@@ -111,7 +111,7 @@ def test_vquest(self):
111111 self .assertEqual (self .post .call_count , 1 )
112112 self .assertEqual (
113113 self .post .call_args .args ,
114- ('http ://www.imgt.org/IMGT_vquest/analysis' , ))
114+ ('https ://www.imgt.org/IMGT_vquest/analysis' , ))
115115 config_used = self .config .copy ()
116116 # Whatever input type was given the actual type submitted to the form
117117 # will be "inline" to allow chunking of sequences if needed. The
@@ -236,6 +236,114 @@ def test_vquest_main_alignment(self):
236236 self .check_missing_defaults_main (lambda : main (["--align" ]))
237237
238238
239+ class TestVquestFasta (TestVquestBase ):
240+ """File-based input with FASTA."""
241+
242+ def setUp (self ):
243+ super ().setUp ()
244+ self .input_path = self .path / "seqs.fasta"
245+ del self .config ["sequences" ]
246+ self .config ["fileSequences" ] = self .input_path
247+
248+ def test_vquest (self ):
249+ """Test that a basic request gives the expected response."""
250+ result = vquest (self .config )
251+ # requests.post should have been called once, with this input.
252+ self .assertEqual (self .post .call_count , 1 )
253+ self .assertEqual (
254+ self .post .call_args .args ,
255+ ('https://www.imgt.org/IMGT_vquest/analysis' , ))
256+ config_used = self .config .copy ()
257+ # Whatever input type was given the actual type submitted to the form
258+ # will be "inline" to allow chunking of sequences if needed. The
259+ # sequences are also reformatted via Biopython when chunked.
260+ config_used ["inputType" ] = "inline"
261+ config_used ["sequences" ] = """>IGKV2-ACR*02
262+ GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCC
263+ ATCTCCTGCAGGTCTAGTCAGAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGG
264+ TACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCTATGAGGTTTCCAACCGGGTC
265+ TCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATC
266+ AGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCT
267+ CC
268+ """
269+ self .assertEqual (
270+ self .post .call_args .kwargs ,
271+ {"data" : config_used })
272+ self .assertEqual (
273+ list (result .keys ()),
274+ ["Parameters.txt" , "vquest_airr.tsv" ])
275+ with open (self .path / "expected/Parameters.txt" ) as f_in :
276+ parameters = f_in .read ()
277+ with open (self .path / "expected/vquest_airr.tsv" ) as f_in :
278+ vquest_airr = f_in .read ()
279+ self .assertEqual (parameters , result ["Parameters.txt" ])
280+ self .assertEqual (vquest_airr , result ["vquest_airr.tsv" ])
281+
282+ def test_vquest_no_collapse (self ):
283+ """test_vquest but with vquest(..., collapse=False)."""
284+ # Also try with collapse=False, for raw output
285+ result = vquest (self .config , collapse = False )
286+ self .assertEqual (self .post .call_count , 1 )
287+ self .assertEqual (len (result ), 1 )
288+ self .assertEqual (
289+ list (result [0 ].keys ()),
290+ ["Parameters.txt" , "vquest_airr.tsv" ])
291+
292+ def test_vquest_main (self ):
293+ """Test that the command-line interface gives the expected response."""
294+ with tempfile .TemporaryDirectory () as tempdir :
295+ os .chdir (tempdir )
296+ with open (self .path / "config.yml" ) as f_in , open ("config.yml" , "wt" ) as f_out :
297+ f_out .write (f_in .read ())
298+ f_out .write (f"fileSequences: { self .input_path } \n " )
299+ main (["config.yml" ])
300+ self .assertTrue (Path ("vquest_airr.tsv" ).exists ())
301+ self .assertTrue (Path ("Parameters.txt" ).exists ())
302+
303+ def test_vquest_main_no_collapse (self ):
304+ """Test command-line interface with --no-collapse."""
305+ with tempfile .TemporaryDirectory () as tempdir :
306+ os .chdir (tempdir )
307+ with open (self .path / "config.yml" ) as f_in , open ("config.yml" , "wt" ) as f_out :
308+ f_out .write (f_in .read ())
309+ f_out .write (f"fileSequences: { self .input_path } \n " )
310+ main (["--no-collapse" , "config.yml" ])
311+ self .assertTrue (Path ("001/vquest_airr.tsv" ).exists ())
312+ self .assertTrue (Path ("001/Parameters.txt" ).exists ())
313+
314+ def test_vquest_main_alignment (self ):
315+ """Try using the --align feature.
316+
317+ In this case the regular output files should not be created and instead
318+ FASTA text should be written to stdout.
319+ """
320+ expected = """>IGKV2-ACR*02
321+ gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc
322+ """
323+ out = StringIO ()
324+ err = StringIO ()
325+ with redirect_stdout (out ), redirect_stderr (err ):
326+ with tempfile .TemporaryDirectory () as tempdir :
327+ os .chdir (tempdir )
328+ with open (self .path / "config.yml" ) as f_in , open ("config.yml" , "wt" ) as f_out :
329+ f_out .write (f_in .read ())
330+ f_out .write (f"fileSequences: { self .input_path } \n " )
331+ main (["config.yml" , "--align" ])
332+ self .assertFalse (Path ("vquest_airr.tsv" ).exists ())
333+ self .assertFalse (Path ("Parameters.txt" ).exists ())
334+ self .assertEqual (out .getvalue (), expected )
335+ self .assertEqual (err .getvalue (), "" )
336+
337+
338+ class TestVquestFastq (TestVquestFasta ):
339+ """File-based input with FASTQ."""
340+
341+ def setUp (self ):
342+ super ().setUp ()
343+ self .input_path = self .path / "seqs.fastq"
344+ self .config ["fileSequences" ] = self .input_path
345+
346+
239347class TestVquestCustom (TestVquestSimple ):
240348 """Try changing one of the configuration options.
241349
@@ -274,7 +382,7 @@ def test_vquest(self):
274382 self .assertEqual (self .post .call_count , 1 )
275383 self .assertEqual (
276384 self .post .call_args .args ,
277- ('http ://www.imgt.org/IMGT_vquest/analysis' , ))
385+ ('https ://www.imgt.org/IMGT_vquest/analysis' , ))
278386
279387 def test_vquest_main (self ):
280388 """Test that an html file with an error message is parsed correctly for cmd-line usage."""
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