GC test

telatin · Jun 5, 2022 · df40240 · df40240
1 parent 22cb875
commit df40240
Showing 1 changed file with 43 additions and 13 deletions.
diff --git a/test/test-stats.sh b/test/test-stats.sh
@@ -9,7 +9,7 @@ SEQS=$(cat "$TMP" | tail -n 1 | cut -f 2)
 TOT=$(cat "$TMP" | tail -n 1 | cut -f 3)
 N50=$(cat "$TMP" | tail -n 1 | cut -f 5)
 
-MSG="[stats] Checking normal output expecting 2 lines: <$WC>"
+MSG="Checking normal output expecting 2 lines: <$WC>"
 if [[ $WC == 2 ]]; then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -19,7 +19,7 @@ else
 fi
 
 
-MSG="[stats] Checking normal output expecting total seqs 78730: <$SEQS>"
+MSG="Checking normal output expecting total seqs 78730: <$SEQS>"
 if [[ $SEQS == 78730 ]]; then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -28,7 +28,7 @@ else
     ERRORS=$((ERRORS+1))
 fi
 
-MSG="[stats] Checking normal output expecting total bases 24299931: <$TOT>"
+MSG="Checking normal output expecting total bases 24299931: <$TOT>"
 if [[ $TOT == 24299931 ]]; then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -37,7 +37,7 @@ else
     ERRORS=$((ERRORS+1))
 fi
 
-MSG="[stats] Checking normal N50 to be 316: <$N50>"
+MSG="Checking normal N50 to be 316: <$N50>"
 if [[ $N50 == 316 ]]; then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -48,7 +48,7 @@ fi
 
 CSV=$("$BINDIR"/seqfu stats --basename --csv $iAmpli > $TMP)
 N50=$(cat "$TMP" | tail -n 1 | cut -f 5 -d ,)
-MSG="[stats] Checking CSV output N50 is 316, got: <$N50>"
+MSG="Checking CSV output N50 is 316, got: <$N50>"
 if [[ $N50 == 316 ]]; then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -61,10 +61,10 @@ fi
 STATS=$("$BINDIR"/seqfu stats --basename --nice $iAmpli > $TMP)
 WC=$(cat "$TMP" | grep . | wc -l | grep -o '\d\+')
 if [[ $WC == 5 ]]; then
-    echo -e "$OK: [stats] Checking nice output expecting 5 lines: <$WC>"
+    echo -e "$OK: Checking nice output expecting 5 lines: <$WC>"
     PASS=$((PASS+1))
 else
-    echo -e "$FAIL: [stats] Checking nice output expecting 5 lines: <$WC>"
+    echo -e "$FAIL: Checking nice output expecting 5 lines: <$WC>"
     ERRORS=$((ERRORS+1))
 fi
 
@@ -74,18 +74,18 @@ STATS=$("$BINDIR"/seqfu stats --basename --json --multiqc $TMP2 $iAmpli > $TMP)
 WC=$(cat "$TMP" | grep . | wc -l | grep -o '\d\+')
 WC2=$(cat "$TMP2" | grep . | wc -l | grep -o '\d\+')
 if [[ $WC2 == 39 ]]; then
-    echo -e "$OK: [stats] Checking MultiQC output expecting 39 lines: <$WC2>"
+    echo -e "$OK: Checking MultiQC output expecting 39 lines: <$WC2>"
     PASS=$((PASS+1))
 else
-    echo -e "$FAIL: [stats] Checking MultiQC output expecting 39 lines: <$WC2>"
+    echo -e "$FAIL: Checking MultiQC output expecting 39 lines: <$WC2>"
     ERRORS=$((ERRORS+1))
 fi
 
 if [[ $WC == 1 ]]; then
-    echo -e "$OK: [stats] Experimental JSON output on 1 line: <$WC>"
+    echo -e "$OK: Experimental JSON output on 1 line: <$WC>"
     PASS=$((PASS+1))
 else
-    echo -e "$FAIL: [stats] Experimental JSON output on 1 line: <$WC>"
+    echo -e "$FAIL: Experimental JSON output on 1 line: <$WC>"
     ERRORS=$((ERRORS+1))
 fi
 # Multi file 
@@ -96,7 +96,7 @@ fi
 "$BINDIR"/seqfu stats --basename  --sort n50 --reverse $iAmpli $iSort $iMini > $TMP2
 
 FILT=$(cat $TMP | head -n 2 | tail -n 1 | cut -f 1)
-MSG="[stats] Checking default starting  by 'filt': <$FILT>"
+MSG="Checking default starting  by 'filt': <$FILT>"
 if [[ $FILT == "filt" ]];  then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -106,7 +106,7 @@ else
 fi
 
 FILT=$(cat $TMP2 | head -n 2 |tail -n 1 | cut -f 1)
-MSG="[stats] Checking default N50 starting by 'sort': <$FILT>"
+MSG="Checking default N50 starting by 'sort': <$FILT>"
 if [[ $FILT == "sort" ]];  then
     echo -e "$OK: $MSG"
     PASS=$((PASS+1))
@@ -157,4 +157,34 @@ if [[ $(tail -n 1 $TMP | cut -f 3 ) == 3300 ]]; then
 else
     echo -e "$FAIL: $MSG:$(head -n 1 $TMP | cut -f 3 ) "
     ERRORS=$((ERRORS+1))
+fi
+
+"$BINDIR"/seqfu stats --gc $FILES/gc/1.fa | grep -v "Total bp" > $TMP
+MSG="%GC check at 1.00"
+if [[ $(cut -f 11 $TMP ) == 1.00 ]]; then
+   echo -e "$OK: $MSG"
+   PASS=$((PASS+1))
+else
+    echo -e "$FAIL: $MSG: $(cut -f 11 $TMP ) "
+    ERRORS=$((ERRORS+1))
+fi
+
+"$BINDIR"/seqfu stats --gc $FILES/gc/2.fa | grep -v "Total bp" > $TMP
+MSG="%GC check at 0.00"
+if [[ $(cut -f 11 $TMP ) == 0.00 ]]; then
+   echo -e "$OK: $MSG"
+   PASS=$((PASS+1))
+else
+    echo -e "$FAIL: $MSG: $(cut -f 11 $TMP ) "
+    ERRORS=$((ERRORS+1))
+fi
+
+"$BINDIR"/seqfu stats --gc $FILES/gc/3.fa | grep -v "Total bp" > $TMP
+MSG="%GC check at 0.50"
+if [[ $(cut -f 11 $TMP ) == 0.50 ]]; then
+   echo -e "$OK: $MSG"
+   PASS=$((PASS+1))
+else
+    echo -e "$FAIL: $MSG: $(cut -f 11 $TMP ) "
+    ERRORS=$((ERRORS+1))
 fi