Testing setting abundance via faked control read file

Author: peterjc

tests/test_prepare-reads.sh

@@ -15,6 +15,22 @@ rm -rf $TMP/DNAMIX_S95_L001.prepared.fasta
 thapbi_pict prepare-reads -o $TMP tests/reads/DNAMIX_S95_L001_*.fastq.gz -a 0
 if [ `grep -c "^>" $TMP/DNAMIX_S95_L001.prepared.fasta` -ne "921" ]; then echo "Wrong FASTA output count"; false; fi
 
+rm -rf $TMP/DNAMIX_S95_L001.prepared.fasta
+thapbi_pict prepare-reads -o $TMP tests/reads/DNAMIX_S95_L001_*.fastq.gz -a 5
+if [ `grep -c "^>" $TMP/DNAMIX_S95_L001.prepared.fasta` -ne "27" ]; then echo "Wrong FASTA output count"; false; fi
+
+echo "Generating mock control file"
+# Using just 50 real reads (50 * 4 = 200 lines)
+zcat tests/reads/DNAMIX_S95_L001_R1_001.fastq.gz | head -n 200 > $TMP/MOCK_CONTROL_R1.fastq
+zcat tests/reads/DNAMIX_S95_L001_R2_001.fastq.gz | head -n 200 > $TMP/MOCK_CONTROL_R2.fastq
+
+rm -rf $TMP/DNAMIX_S95_L001.prepared.fasta
+rm -rf $TMP/MOCK_CONTROL.prepared.fasta
+# Starting low threshold, should be increased to 19, so get new output count...
+thapbi_pict prepare-reads -o $TMP tests/reads/DNAMIX_S95_L001_*.fastq.gz -a 5 -c $TMP/MOCK_CONTROL_R?.fastq
+if [ `grep -c "^>" $TMP/MOCK_CONTROL.prepared.fasta` -ne "16" ]; then echo "Wrong FASTA control output count"; false; fi
+if [ `grep -c "^>" $TMP/DNAMIX_S95_L001.prepared.fasta` -ne "9" ]; then echo "Wrong FASTA output count"; false; fi
+
 rm -rf $TMP/DNAMIX_S95_L001.prepared.fasta
 thapbi_pict prepare-reads -o $TMP tests/reads/DNAMIX_S95_L001_*.fastq.gz -a 100
 if [ `grep -c "^>" $TMP/DNAMIX_S95_L001.prepared.fasta` -ne "7" ]; then echo "Wrong FASTA output count"; false; fi