From 460f8a1c318c6b9d3741a9fbbc242e22f48b5167 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 13 Oct 2011 12:14:37 +0000 Subject: [PATCH] fixed last of fasta problems git-svn-id: http://biopieces.googlecode.com/svn/trunk@1564 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/digest_seq | 1 - bp_bin/find_genes | 6 +++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq index 7399ae0..56fa322 100755 --- a/bp_bin/digest_seq +++ b/bp_bin/digest_seq @@ -30,7 +30,6 @@ require 'maasha/biopieces' -require 'maasha/fasta' require 'maasha/seq' casts = [] diff --git a/bp_bin/find_genes b/bp_bin/find_genes index a7dda28..a1257c9 100755 --- a/bp_bin/find_genes +++ b/bp_bin/find_genes @@ -47,7 +47,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| Fasta.open(infile, mode="w") do |fasta_io| input.each_record do |record| output.puts record - fasta_io.puts record + + if record[:SEQ_NAME] and record[:SEQ] + seq = Seq.new_bp(record) + fasta_io.puts seq.to_fasta + end end end -- 2.39.2