ setup( ...@@ -71,8 +71,8 @@ setup(
packages=[package], packages=[package],
install_requires=dependencies, install_requires=dependencies,
entry_points={ entry_points={
'console_scripts': ['{0} = {0}.{0}:main'.format(package)] 'console_scripts': ['{0} = {0}.cli:main'.format(package)]
}, },
classifiers=classifiers, classifiers=classifiers,
keywords=' '.join(keywords) keywords=' '.join(keywords)
) )
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