Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-entrez-direct
Commits:
509e0c27 by Aaron M. Ucko at 2021-02-24T21:04:50-05:00
New upstream version 14.6.20210224+dfsg
- - - - -
4 changed files:
- ecommon.sh
- efetch
- esample
- transmute.go
Changes:
=====================================
ecommon.sh
=====================================
@@ -975,6 +975,14 @@ LookupSpecialAccessions() {
ids=$( echo "$rem $lcl" | fmt -w 1 | sort -n | uniq )
fi
;;
+ taxonomy )
+ acc=$( ExtractAccns )
+ if [ -n "$acc" ]
+ then
+ echo "ERROR: Taxonomy database does not index sequence accession
numbers" >&2
+ exit 1
+ fi
+ ;;
esac
if [ -n "$fld" ]
then
=====================================
efetch
=====================================
@@ -1004,6 +1004,7 @@ case "$format:$dbase:$mode:$isSequence" in
docsum:gtr:json:* ) chunk=50 ;;
docsum:*:json:* ) chunk=500 ;;
bioc:* ) chunk=100 ;;
+ ipg:* ) chunk=1 ;;
json:snp:* ) chunk=10 ;;
*:*:true ) chunk=100 ;;
* ) chunk=1000 ;;
=====================================
esample
=====================================
@@ -1649,6 +1649,8 @@ EOF
do_gencode() {
cat <<EOF
+Standard Genetic Code Table
+
Second Position
First T C A G Third
-----------------------------------------------------------------
@@ -1673,6 +1675,8 @@ do_gencode() {
GTG Val [V] GCG Ala [A] GAG Glu [E] GGG Gly [G] G
-----------------------------------------------------------------
+Amino Acid Abbreviations
+
Alanine Ala A | A Ala Alanine
Arginine Arg R R-ginine | B Asx Asp or Asn
Asparagine Asn N asparagiNe | C Cys Cysteine
@@ -1703,6 +1707,8 @@ do_gencode() {
-----------------------------------------------------------------
+Nucleotide Abbreviations
+
R AG puRine | H ACT not G
Y CT pYrimidine | B CGT not A
M AC aMino | V ACG not T
@@ -1710,6 +1716,37 @@ do_gencode() {
S CG Strong | N ACGT unkNown
W AT Weak | X ACGT unknown
+Genetic Code Names
+
+ 1: Standard
+ 2: Vertebrate Mitochondrial
+ 3: Yeast Mitochondrial
+ 4: Mold Mitochondrial; Protozoan Mitochondrial;
+ Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
+ 5: Invertebrate Mitochondrial
+ 6: Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
+ 9: Echinoderm Mitochondrial; Flatworm Mitochondrial
+ 10: Euplotid Nuclear
+ 11: Bacterial, Archaeal and Plant Plastid
+ 12: Alternative Yeast Nuclear
+ 13: Ascidian Mitochondrial
+ 14: Alternative Flatworm Mitochondrial
+ 15: Blepharisma Macronuclear
+ 16: Chlorophycean Mitochondrial
+ 21: Trematode Mitochondrial
+ 22: Scenedesmus obliquus Mitochondrial
+ 23: Thraustochytrium Mitochondrial
+ 24: Rhabdopleuridae Mitochondrial
+ 25: Candidate Division SR1 and Gracilibacteria
+ 26: Pachysolen tannophilus Nuclear
+ 27: Karyorelict Nuclear
+ 28: Condylostoma Nuclear
+ 29: Mesodinium Nuclear
+ 30: Peritrich Nuclear
+ 31: Blastocrithidia Nuclear
+ 32: Balanophoraceae Plastid
+ 33: Cephalodiscidae Mitochondrial
+
EOF
}
=====================================
transmute.go
=====================================
@@ -4589,35 +4589,30 @@ func ReadAllIntoSequence(inp io.Reader) string {
return ""
}
- var buffer strings.Builder
-
- scanr := bufio.NewScanner(inp)
-
- for scanr.Scan() {
-
- str := scanr.Text()
+ data, _ := ioutil.ReadAll(inp)
+ txt := string(data)
- // skip FASTA definition line
- if strings.HasPrefix(str, ">") {
- continue
+ // skip past FASTA definition line
+ if len(txt) > 0 && txt[0] == '>' {
+ pos := strings.Index(txt, "\n")
+ if pos > 0 {
+ txt = txt[:pos+1]
}
- // convert everything to upper case
- str = strings.ToUpper(str)
-
- // leave only upper case letters or asterisk
- str = strings.Map(func(c rune) rune {
- if (c < 'A' || c > 'Z') && c != '*' && c != '-' {
- return -1
- }
- return c
- }, str)
+ }
- buffer.WriteString(str)
+ if txt == "" {
+ return ""
}
- txt := buffer.String()
+ // convert letters to upper case, leave only upper case letters,
asterisk, or hyphen
+ str := strings.Map(func(c rune) rune {
+ if (c < 'A' || c > 'Z') && c != '*' && c != '-' {
+ return -1
+ }
+ return c
+ }, strings.ToUpper(txt))
- return txt
+ return str
}
func ReadFromFileIntoSequence(fname string) string {
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/509e0c274178abf9d5c16abde65bf7b08d9352cd
--
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/509e0c274178abf9d5c16abde65bf7b08d9352cd
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