From 8466d8cfa486fb30d1755c4261b781135083787b Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@robocracy.org>
Date: Mon, 20 Feb 2017 00:05:29 -0800
Subject: Import Upstream version 3a1

---
 ncbi-dna.txi | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 ncbi-dna.txi

(limited to 'ncbi-dna.txi')

diff --git a/ncbi-dna.txi b/ncbi-dna.txi
new file mode 100644
index 0000000..9a5babc
--- /dev/null
+++ b/ncbi-dna.txi
@@ -0,0 +1,54 @@
+
+@defun ncbi:read-dna-sequence port
+
+Reads the NCBI-format DNA sequence following the word @samp{ORIGIN}
+from @var{port}.
+@end defun
+
+@defun ncbi:read-file file
+
+Reads the NCBI-format DNA sequence following the word @samp{ORIGIN}
+from @var{file}.
+@end defun
+
+@defun mrna<-cdna str
+
+Replaces @samp{T} with @samp{U} in @var{str}
+@end defun
+
+@defun codons<-cdna cdna
+
+Returns a list of three-letter symbol codons comprising the protein
+sequence encoded by @var{cdna} starting with its first occurence of
+@samp{atg}.
+@end defun
+
+@defun protein<-cdna cdna
+
+Returns a list of three-letter symbols for the protein sequence
+encoded by @var{cdna} starting with its first occurence of @samp{atg}.
+@end defun
+
+@defun p<-cdna cdna
+
+Returns a string of one-letter amino acid codes for the protein
+sequence encoded by @var{cdna} starting with its first occurence of
+@samp{atg}.
+@end defun
+
+These cDNA count routines provide a means to check the nucleotide
+sequence with the @samp{BASE COUNT} line preceding the sequence from
+NCBI.
+
+
+@defun cdna:base-count cdna
+
+Returns a list of counts of @samp{a}, @samp{c}, @samp{g}, and
+@samp{t} occurrencing in @var{cdna}.
+@end defun
+
+@defun cdna:report-base-count cdna
+
+Prints the counts of @samp{a}, @samp{c}, @samp{g}, and @samp{t}
+occurrencing in @var{cdna}.
+@end defun
-- 
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