Fix 2060A microtest sample by making the overlap longer.

Also improve error message when Kive API isn't installed.
cfe-lab · Jun 14, 2017 · b870046 · b870046
1 parent 5e60fcb
commit b870046
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Showing 4 changed files with 25 additions and 23 deletions.
diff --git a/micall/monitor/kive_download.py b/micall/monitor/kive_download.py
@@ -48,6 +48,8 @@ def parse_args():
 
 
 def kive_login(server_url, user, password):
+    if KiveAPI is None:
+        raise ImportError('Kive API failed to import. Is it installed?')
     kive = KiveAPI(server_url)
     kive.mount('https://', HTTPAdapter(max_retries=20))
     kive.login(user, password)

diff --git a/micall/tests/microtest/2060A-V3LOOP_S8_L001_R1_001.fastq b/micall/tests/microtest/2060A-V3LOOP_S8_L001_R1_001.fastq
@@ -1,40 +1,40 @@
-@M01234:01:000000000-AAAAA:1:1101:02060:0001 1:N:0:8:clean_read_tests_g2p_with_three_codon_overlap_between_forward_and_reverse
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+@M01234:01:000000000-AAAAA:1:1101:02060:0001 1:N:0:8:clean_read_tests_g2p_with_four_codon_overlap_between_forward_and_reverse
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0002 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0003 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0004 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0005 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0006 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0007 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0008 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0009 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 @M01234:01:000000000-AAAAA:1:1101:02060:0010 1:N:0:8
-AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCA
+AATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGACAAGCATTC
 +
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
diff --git a/micall/tests/microtest/2060A-V3LOOP_S8_L001_R2_001.fastq b/micall/tests/microtest/2060A-V3LOOP_S8_L001_R2_001.fastq
@@ -1,4 +1,4 @@
-@M01234:01:000000000-AAAAA:1:1101:02060:0001 2:N:0:8:clean_read_tests_g2p_with_three_codon_overlap_between_forward_and_reverse
+@M01234:01:000000000-AAAAA:1:1101:02060:0001 2:N:0:8:clean_read_tests_g2p_with_four_codon_overlap_between_forward_and_reverse
 ACAATGTGCCTGTCTTATATCTCCTACTATGTCTCCTGTTGCATAGAATGCTTGTCC
 +
 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

diff --git a/micall/tests/microtest/README.md b/micall/tests/microtest/README.md
@@ -21,7 +21,7 @@ The scenarios that each file tests are:
 * 2040-HLA-B - exon2 of HLA-B, half have a changed base at position 7 to test
   mixtures in the consensus
 * 2050-V3LOOP - low quality
-* 2060A-V3LOOP - clean read tests g2p with three codon overlap between forward
+* 2060A-V3LOOP - clean read tests g2p with four codon overlap between forward
   and reverse
 * 2070A-PR - seven reads with two deletions and three with one deletion
 * 2080A-V3LOOP - PR contamination below remap threshold