0.9.6

clean.sh

@@ -0,0 +1,17 @@
+MIN=1000
+
+DEL=0
+KEEP=0
+
+for i in ~/git/dadaist2/data/its-mock/split/*.fq; 
+do 
+  c=$(wc -l $i| perl -ne 'print $1 if ($_=~/(\d+)/)'); 
+  if [ $c -lt $MIN ]; then
+    DEL=$((DEL+1))
+    rm $i
+  else
+    KEEP=$((KEEP+1))
+  fi
+done
+
+echo "Kept $KEEP, deleted $DEL"

seqfu.nimble

@@ -1,5 +1,5 @@
 # Package
-version       = "0.9.5"
+version       = "0.9.6"
 author        = "Andrea Telatin"
 description   = "SeqFU command-line tools"
 license       = "MIT"

src/fu_sw.nim

@@ -282,7 +282,15 @@ proc main(args: var seq[string]): int =
     query = $args["--query"]
     target = $args["--target"] 
     pctid = parseFloat($args["--pct-id"])
-
+
+  if not fileExists(query):
+    stderr.writeLine("ERROR: Query file not found: ", query)
+    quit(1)
+
+
+  if not fileExists(target):
+    stderr.writeLine("ERROR: Target file not found: ", target)
+    quit(1)
 
   poolSize = parseInt($args["--pool-size"])
 

src/seqfu_utils.nim

@@ -1,7 +1,7 @@
 import klib, readfq
-
 import  strutils, os, re
-
+when not defined(windows):
+  import posix
 const NimblePkgVersion {.strdefine.} = "<NimblePkgVersion>"
 proc version*(): string =
   return NimblePkgVersion
@@ -361,6 +361,7 @@ proc main_helper*(main_func: var seq[string] -> int) =
       stderr.writeLine( getCurrentExceptionMsg() )
       quit(2)   
   else:
+
     signal(SIG_PIPE, SIG_IGN)
     # Handle Ctrl+C interruptions and pipe breaks
     type EKeyboardInterrupt = object of CatchableError

src/sfu.nim

@@ -4,7 +4,7 @@ import strutils
 import tables
 import algorithm
 import docopt
-import posix
+
 
 
 
@@ -96,7 +96,7 @@ proc main(args: var seq[string]): int =
       echo format("	• $1: $2", k & repeat(" ", 20 - len(k)), helps_last[k])
 
     echo "\nAdd --help after each command to print usage"
-    1
+    0
   else:
     var p = args[0]
     var pargs = args[1 .. ^1]

test/mini.sh

@@ -5,7 +5,8 @@ PLATFORM=""
 #if [[ $(uname) == "Darwin" ]]; then
 # PLATFORM="_mac"
 #fi
-BIN=$DIR/../bin/seqfu${PLATFORM}
+BINDIR="$DIR/../bin/"
+BIN="$BINDIR"/seqfu
 FILES=$DIR/../data/
 
 iInterleaved=$FILES/interleaved.fq.gz
@@ -18,9 +19,15 @@ ERRORS=0
 echo "# Minimal test suite"
 
 # Binary works
-$BIN > /dev/null|| { echo "Binary not working"; exit 1; }
-echo "OK: Running"
+$BIN > /dev/null || { echo "Binary not working: $BIN"; exit 1; }
+echo "OK: Binary running"
 
+for MOD in head tail view qual derep sort count stats grep rc interleave deinterleave count;
+do
+  echo " - $MOD"
+  $BIN $MOD --help >/dev/null  2>&1 || {  echo "Help for $MOD returned non-zero"; exit 1; }
+
+done
 # Dereiplicate
 if [[ $($BIN derep $iAmpli  | grep -c '>') -eq "18664" ]]; then
 	echo "OK: Dereplicate"
@@ -85,13 +92,80 @@ else
   ERRORS=$((ERRORS+1))
 fi
 
+## Head 
+if [[ $($BIN head -n 1 $iInterleaved | wc -l) -eq 4 ]]; then
+  echo "OK: Head 1 sequence"
+else
+  echo "ERR: Head failed"
+  ERRORS=$((ERRORS+1))
+fi
+
+
+
+## Tail 
+if [[ $($BIN tail -n 1 $iInterleaved | wc -l) -eq 4 ]]; then
+  echo "OK: tail 1 sequence"
+else
+  echo "ERR: Tail failed"
+  ERRORS=$((ERRORS+1))
+fi
+
+
+
+##QUal
+if [[ $($BIN qual  $iInterleaved | grep 'Illumina-1.8' | wc -l ) -eq 1 ]]; then
+  echo "OK: qual tested"
+else
+  echo "ERR: qual failed"
+  ERRORS=$((ERRORS+1))
+fi
+## External
+
+if [[ $($BINDIR/fu-orf -1 $iPair1 -m 29 | grep -c '>') -eq 5 ]]; then
+  echo "OK: fu-orf tested"
+else
+  echo "ERR: fu-orf test failed: $($BINDIR/fu-orf -1 $iPair1 -m 29 | grep -c '>') != 5"
+  ERRORS=$((ERRORS+1))
+fi
+
+if [[ $($BINDIR/fu-sw -q $FILES/query.fa -t $FILES/target.fa | grep -c 'Score') -eq 2 ]]; then
+  echo "OK: fu-sw tested"
+else
+  echo "ERR: fu-sw test failed: $BINDIR/fu-sw -q $DATA/query.fa -t $DATA/target.fa | grep -c 'Score' != 2"
+  ERRORS=$((ERRORS+1))
+fi
+## STREAMING
+
+if [[ $(cat  $iInterleaved | gzip -d | $BIN head -n 1 2>/dev/null | wc -l) -eq 4 ]]; then
+  echo "OK: Head 1 sequence (stream)"
+else
+  echo "ERR: Head failed"
+  ERRORS=$((ERRORS+1))
+fi
+
+if [[ $(cat  $iInterleaved | gzip -d | $BIN tail -n 1 2>/dev/null | wc -l) -eq 4 ]]; then
+  echo "OK: tail 1 sequence (stream)"
+else
+  echo "ERR: tail failed"
+  ERRORS=$((ERRORS+1))
+fi
+
+if [[ $($BIN head -n 6  $iInterleaved | $BIN tail -n 2 2>/dev/null | wc -l) -eq 8 ]]; then
+  echo "OK: head/tail 1 sequence (stream)"
+else
+  echo "ERR: head/tail failed"
+  ERRORS=$((ERRORS+1))
+fi
+
+### Check failures
 if  [[ $ERRORS -gt 0 ]]; then
 	echo "FAIL: $ERRORS test failed."
 	exit 1
 else
 	echo "PASS"
 fi
 
+
 echo ""
 for TEST in $DIR/*.sh;
 do