Merge pull request #38 from ShawHahnLab/release-0.0.10

Release 0.0.10

CHANGELOG.md

@@ -1,5 +1,24 @@
 # Changelog
 
+## 0.0.10 - 2022-10-11
+
+### Added
+
+ * FASTQ support ([#37])
+
+### Changed
+
+ * Repository now at <https://github.com/ShawHahnLab/vquest> ([#36])
+
+### Fixed
+
+ * Usage example now matches packaged structure ([#36])
+ * Requests to the IMGT server now use HTTPS ([#34])
+
+[#37]: https://github.com/ShawHahnLab/vquest/pull/37
+[#36]: https://github.com/ShawHahnLab/vquest/pull/36
+[#34]: https://github.com/ressy/vquest/pull/34
+
 ## 0.0.9 - 2021-07-20
 
 ### Added

README.md

@@ -1,6 +1,6 @@
 # Automate IMGT V-QUEST usage on imgt.org
 
-[![vquest](https://circleci.com/gh/ressy/vquest.svg?style=shield)](https://circleci.com/gh/ressy/vquest)
+[![vquest](https://circleci.com/gh/ShawHahnLab/vquest.svg?style=shield)](https://circleci.com/gh/ShawHahnLab/vquest)
 
 [IMGT](http://imgt.org)'s [V-QUEST](http://www.imgt.org/IMGT_vquest/analysis)
 is only available via a web interface.  This Python package automates V-QUEST
@@ -23,7 +23,7 @@ Here the aligned FASTA text is printed directly to standard output.
 
 Example Python usage:
 
-    >>> from vquest import *
+    >>> from vquest.vq import *
     >>> config = layer_configs(DEFAULTS, {"species": "rhesus-monkey", "receptorOrLocusType": "IG", "fileSequences": "seqs.fasta"})
     >>> result = vquest(config)
     >>> result.keys()

setup.py

@@ -12,7 +12,7 @@
     description="Automate IMGT V-QUEST usage on imgt.org",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url="https://github.com/ressy/vquest",
+    url="https://github.com/shawhahnlab/vquest",
     packages=setuptools.find_packages(),
     package_data={"vquest": ["data/*"]},
     entry_points={"console_scripts": [

test_vquest/data/test_vquest/TestVquestFasta/config.yml

@@ -0,0 +1,2 @@
+species: rhesus-monkey
+receptorOrLocusType: IG

test_vquest/data/test_vquest/TestVquestFasta/config_inline.yml

@@ -0,0 +1,10 @@
+species: rhesus-monkey
+receptorOrLocusType: IG
+resultType: excel
+xv_outputtype: 3
+sequences: |
+  >IGKV2-ACR*02
+  GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCCATCTCCTGCAGGTCTAGTCA
+  GAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGGTACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCT
+  ATGAGGTTTCCAACCGGGTCTCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATC
+  AGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCTCC

test_vquest/data/test_vquest/TestVquestFasta/expected/Parameters.txt

@@ -0,0 +1,12 @@
+Date	Tue Dec 01 22:08:11 CET 2020	
+IMGT/V-QUEST program version	3.5.21	
+IMGT/V-QUEST reference directory release	202049-2	
+Species	Macaca mulatta	
+Receptor type or locus	IG	
+IMGT/V-QUEST reference directory set	F+ORF+ in-frame P	
+Search for insertions and deletions	no	
+Nb of nucleotides to add (or exclude) in 3' of the V-REGION for the evaluation of the alignment score	0	
+Nb of nucleotides to exclude in 5' of the V-REGION for the evaluation of the nb of mutations	0	
+Analysis of scFv	no	
+Number of submitted sequences	1	
+

