--- a/tools/fasta_tools/fasta_filter_by_id.py	Tue Jun 07 17:22:24 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.py	Tue Jun 07 17:22:48 2011 -0400
@@ -3,8 +3,9 @@
 
 Takes five command line options, tabular filename, ID column numbers
 (comma separated list using one based counting), input FASTA filename, and
-two output FASTA filenames (for records with and without any BLAST hits).
-If the either output filename is just a minus sign, that file is not created.
+two output FASTA filenames (for records with and without the given IDs).
+
+If either output filename is just a minus sign, that file is not created.
 This is intended to allow output for just the matched (or just the non-matched)
 records.
 
@@ -51,7 +52,7 @@
     print "Using %i IDs from tabular file" % (len(ids))
 handle.close()
 
-#Write filtered FASTA file based on IDs from BLAST file
+#Write filtered FASTA file based on IDs from tabular file
 reader = fastaReader(open(in_file, "rU"))
 if out_positive_file != "-" and out_negative_file != "-":
     print "Generating two FASTA files"