tools/pear_structured_log: add and update tests

link to #3054

tools/tests/data/pear_log.log

+=== Pre-process 2 ===
+python pear.py /home/vidjil-ci/opt sequence_R1.fastq sequence_R2.fastq demo_set.fastq -r2
+===============
+Output log in demo_set.fastq.pre.log
+ ____  _____    _    ____ 
+|  _ \| ____|  / \  |  _ \
+| |_) |  _|   / _ \ | |_) |
+|  __/| |___ / ___ \|  _ <
+|_|   |_____/_/   \_\_| \_\
+
+PEAR v0.9.10 [May 30, 2016]
+
+Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
+Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593
+
+Forward reads file.................: sequence_R1.fastq
+Reverse reads file.................: sequence_R2.fastq
+PHRED..............................: 33
+Using empirical frequencies........: YES
+Statistical method.................: OES
+Maximum assembly length............: 999999
+Minimum assembly length............: 50
+p-value............................: 0.010000
+Quality score threshold (trimming).: 0
+Minimum read size after trimming...: 1
+Maximal ratio of uncalled bases....: 1.000000
+Minimum overlap....................: 10
+Scoring method.....................: Scaled score
+Threads............................: 1
+
+Allocating memory..................: 200,000,000 bytes
+Computing empirical frequencies....: DONE
+  A: 0.269874
+  C: 0.257653
+  G: 0.238808
+  T: 0.233665
+  9000 uncalled bases
+Assemblying reads: 0%Assemblying reads: 100%
+
+Assembled reads ...................: 2,972 / 3,000 (99.067%)
+Discarded reads ...................: 0 / 3,000 (0.000%)
+Not assembled reads ...............: 28 / 3,000 (0.933%)
+Assembled reads file...............: demo_set.fastq.assembled.fastq
+Discarded reads file...............: demo_set.fastq.discarded.fastq
+Unassembled forward reads file.....: demo_set.fastq.unassembled.forward.fastq
+Unassembled reverse reads file.....: demo_set.fastq.unassembled.reverse.fastq

tools/tests/data/pear_log_warning.log

+=== Pre-process 2 ===
+python pear.py /home/vidjil-ci/opt sequence_R1.fastq sequence_R2.fastq demo_set.fastq -r2
+===============
+Output log in /mnt/vda/prod/result/tmp/pre/out-039723//demo_set_R_6.fastq.pre.log
+ ____  _____    _    ____ 
+|  _ \| ____|  / \  |  _ \
+| |_) |  _|   / _ \ | |_) |
+|  __/| |___ / ___ \|  _ <
+|_|   |_____/_/   \_\_| \_\
+
+PEAR v0.9.10 [May 30, 2016]
+
+Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
+Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593
+
+Forward reads file.................: sequence_R1.fastq
+Reverse reads file.................: sequence_R2.fastq
+PHRED..............................: 33
+Using empirical frequencies........: YES
+Statistical method.................: OES
+Maximum assembly length............: 999999
+Minimum assembly length............: 50
+p-value............................: 0.010000
+Quality score threshold (trimming).: 0
+Minimum read size after trimming...: 1
+Maximal ratio of uncalled bases....: 1.000000
+Minimum overlap....................: 10
+Scoring method.....................: Scaled score
+Threads............................: 1
+
+Allocating memory..................: 200,000,000 bytes
+Computing empirical frequencies....: DONE
+  A: 0.269874
+  C: 0.257653
+  G: 0.238808
+  T: 0.233665
+  9000 uncalled bases
+Assemblying reads: 0%Assemblying reads: 100%
+
+Assembled reads ...................: 972 / 3,000 (32.400%)
+Discarded reads ...................: 500 / 3,000 (16.666%)
+Not assembled reads ...............: 1528 / 3,000 (50.933%)
+Assembled reads file...............: demo_set.fastq.assembled.fastq
+Discarded reads file...............: demo_set.fastq.discarded.fastq
+Unassembled forward reads file.....: demo_set.fastq.unassembled.forward.fastq
+Unassembled reverse reads file.....: demo_set.fastq.unassembled.reverse.fastq

tools/tests/should-get-tests/pear_structured_log.should-get

-!LAUNCH: python ../../pear_structured_log.py -i pear_log.log
+!LAUNCH: python ../../pear_structured_log.py -i ../data/pear_log.log -o ../data/pear_strucured.json; cat ../data/pear_strucured.json
 
-$ Clone id-1 has a different number of reads 
-1:Not the same number or reads: id-1
+$ Correct number of assembled reads
+1:"reads_assembled_number": 2972
 
-$ Clone id-2 is not in the second file
-1:[-] .* Clone not present: .* id-2
+1:"reads_total_number": 3000
 
-$ Clone id-3 is not in the first file
-1:[+] .* Clone not present: .* id-3
+$ Correct number of unassembled reads
+1:"reads_not_assembled_number": 28
+
+$ Correct information on input files used by pear
+1:"assembled_reads": "demo_set.fastq.assembled.fastq", 
+1:"discarded_reads": "demo_set.fastq.discarded.fastq", 
+1:"unassembled_forward": "demo_set.fastq.unassembled.forward.fastq", 
+1:"unassembled_reverse": "demo_set.fastq.unassembled.reverse.fastq"
+
+$ Correct parameter return
+1:"forward_file": "sequence_R1.fastq", 
+1:"minimum_overlap": "10", 
+1:"phred": "33", 
+1:"reverse_file": "sequence_R2.fastq", 
+1:"scoring_methode": "Scaled score", 
+1:"version": "PEAR v0.9.10 \[May 30, 2016\]"
+
+
+$ Correct nucleotides frequencies
+1:"base_frequency_a": "0.269874", 
+1:"base_frequency_c": "0.257653", 
+1:"base_frequency_g": "0.238808", 
+1:"base_frequency_t": "0.233665", 
\ No newline at end of file

tools/tests/should-get-tests/pear_structured_log_with_warning.should-get

+!LAUNCH: python ../../pear_structured_log.py -i ../data/pear_log_warning.log -o ../data/pear_strucured_waring.json; cat ../data/pear_strucured_waring.json
+
+$ Correct percentage of reads
+1:"percentage_assembled": 32.4, 
+1:"percentage_discarded": 16.666666666666668, 
+1:"percentage_not_assembled": 50.93333333333333, 
+
+$ Correct number of reads
+1:"reads_assembled_number": 972, 
+1:"reads_discarded_number": 500, 
+1:"reads_not_assembled_number": 1528, 
+1:"reads_total_number": 3000
+
+$ correct add of warning into the structured log
+1:"Very few reads assembled"
+1:"High level of discarded reads"