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View Code? Open in Web Editor NEWCode for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
License: MIT License
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Chapter 6 solution 1: two questions
Dear Ken: from one Perl hack to his better, I cannot thank you enough for this book!
I have two likely trivial questions:
- At the bottom of p. 142, I had initially tried the following:
distance += 1 if seq1[i] != seq2[i]
However, this fails. Would you be willing to help help me understand why this does not work in Python?
- On p. 142-143, you copy the two sequences into variables rather than using them directly as
args.seq1andargs.seq2. Is there a computational or other advantage to doing this? I ask because I am always afraid of making multiple copies of sequences in case they're too long.
Very grateful for this book, and for your help!
Chase
new-py
hi, I would like to know if I have to add the path of new-py to variables environments to be able to use it. the command is not working for me
Chapter 1 `make test` failed
Hi there,
It seems that the tests/dna_test.py file didn't pass pylint on my end as shown below. I was wondering if you would take a look when you have time? I could also submit a PR if that works for you.
Thanks very much,
Yuan
dna.py::PYLINT SKIPPED (file(s) previously passed pylint checks) [ 8%]
dna.py::mypy PASSED [ 16%]
dna.py::mypy-status PASSED [ 25%]
dna.py::FLAKE8 SKIPPED (file(s) previously passed FLAKE8 checks) [ 33%]
tests/dna_test.py::PYLINT FAILED [ 41%]
===================================================================================================================== FAILURES ======================================================================================================================
____________________________________________________________________________________________________________ [pylint] tests/dna_test.py _____________________________________________________________________________________________________________
R: 45,14: Consider using 'with' for resource-allocating operations (consider-using-with)
======================================================================================================================= mypy ========================================================================================================================
Success: no issues found in 2 source files
============================================================================================================== short test summary info ==============================================================================================================
FAILED tests/dna_test.py::PYLINT
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
====================================================================================================== 1 failed, 2 passed, 2 skipped in 0.52s =======================================================================================================
Makefile:4: recipe for target 'test' failed
make: *** [test] Error 1
wget in fetch_fasta.sh bash script, chapter 11
Dear Ken:
When running ./fetch_fasta.sh tests/inputs/1.txt from inside /biofx_python/11_mprt/, four empty FASTA files were being created in the /fasta/ directory. It's possible I have a different version of wget; mine is iGNU Wget 1.21.1 built on darwin19.6.0. However, I got it working as follows:
- Add a ".fasta" suffix to the end of
$URL, i.e.:
URL="https://www.uniprot.org/uniprot/${PROT_ID}.fasta"
- Change the
-oto-Oin thewgetcall, i.e.:
wget -q -O "$OUT_FILE" "$URL"
Does that seem correct, or do you think my problem lies elsewhere?
Many thanks!
Chase
Why use ''.join() in chapter 14, solution 1, find_orfs()?
For the following line in chapter 14, solution 1, find_orfs(), from page 281:
orfs.append(''.join(aa[start:stop]))
Could you help me understand why one would not use the following (presumably simpler?):
orfs.append(aa[start:stop])
In other words, what is the advantage of joining on the empty string in this situation?
Thanks as always!
Chase
Figure 16-3
Greetings! I am wondering if there should be one additional arrow in Figure 16-3, namely an arrow pointing from the second circle to the last circle, and labelled 'a'? The second circle would then have two arrows emanating from it, one labelled 'n' and one labelled 'a'. (It's totally possible I have a misunderstanding due to unfamiliarity with finite state machine diagrams!)
Many thanks,
Chase
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