test_vquest/data/test_vquest/TestVquestFasta/expected/vquest_airr.tsv

@@ -0,0 +1,2 @@
+sequence_id	sequence	sequence_aa	rev_comp	productive	complete_vdj	vj_in_frame	stop_codon	locus	v_call	d_call	j_call	c_call	sequence_alignment	sequence_alignment_aa	germline_alignment	germline_alignment_aa	junction	junction_aa	np1	np1_aa	np2	np2_aa	cdr1	cdr1_aa	cdr2	cdr2_aa	cdr3	cdr3_aa	fwr1	fwr1_aa	fwr2	fwr2_aa	fwr3	fwr3_aa	fwr4	fwr4_aa	v_score	v_identity	v_support	v_cigar	d_score	d_identity	d_support	d_cigar	j_score	j_identity	j_support	j_cigar	c_score	c_identity	c_support	c_cigar	v_sequence_start	v_sequence_end	v_germline_start	v_germline_end	v_alignment_start	v_alignment_end	d_sequence_start	d_sequence_end	d_germline_start	d_germline_end	d_alignment_start	d_alignment_end	j_sequence_start	j_sequence_end	j_germline_start	j_germline_end	j_alignment_start	j_alignment_end	cdr1_start	cdr1_end	cdr2_start	cdr2_end	cdr3_start	cdr3_end	fwr1_start	fwr1_end	fwr2_start	fwr2_end	fwr3_start	fwr3_end	fwr4_start	fwr4_end	v_sequence_alignment	v_sequence_alignment_aa	d_sequence_alignment	d_sequence_alignment_aa	j_sequence_alignment	j_sequence_alignment_aa	c_sequence_alignment	c_sequence_alignment_aa	v_germline_alignment	v_germline_alignment_aa	d_germline_alignment	d_germline_alignment_aa	j_germline_alignment	j_germline_alignment_aa	c_germline_alignment	c_germline_alignment_aa	junction_length	junction_aa_length	np1_length	np2_length	n1_length	n2_length	p3v_length	p5d_length	p3d_length	p5j_length	consensus_count	duplicate_count	cell_id	clone_id	rearrangement_id	repertoire_id	rearrangement_set_id	sequence_analysis_category	d_number	5prime_trimmed_n_nb	3prime_trimmed_n_nb	insertions	deletions	junction_decryption
+IGKV2-ACR*02	gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagtgacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtttccaaccgggtctctggagtccctgacaggttcagtggcagtgggtcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc		F	F				IGK	Macmul IGKV2S20*01 F				gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDS.DGYTCLDWYLQKPGQSPQLLIYEV.......SNRVSGVP.DRFSGSG..SXTDFTLKISRVEAEDVGVYYCMQSIEFP	gatattgtgatgacccagactccactctccctgccagtcacccctggagagccggcctccatctcctgcaggtctagtcagagcctcttggatagtgaggatggaaacacctatttggaatggtacctgcagaagccaggccagtctccacagcccttgatttatgaggtt.....................tccaaccgggcctctggagtccca...gacaggttcagtggcagtggg......tcagacactgatttcacactgaaaatcagcagagtggaggctgaggatgttggggtttattactgcatgcaaggtatagagtatcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSEDGNTYLEWYLQKPGQSPQPLIYEV.......SNRASGVP.DRFSGSG..SDTDFTLKISRVEAEDVGVYYCMQGIEYP							cagagcctcttggatagtgacgggtacacctgt	QSLLDSDGYTC	gaggtttcc	EVS	atgcaaagtatagagtttcctcc	MQSIEFP	gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagt	DIVMTQTPLSLPVTPGEPASISCRSS	ttggactggtacctgcagaagccaggccagtctccacagctcctgatctat	LDWYLQKPGQSPQLLIY	aaccgggtctctggagtccctgacaggttcagtggcagtgggtcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgt	NRVSGVPDRFSGSGSXTDFTLKISRVEAEDVGVYYC			1294	93.20		2=1X32=1X17=1X42=3D2=1X2=2X6=1X6=1X34=1X1=1X4=1X19=1X12=1X25=1M25=1X1=1X5=1X17=1X8=1X6=1X9=1X6=													1	302	1	335	1	335													79	111	163	171	280	302	1	78	112	162	172	279			gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDS.DGYTCLDWYLQKPGQSPQLLIYEV.......SNRVSGVP.DRFSGSG..SXTDFTLKISRVEAEDVGVYYCMQSIEFP							gatattgtgatgacccagactccactctccctgccagtcacccctggagagccggcctccatctcctgcaggtctagtcagagcctcttggatagtgaggatggaaacacctatttggaatggtacctgcagaagccaggccagtctccacagcccttgatttatgaggtt.....................tccaaccgggcctctggagtccca...gacaggttcagtggcagtggg......tcagacactgatttcacactgaaaatcagcagagtggaggctgaggatgttggggtttattactgcatgcaaggtatagagtatcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSEDGNTYLEWYLQKPGQSPQPLIYEV.......SNRASGVP.DRFSGSG..SDTDFTLKISRVEAEDVGVYYCMQGIEYP									0		0		0	0	0	0								1 (noindelsearch)	0	0	0			

