0.9.2

docs/1_install.md

@@ -8,7 +8,8 @@ permalink: /installation
 
 ## Install via Miniconda
 
-The recommended installation method is via BioConda. If you have _conda_ installed ([how to install it](https://docs.conda.io/en/latest/miniconda.html)):
+The **recommended** installation method is via BioConda. 
+If you have _conda_ installed ([how to install it](https://docs.conda.io/en/latest/miniconda.html)):
 
 ```
 conda install -c conda-forge -c bioconda seqfu
@@ -18,6 +19,6 @@ More info on [installing conda](https://telatin.github.io/microbiome-bioinformat
 
 ## Pre-compiled binaries
 
-Pre-compiled binaries are distributed with the [stable releases](https://github.com/telatin/qax/releases).  
+Pre-compiled binaries are distributed with the [stable releases](https://github.com/telatin/seqfu2/releases).  
 
 

docs/tools/2.12_usage_rc.md

@@ -35,6 +35,12 @@ CTGCWGCCNCCCGTAGG
 GGATTAGATACCCBDGTAGTCC
 ```
 
+**Note**: if a single sequence (string) is provided, the output is not in FASTA format but a plain string. This makes easier
+a programmatic use like:
+```bash
+removePrimersScript.sh --for $FOR --rev $(seqfu rc $REV)
+```
+
 ## Reverse commplement files
 When supplying input files, the whole file will be complemented. If the file is in FASTQ format the 
 quality will be reversed as well. The program can process multiple files.

src/fastx_rc.nim

@@ -44,8 +44,12 @@ Options:
       if not fileExists(filename):
         # Process as string
         stringCount += 1
-        echo ">", seqDefaultName, "_" , $stringCount, "\n", revcompl(filename)
-        continue
+        if len(files) == 1:
+          echo revcompl(filename)
+          continue
+        else:
+          echo ">", seqDefaultName, "_" , $stringCount, "\n", revcompl(filename)
+          continue
       else:
         echoVerbose(filename, verbose)
 

src/fastx_view.nim

@@ -101,27 +101,46 @@ proc qualToColor(s: string, v: seq[int], color = false): string =
       else:
         result &= i
 
-proc highlight(r: string, matches: seq[seq[int]], l:int, color: proc) =
+proc isOnlySpaces(s: string): bool =
+  for c in s:
+    if c != ' ':
+      return false
+  return true
+
+proc highlightOligoMatches(r: string, matches: seq[seq[int]], oligo_length:int, color: proc): string =
+  var
+    glyphs = newSeq[string](len(r))
+
+  for i in 0 ..< len(r):
+    glyphs[i] = " "
+
+
   if len(matches[0]) > 0:
     for m in matches[0]:
       let 
-        stop = if m >= 0: l
-               else: l + m
+        stop = if m >= 0: oligo_length
+               else: oligo_length + m
         start = if m >= 0: m
               else: 0
-      echo ' '.repeat(start) & "ᐅ".color.fgWhite.repeat(stop)
+      for i in start ..< start+stop:
+        if i < len(glyphs):
+          glyphs[i] = "ᐅ".color.fgWhite
 
   #echo r
-
   if len(matches[1]) > 0:
     for m in matches[1]:
       let 
-        stop = if m >= 0: l
-               else: l + m
+        stop = if m >= 0: oligo_length
+               else: oligo_length + m
         start = if m >= 0: m
               else: 0
-      echo ' '.repeat(start) & "ᐊ".color.fgWhite.repeat(stop)
-
+      #echo "?", ' '.repeat(start) & "ᐊ".color.fgWhite.repeat(stop)
+      for i in start ..< start+stop:
+        if i < len(glyphs):
+          glyphs[i] = "ᐊ".color.fgWhite
+
+  return glyphs.join("")
+
 proc fastx_view(argv: var seq[string]): int =
   let args = docopt("""
 Usage: view [options] <inputfile> [<input_reverse>]
@@ -192,10 +211,14 @@ Options:
 
     if $args["--oligo1"] != "nil":
       let matches = findPrimerMatches(read.seq, $args["--oligo1"], matchThs, maxMismatches, minMatches)
-      highlight(read.seq, matches, len($args["--oligo1"]), bgBlue)
+      let forString = highlightOligoMatches(read.seq, matches, len($args["--oligo1"]), bgBlue)
+      if forString.isOnlySpaces == false:
+        echo forString
     if $args["--oligo2"] != "nil":
       let matches = findPrimerMatches(read.seq, $args["--oligo2"], matchThs, maxMismatches, minMatches)
-      highlight(read.seq, matches, len($args["--oligo2"]), bgRed)
+      let revString = highlightOligoMatches(read.seq, matches, len($args["--oligo2"]), bgRed)
+      if revString.isOnlySpaces == false:
+        echo revString
     echo read.seq
     if args["--qual-chars"]:
       echo qualToColor(read.qual, thresholdValues, colorOutput)