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import os
import parasail
from unittest import TestCase, main
from tempfile import NamedTemporaryFile
def create_input_file(filename):
with open(filename, 'w') as fp:
fp.write('''>AF0017_1 COG1250 # Protein_GI_number: 11497638 # Func_class: I Lipid transport and metabolism # Function: 3-hydroxyacyl-CoA dehydrogenase # Organism: Archaeoglobus fulgidus
MMVLEIRNVAVIGAGSMGHAIAEVVAIHGFNVKLMDVSEDQLKRAMEKIEEGLRKSYERGYISEDPEKVLKRIEATADLIEVAKDADLVIEAIPEIFDLKKKVFSEIEQYCPDHTIFATNTSSLSITKLAEATKRPEKFIGMHFFNPPKILKLLEIVWGEKTSEETIRIVEDFARKIDRIIIHVRKDVPGFIVNRIFVTMSNEASWAVEMGEGTIEEIDSAVKYRLGLPMGLFELHDVLGGGSVDVSYHVLEYYRQTLGESYRPSPLFERLFKAGHYGKKTGKGFYDWSEGKTNEVPLRAGANFDLLRLVAPAVNEAAWLIEKGVASAEEIDLAVLHGLNYPRGLLRMADDFGIDSIVKKLNELYEKYNGEERYKVNPVLQKMVEEGKLGRTTGEGFYKYGD
>AF0017_2_COG1024_#_Protein_GI_number: 11497638 # Func_class: I Lipid transport and metabolism # Function: Enoyl-CoA hydratase/carnithine racemase # Organism: Archaeoglobus fulgidus
GNYEFVKVEKEGKVGVLKLNRPRRANALNPTFLKEVEDALDLLERDEEVRAIVIAGEGKNFCAGADIAMFASGRPEMVTEFSQLGHKVFRKIEMLSKPVIAAIHGAAVGGGFELAMACDLRVMSERAFLGLPELNLGIIPGWGGTQRLAYYVGVSKLKEVIMLKRNIKPEEAKNLGLVAEVFPQERFWDEVMKLAREVAELPPLAVKYLKKVIALGTMPALETGNLAESEAGAVIALTDDVAEGIQAFNYRRKPNFRGR
''')
class Tests(TestCase):
def setUp(self):
self.tmpfile = NamedTemporaryFile()
create_input_file(self.tmpfile.name)
def tearDown(self):
os.unlink(self.tmpfile.name)
os.path.exists(self.tempfile.name)
def work(self):
sequences = parasail.sequences_from_file(self.tmpfile)
print(len(sequences))
print(len(sequences[0]))
print(sequences[0])
print(len(sequences[-1]))
print(sequences[-1])
print(sequences[0][0])
with self.assertRaises(TypeError):
print(sequences['asdf'])
with self.assertRaises(TypeError):
print(sequences[0]['asdf'])
with self.assertRaises(IndexError):
print(sequences[1000000])
with self.assertRaises(IndexError):
print(sequences[-1000000])
with self.assertRaises(IndexError):
print(sequences[0][1000000])
with self.assertRaises(IndexError):
print(sequences[0][-1000000])
print("name: '{}'".format(sequences[0].name))
print("comment: '{}'".format(sequences[0].comment))
print("seq: '{}'".format(sequences[0].seq))
print("qual: '{}'".format(sequences[0].qual))
print("characters: {}".format(sequences.characters))
print("shortest: {}".format(sequences.shortest))
print("longest: {}".format(sequences.longest))
print("mean: {}".format(sequences.mean))
print("stddev: {}".format(sequences.stddev))
result = parasail.sw(str(sequences[0]), str(sequences[1]), 10, 1, parasail.blosum62)
print(result.score)
result = parasail.sw(sequences[0], sequences[1], 10, 1, parasail.blosum62)
print(result.score)
if __name__ == '__main__':
main()
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