Merge pull request #486 from ged-lab/update/extract-long-seqs

updated extract-long sequence to extract 200 bp sequences by default

ChangeLog

@@ -1,11 +1,17 @@
+2014-06-14  Titus Brown  <t@idyll.org>
+
+    * doc/scripts.txt: added extract-long-sequences.py doc reference.
+    * scripts/extract-long-sequences.py: set default sequence length to
+	extract to 200 bp.
+
 2014-06-13  Michael R. Crusoe  <mcrusoe@msu.edu>
 
     * Makefile: split coverity target in two: -build and -upload. Added
     configuration target
 
-2014-06-13  Titus Brown  <t@Titus-MacBook-Air-2.local>
+2014-06-13  Titus Brown  <t@idyll.org>
 
-    * doc/install.txt: updated virtuaenv command to use python2 explicitly,
+    * doc/install.txt: updated virtualenv command to use python2 explicitly,
 	for arch support.
 
 2014-06-13  Titus Brown  <t@idyll.org>
@@ -21,7 +27,7 @@
 2014-06-11  Michael Wright <wrigh517@msu.edu>
 
     * scripts/load-into-counting: Fixed docstring misnomer to 
-    load-into-counting.py
+	load-into-counting.py
 
 2014-06-10  Michael R. Crusoe  <mcrusoe@msu.edu>
 

doc/scripts.txt

@@ -114,20 +114,23 @@ Digital normalization
 Read handling: interleaving, splitting, etc.
 ============================================
 
-.. autoprogram:: sweep-reads-buffered:get_parser()
-        :prog: sweep-reads-buffered.py
+.. autoprogram:: extract-long-sequences:get_parser()
+        :prog: extract-long-sequences.py
 
 .. autoprogram:: extract-paired-reads:get_parser()
         :prog: extract-paired-reads.py
 
+.. autoprogram:: fastq-to-fasta:get_parser()
+        :prog: fastq-to-fasta.py
+
 .. autoprogram:: interleave-reads:get_parser()
         :prog: interleave-reads.py
 
+.. autoprogram:: sample-reads-randomly:get_parser()
+        :prog: sample-reads-randomly.py
+
 .. autoprogram:: split-paired-reads:get_parser()
         :prog: split-paired-reads.py
 
-.. autoprogram:: fastq-to-fasta:get_parser()
-        :prog: fastq-to-fasta.py
-
-.. autoprogram:: sample-reads-randomly:get_parser()
-        :prog: sample-reads-randomly.py
+.. autoprogram:: sweep-reads-buffered:get_parser()
+        :prog: sweep-reads-buffered.py

scripts/extract-long-sequences.py

@@ -11,7 +11,7 @@
 Write out lines of FASTQ and FASTA files that exceed an argument-specified
 length.
 
-% scripts/extract-long-sequences.py [-h] [-o OUTPUT] -l LENGTH
+% scripts/extract-long-sequences.py [-h] [-o OUTPUT] [-l LENGTH]
                                  input_filenames [input_filenames ...]
 
 Use '-h' for parameter help.
@@ -23,17 +23,17 @@
 
 def get_parser():
     parser = argparse.ArgumentParser(
-        description='Extracts FASTQ or FASTA sequences longer than argument'
-        ' specified length.',
+        description='Extract FASTQ or FASTA sequences longer than'
+        ' specified length (default: 200 bp).',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
     parser.add_argument('input_filenames', help='Input FAST[AQ]'
                         ' sequence filename.', nargs='+')
     parser.add_argument('-o', '--output', help='The name of the output'
                         ' sequence file.', default="/dev/stdout")
     parser.add_argument('-l', '--length', help='The minimum length of'
-                        ' the sequence file. Required argument.',
-                        type=int, required=True)
+                        ' the sequence file.',
+                        type=int, default=200)
     return parser