test_vquest/data/test_vquest/TestVquestFasta/seqs.fasta

@@ -0,0 +1,5 @@
+>IGKV2-ACR*02
+GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCCATCTCCTGCAGGTCTAGTCA
+GAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGGTACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCT
+ATGAGGTTTCCAACCGGGTCTCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATC
+AGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCTCC

test_vquest/data/test_vquest/TestVquestFastq/config.yml

@@ -0,0 +1,2 @@
+species: rhesus-monkey
+receptorOrLocusType: IG

test_vquest/data/test_vquest/TestVquestFastq/config_inline.yml

@@ -0,0 +1,10 @@
+species: rhesus-monkey
+receptorOrLocusType: IG
+resultType: excel
+xv_outputtype: 3
+sequences: |
+  >IGKV2-ACR*02
+  GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCCATCTCCTGCAGGTCTAGTCA
+  GAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGGTACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCT
+  ATGAGGTTTCCAACCGGGTCTCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATC
+  AGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCTCC

test_vquest/data/test_vquest/TestVquestFastq/expected/Parameters.txt

@@ -0,0 +1,12 @@
+Date	Tue Dec 01 22:08:11 CET 2020	
+IMGT/V-QUEST program version	3.5.21	
+IMGT/V-QUEST reference directory release	202049-2	
+Species	Macaca mulatta	
+Receptor type or locus	IG	
+IMGT/V-QUEST reference directory set	F+ORF+ in-frame P	
+Search for insertions and deletions	no	
+Nb of nucleotides to add (or exclude) in 3' of the V-REGION for the evaluation of the alignment score	0	
+Nb of nucleotides to exclude in 5' of the V-REGION for the evaluation of the nb of mutations	0	
+Analysis of scFv	no	
+Number of submitted sequences	1	
+

