fixup! updated test files to match output of bowtie2 V2.5.2

tests/test_fastq.py

@@ -754,7 +754,7 @@ def test_PairedEndPipeline_import():
                        **{'allow_indels': True, 'any_position_adapters_r1': None, 'any_position_adapters_r2': None,
                           'discard_untrimmed_reads': False,
                           'error_tolerance': 0.1, 'five_prime_adapters_r1': None, 'five_prime_adapters_r2': None,
-                          'maximum_read_length': None, 'pair_filter_if': 'both',
+                          'maximum_read_length': None, 'pair_filter_if': 'any',
                           'minimum_overlap': 3, 'minimum_read_length': 10, 'parallel': True, 'quality_trimming': 20,
                           'three_prime_adapters_r1': 'ATGGGTATATGGGT',
                           'three_prime_adapters_r2': 'AGTTTACCGTTGT', 'trim_n': True, 'gzip_output': False})

tests/test_files/fastq_pipeline_tests/paired/truth/01_trim_adapters_paired_end/reads_1_trimmed.fastq

@@ -1,7 +1,3 @@
-@1:NM_014620:16:182
-
-+
-
 @2:NM_014620:1094:172
 ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA
 +
@@ -22,18 +18,10 @@ IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
 GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA
 +
 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@7:NM_022658:1912:184
-
-+
-
 @8:NM_022658:304:172
 AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC
 +
 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@9:NM_174914:46:212
-
-+
-
 @10:NM_022658:25:186
 CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC
 +

tests/test_files/fastq_pipeline_tests/paired/truth/01_trim_adapters_paired_end/reads_2_trimmed.fastq

@@ -1,7 +1,3 @@
-@1:NM_014620:16:182
-ATGGGTATATGGGTCCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
 @2:NM_014620:1094:172
 ATGGGTATATGGGTAGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG
 +
@@ -22,18 +18,10 @@ IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
 GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA
 +
 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@7:NM_022658:1912:184
-ATGGGTATATGGGTGTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
 @8:NM_022658:304:172
 CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT
 +
 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@9:NM_174914:46:212
-GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
 @10:NM_022658:25:186
 GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC
 +

tests/test_files/fastq_pipeline_tests/paired/truth/02_bowtie2_align_paired_end/bowtie2-align_reads_1_trimmed_reads_2_trimmed.log

@@ -1,12 +1,15 @@
-Warning: minimum score function gave negative number in --local mode for mate #1 of read '1:NM_014620:16:182; setting to 0 instead
-Warning: skipping mate #1 of read '1:NM_014620:16:182' because length (0) <= # seed mismatches (0)
-Warning: skipping mate #1 of read '1:NM_014620:16:182' because it was < 2 characters long
-Warning: minimum score function gave negative number in --local mode for mate #1 of read '7:NM_022658:1912:184; setting to 0 instead
-Warning: skipping mate #1 of read '7:NM_022658:1912:184' because length (0) <= # seed mismatches (0)
-Warning: skipping mate #1 of read '7:NM_022658:1912:184' because it was < 2 characters long
-Warning: minimum score function gave negative number in --local mode for mate #1 of read '9:NM_174914:46:212; setting to 0 instead
-Warning: skipping mate #1 of read '9:NM_174914:46:212' because length (0) <= # seed mismatches (0)
-Warning: skipping mate #1 of read '9:NM_174914:46:212' because it was < 2 characters long
-Error, fewer reads in file specified with -1 than in file specified with -2
-terminate called after throwing an instance of 'int'
-(ERR): bowtie2-align exited with value 3
+9997 reads; of these:
+  9997 (100.00%) were paired; of these:
+    872 (8.72%) aligned concordantly 0 times
+    6431 (64.33%) aligned concordantly exactly 1 time
+    2694 (26.95%) aligned concordantly >1 times
+    ----
+    872 pairs aligned concordantly 0 times; of these:
+      0 (0.00%) aligned discordantly 1 time
+    ----
+    872 pairs aligned 0 times concordantly or discordantly; of these:
+      1744 mates make up the pairs; of these:
+        1477 (84.69%) aligned 0 times
+        257 (14.74%) aligned exactly 1 time
+        10 (0.57%) aligned >1 times
+92.61% overall alignment rate

tests/test_files/fastq_pipeline_tests/paired/truth/03_featurecounts_paired_end/featureCounts_stats.csv

@@ -1,15 +1,15 @@
 ,Status,reads_1_trimmed_reads_2_trimmed
 1,Assigned,0
-2,Unassigned_Unmapped,132
+2,Unassigned_Unmapped,606
 3,Unassigned_Read_Type,0
-4,Unassigned_Singleton,2657
+4,Unassigned_Singleton,265
 5,Unassigned_MappingQuality,0
-6,Unassigned_Chimera,15014
+6,Unassigned_Chimera,1
 7,Unassigned_FragmentLength,0
 8,Unassigned_Duplicate,0
 9,Unassigned_MultiMapping,0
 10,Unassigned_Secondary,0
 11,Unassigned_NonSplit,0
-12,Unassigned_NoFeatures,2056
+12,Unassigned_NoFeatures,9125
 13,Unassigned_Overlapping_Length,0
 14,Unassigned_Ambiguity,0

tests/test_files/test_paired_end_pipeline.yaml

@@ -19,7 +19,7 @@ params:
     maximum_read_length: null
     minimum_overlap: 3
     minimum_read_length: 10
-    pair_filter_if: both
+    pair_filter_if: any
     parallel: true
     quality_trimming: 20
     three_prime_adapters_r1: ATGGGTATATGGGT

tests/test_io.py

@@ -1174,6 +1174,7 @@ def test_none_mapping_dict(self):
         with pytest.raises(KeyError):
             ortholog_dict['gene1']
 
+
 class TestPhylomeDBOrthologMapper:
 
     # Define a fixture to create an instance of PhylomeDBOrthologMapper for testing