Write a program called blastomatic.py that will select BLAST hits above a given percent ID and will merge them with annotations and print the query sequence ID, the percent ID, the depth, and the lat/lon:
$ ./blastomatic.py -a tests/inputs/meta.csv -b tests/inputs/hits1.csv -p 99
Exported 22 to "out.csv".
$ head out.csv
qseqid,pident,depth,lat_lon
"JCVI_READ_1095913011720","100.000","12","41.485832,-71.35111"
"JCVI_READ_1095900076806","100.000","32","41.09111,-71.60222"
"JCVI_READ_1095900076806","100.000","32","41.09111,-71.60222"
"JCVI_READ_1095901257294","100.000","32","41.09111,-71.60222"
"JCVI_READ_1095899227776","100.000","25","38.946945,-76.41722"
"JCVI_READ_1093012135235","100.000","20","36.003887,-75.39472"
"JCVI_READ_1093012135235","100.000","20","36.003887,-75.39472"
"JCVI_READ_1093012135235","100.000","20","36.003887,-75.39472"
"JCVI_READ_1093012135235","100.000","20","36.003887,-75.39472"
The program should produce a usage:
$ ./blastomatic.py -h
usage: blastomatic.py [-h] -b FILE -a FILE [-o FILE] [-d DELIM] [-p PCTID]
Annotate BLAST output
optional arguments:
-h, --help show this help message and exit
-b FILE, --blasthits FILE
BLAST -outfmt 6 (default: None)
-a FILE, --annotations FILE
Annotations file (default: None)
-o FILE, --outfile FILE
Output file (default: out.csv)
-d DELIM, --delimiter DELIM
Output field delimiter (default: )
-p PCTID, --pctid PCTID
Minimum percent identity (default: 0.0)
A passing test suite looks like this:
$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint
--mypy blastomatic.py tests/*_test.py
============================= test session starts ==============================
...
collected 15 items
blastomatic.py::FLAKE8 SKIPPED [ 6%]
blastomatic.py::mypy PASSED [ 12%]
tests/blastomatic_test.py::FLAKE8 SKIPPED [ 18%]
tests/blastomatic_test.py::mypy PASSED [ 25%]
tests/blastomatic_test.py::test_exists PASSED [ 31%]
tests/blastomatic_test.py::test_usage PASSED [ 37%]
tests/blastomatic_test.py::test_bad_annotations PASSED [ 43%]
tests/blastomatic_test.py::test_bad_input_file PASSED [ 50%]
tests/blastomatic_test.py::test_good_input PASSED [ 56%]
tests/blastomatic_test.py::test_delimiter PASSED [ 62%]
tests/blastomatic_test.py::test_guess_delimiter PASSED [ 68%]
tests/blastomatic_test.py::test_pctid PASSED [ 75%]
tests/unit_test.py::FLAKE8 SKIPPED [ 81%]
tests/unit_test.py::mypy PASSED [ 87%]
tests/unit_test.py::test_guess_delimiter PASSED [ 93%]
::mypy PASSED [100%]
===================================== mypy =====================================
Success: no issues found in 3 source files
======================== 13 passed, 3 skipped in 2.84s =========================
Ken Youens-Clark [email protected]