test_vquest/data/test_vquest/TestVquestFastq/expected/vquest_airr.tsv

@@ -0,0 +1,2 @@
+sequence_id	sequence	sequence_aa	rev_comp	productive	complete_vdj	vj_in_frame	stop_codon	locus	v_call	d_call	j_call	c_call	sequence_alignment	sequence_alignment_aa	germline_alignment	germline_alignment_aa	junction	junction_aa	np1	np1_aa	np2	np2_aa	cdr1	cdr1_aa	cdr2	cdr2_aa	cdr3	cdr3_aa	fwr1	fwr1_aa	fwr2	fwr2_aa	fwr3	fwr3_aa	fwr4	fwr4_aa	v_score	v_identity	v_support	v_cigar	d_score	d_identity	d_support	d_cigar	j_score	j_identity	j_support	j_cigar	c_score	c_identity	c_support	c_cigar	v_sequence_start	v_sequence_end	v_germline_start	v_germline_end	v_alignment_start	v_alignment_end	d_sequence_start	d_sequence_end	d_germline_start	d_germline_end	d_alignment_start	d_alignment_end	j_sequence_start	j_sequence_end	j_germline_start	j_germline_end	j_alignment_start	j_alignment_end	cdr1_start	cdr1_end	cdr2_start	cdr2_end	cdr3_start	cdr3_end	fwr1_start	fwr1_end	fwr2_start	fwr2_end	fwr3_start	fwr3_end	fwr4_start	fwr4_end	v_sequence_alignment	v_sequence_alignment_aa	d_sequence_alignment	d_sequence_alignment_aa	j_sequence_alignment	j_sequence_alignment_aa	c_sequence_alignment	c_sequence_alignment_aa	v_germline_alignment	v_germline_alignment_aa	d_germline_alignment	d_germline_alignment_aa	j_germline_alignment	j_germline_alignment_aa	c_germline_alignment	c_germline_alignment_aa	junction_length	junction_aa_length	np1_length	np2_length	n1_length	n2_length	p3v_length	p5d_length	p3d_length	p5j_length	consensus_count	duplicate_count	cell_id	clone_id	rearrangement_id	repertoire_id	rearrangement_set_id	sequence_analysis_category	d_number	5prime_trimmed_n_nb	3prime_trimmed_n_nb	insertions	deletions	junction_decryption
+IGKV2-ACR*02	gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagtgacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtttccaaccgggtctctggagtccctgacaggttcagtggcagtgggtcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc		F	F				IGK	Macmul IGKV2S20*01 F				gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDS.DGYTCLDWYLQKPGQSPQLLIYEV.......SNRVSGVP.DRFSGSG..SXTDFTLKISRVEAEDVGVYYCMQSIEFP	gatattgtgatgacccagactccactctccctgccagtcacccctggagagccggcctccatctcctgcaggtctagtcagagcctcttggatagtgaggatggaaacacctatttggaatggtacctgcagaagccaggccagtctccacagcccttgatttatgaggtt.....................tccaaccgggcctctggagtccca...gacaggttcagtggcagtggg......tcagacactgatttcacactgaaaatcagcagagtggaggctgaggatgttggggtttattactgcatgcaaggtatagagtatcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSEDGNTYLEWYLQKPGQSPQPLIYEV.......SNRASGVP.DRFSGSG..SDTDFTLKISRVEAEDVGVYYCMQGIEYP							cagagcctcttggatagtgacgggtacacctgt	QSLLDSDGYTC	gaggtttcc	EVS	atgcaaagtatagagtttcctcc	MQSIEFP	gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagt	DIVMTQTPLSLPVTPGEPASISCRSS	ttggactggtacctgcagaagccaggccagtctccacagctcctgatctat	LDWYLQKPGQSPQLLIY	aaccgggtctctggagtccctgacaggttcagtggcagtgggtcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgt	NRVSGVPDRFSGSGSXTDFTLKISRVEAEDVGVYYC			1294	93.20		2=1X32=1X17=1X42=3D2=1X2=2X6=1X6=1X34=1X1=1X4=1X19=1X12=1X25=1M25=1X1=1X5=1X17=1X8=1X6=1X9=1X6=													1	302	1	335	1	335													79	111	163	171	280	302	1	78	112	162	172	279			gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDS.DGYTCLDWYLQKPGQSPQLLIYEV.......SNRVSGVP.DRFSGSG..SXTDFTLKISRVEAEDVGVYYCMQSIEFP							gatattgtgatgacccagactccactctccctgccagtcacccctggagagccggcctccatctcctgcaggtctagtcagagcctcttggatagtgaggatggaaacacctatttggaatggtacctgcagaagccaggccagtctccacagcccttgatttatgaggtt.....................tccaaccgggcctctggagtccca...gacaggttcagtggcagtggg......tcagacactgatttcacactgaaaatcagcagagtggaggctgaggatgttggggtttattactgcatgcaaggtatagagtatcctcc	DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSEDGNTYLEWYLQKPGQSPQPLIYEV.......SNRASGVP.DRFSGSG..SDTDFTLKISRVEAEDVGVYYCMQGIEYP									0		0		0	0	0	0								1 (noindelsearch)	0	0	0			

test_vquest/data/test_vquest/TestVquestFastq/seqs.fastq

@@ -0,0 +1,4 @@
+@IGKV2-ACR*02
+GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGGTACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCTATGAGGTTTCCAACCGGGTCTCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATCAGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCTCC
++
+JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

test_vquest/test_vquest.py

@@ -111,7 +111,7 @@ def test_vquest(self):
         self.assertEqual(self.post.call_count, 1)
         self.assertEqual(
             self.post.call_args.args,
-            ('http://www.imgt.org/IMGT_vquest/analysis', ))
+            ('https://www.imgt.org/IMGT_vquest/analysis', ))
         config_used = self.config.copy()
         # Whatever input type was given the actual type submitted to the form
         # will be "inline" to allow chunking of sequences if needed.  The
@@ -236,6 +236,114 @@ def test_vquest_main_alignment(self):
         self.check_missing_defaults_main(lambda: main(["--align"]))
 
