From b87004684411fc58b86a29cbd7320d2b996c1564 Mon Sep 17 00:00:00 2001 From: don Date: Wed, 14 Jun 2017 14:51:00 -0700 Subject: [PATCH] Fix 2060A microtest sample by making the overlap longer. Also improve error message when Kive API isn't installed. --- micall/monitor/kive_download.py | 2 + .../2060A-V3LOOP_S8_L001_R1_001.fastq | 42 +++++++++---------- .../2060A-V3LOOP_S8_L001_R2_001.fastq | 2 +- micall/tests/microtest/README.md | 2 +- 4 files changed, 25 insertions(+), 23 deletions(-) diff --git a/micall/monitor/kive_download.py b/micall/monitor/kive_download.py index d3c9a6214..437fa6105 100644 --- 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 index c652b7c4b..420087d6f 100644 --- 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 index 617fae4bc..7dc00982b 100644 --- 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 index 3cb65e3c2..8a22dd43c 100644 --- 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