 
+class TestVquestFasta(TestVquestBase):
+    """File-based input with FASTA."""
+
+    def setUp(self):
+        super().setUp()
+        self.input_path = self.path/"seqs.fasta"
+        del self.config["sequences"]
+        self.config["fileSequences"] = self.input_path
+
+    def test_vquest(self):
+        """Test that a basic request gives the expected response."""
+        result = vquest(self.config)
+        # requests.post should have been called once, with this input.
+        self.assertEqual(self.post.call_count, 1)
+        self.assertEqual(
+            self.post.call_args.args,
+            ('https://www.imgt.org/IMGT_vquest/analysis', ))
+        config_used = self.config.copy()
+        # Whatever input type was given the actual type submitted to the form
+        # will be "inline" to allow chunking of sequences if needed.  The
+        # sequences are also reformatted via Biopython when chunked.
+        config_used["inputType"] = "inline"
+        config_used["sequences"] = """>IGKV2-ACR*02
+GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCC
+ATCTCCTGCAGGTCTAGTCAGAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGG
+TACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCTATGAGGTTTCCAACCGGGTC
+TCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATC
+AGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCT
+CC
+"""
+        self.assertEqual(
+            self.post.call_args.kwargs,
+            {"data": config_used})
+        self.assertEqual(
+            list(result.keys()),
+            ["Parameters.txt", "vquest_airr.tsv"])
+        with open(self.path / "expected/Parameters.txt") as f_in:
+            parameters = f_in.read()
+        with open(self.path / "expected/vquest_airr.tsv") as f_in:
+            vquest_airr = f_in.read()
+        self.assertEqual(parameters, result["Parameters.txt"])
+        self.assertEqual(vquest_airr, result["vquest_airr.tsv"])
+
+    def test_vquest_no_collapse(self):
+        """test_vquest but with vquest(..., collapse=False)."""
+        # Also try with collapse=False, for raw output
+        result = vquest(self.config, collapse=False)
+        self.assertEqual(self.post.call_count, 1)
+        self.assertEqual(len(result), 1)
+        self.assertEqual(
+            list(result[0].keys()),
+            ["Parameters.txt", "vquest_airr.tsv"])
+
+    def test_vquest_main(self):
+        """Test that the command-line interface gives the expected response."""
+        with tempfile.TemporaryDirectory() as tempdir:
+            os.chdir(tempdir)
+            with open(self.path / "config.yml") as f_in, open("config.yml", "wt") as f_out:
+                f_out.write(f_in.read())
+                f_out.write(f"fileSequences: {self.input_path}\n")
+            main(["config.yml"])
+            self.assertTrue(Path("vquest_airr.tsv").exists())
+            self.assertTrue(Path("Parameters.txt").exists())
+
+    def test_vquest_main_no_collapse(self):
+        """Test command-line interface with --no-collapse."""
+        with tempfile.TemporaryDirectory() as tempdir:
+            os.chdir(tempdir)
+            with open(self.path / "config.yml") as f_in, open("config.yml", "wt") as f_out:
+                f_out.write(f_in.read())
+                f_out.write(f"fileSequences: {self.input_path}\n")
+            main(["--no-collapse", "config.yml"])
+            self.assertTrue(Path("001/vquest_airr.tsv").exists())
+            self.assertTrue(Path("001/Parameters.txt").exists())
+
+    def test_vquest_main_alignment(self):
+        """Try using the --align feature.
+
+        In this case the regular output files should not be created and instead
+        FASTA text should be written to stdout.
+        """
+        expected = """>IGKV2-ACR*02
+gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc
+"""
+        out = StringIO()
+        err = StringIO()
+        with redirect_stdout(out), redirect_stderr(err):
+            with tempfile.TemporaryDirectory() as tempdir:
+                os.chdir(tempdir)
+                with open(self.path / "config.yml") as f_in, open("config.yml", "wt") as f_out:
+                    f_out.write(f_in.read())
+                    f_out.write(f"fileSequences: {self.input_path}\n")
+                main(["config.yml", "--align"])
+                self.assertFalse(Path("vquest_airr.tsv").exists())
+                self.assertFalse(Path("Parameters.txt").exists())
+        self.assertEqual(out.getvalue(), expected)
+        self.assertEqual(err.getvalue(), "")
+
+
+class TestVquestFastq(TestVquestFasta):
+    """File-based input with FASTQ."""
+
+    def setUp(self):
+        super().setUp()
+        self.input_path = self.path/"seqs.fastq"
+        self.config["fileSequences"] = self.input_path
+
+
 class TestVquestCustom(TestVquestSimple):
     """Try changing one of the configuration options.
 
@@ -274,7 +382,7 @@ def test_vquest(self):
         self.assertEqual(self.post.call_count, 1)
         self.assertEqual(
             self.post.call_args.args,
-            ('http://www.imgt.org/IMGT_vquest/analysis', ))
+            ('https://www.imgt.org/IMGT_vquest/analysis', ))
 
     def test_vquest_main(self):
         """Test that an html file with an error message is parsed correctly for cmd-line usage."""