[med-svn] [ncbi-entrez-direct] 01/05: New upstream version 6.80.20170608+ds
Aaron M. Ucko
ucko at moszumanska.debian.org
Fri Jun 9 22:06:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
ucko pushed a commit to branch experimental
in repository ncbi-entrez-direct.
commit be988e442b6112db8f160acdaa8645b446d7a267
Author: Aaron M. Ucko <ucko at debian.org>
Date: Fri Jun 9 17:43:54 2017 -0400
New upstream version 6.80.20170608+ds
---
asp-cp | 22 ++-
asp-ls | 26 +++
edirect.pl | 2 +-
entrez-phrase-search | 4 +-
ftp-cp | 31 +++-
gbf2xml | 515 +++++++++++++++++++++++++++++++++++++++++++++++++++
xtract.go | 71 ++-----
7 files changed, 605 insertions(+), 66 deletions(-)
diff --git a/asp-cp b/asp-cp
index a2b64f5..73b526d 100755
--- a/asp-cp
+++ b/asp-cp
@@ -84,11 +84,11 @@ EOF
fi
failed=""
-while read fl
-do
+if [ "$#" -gt 1 ]
+then
+ fl="$2"
if [ ! -f "$fl" ]
then
- echo "$fl"
"$APPPATH/ascp" -T -q -k 1 -l 500m -i "$KEYPATH/$KEYNAME" \
"anonftp at ftp.ncbi.nlm.nih.gov:/$DATAPATH/$fl" "."
fi
@@ -96,7 +96,21 @@ do
then
failed="$failed\n$fl"
fi
-done
+else
+ while read fl
+ do
+ if [ ! -f "$fl" ]
+ then
+ echo "$fl"
+ "$APPPATH/ascp" -T -q -k 1 -l 500m -i "$KEYPATH/$KEYNAME" \
+ "anonftp at ftp.ncbi.nlm.nih.gov:/$DATAPATH/$fl" "."
+ fi
+ if [ ! -f "$fl" ]
+ then
+ failed="$failed\n$fl"
+ fi
+ done
+fi
if [ -n "$failed" ]
then
echo -e "\nFAILED TO DOWNLOAD:\n$failed\n" >&2
diff --git a/asp-ls b/asp-ls
new file mode 100755
index 0000000..c2a109f
--- /dev/null
+++ b/asp-ls
@@ -0,0 +1,26 @@
+#!/usr/bin/perl -w
+# Usage: asp-ls PATH
+
+use strict;
+
+use Net::FTP;
+
+my $server = "ftp.ncbi.nlm.nih.gov";
+my $dir = shift;
+my $ftp = new Net::FTP($server, Passive => 1)
+ or die "Unable to connect to FTP server: $!";
+
+$ftp->login or die "Unable to log in to FTP server";
+$ftp->cwd($dir) or die "Unable to change to $dir";
+my $contents = $ftp->dir;
+die "Unable to list contents" unless defined $contents;
+
+for (@$contents) {
+ if (/^-.*?(\S*)$/) {
+ print "$1\n";
+ } elsif (/^d.*?(\S*)$/) {
+ print "$1/\n";
+ } elsif (/^l.*?(\S*) -> \S*$/) {
+ print "$1@\n";
+ }
+}
diff --git a/edirect.pl b/edirect.pl
index c3cd694..7c59db4 100755
--- a/edirect.pl
+++ b/edirect.pl
@@ -87,7 +87,7 @@ use constant true => 1;
# EDirect version number
-$version = "6.70";
+$version = "6.80";
# URL address components
diff --git a/entrez-phrase-search b/entrez-phrase-search
index 62baead..1559104 100755
--- a/entrez-phrase-search
+++ b/entrez-phrase-search
@@ -143,13 +143,13 @@ fi
case "$mode" in
help | usage )
- echo "<<EOF
+ cat <<EOF
USAGE: $0
[-count|-counts|-string]
[-db database|-database database]
[-field field]
query
-EOF"
+EOF
if [ $mode = usage ]
then
exit 1
diff --git a/ftp-cp b/ftp-cp
index 8e0123e..45824eb 100755
--- a/ftp-cp
+++ b/ftp-cp
@@ -10,9 +10,36 @@ my $dir = shift;
my $ftp = new Net::FTP($server, Passive => 1)
or die "Unable to connect to FTP server: $!";
+my @failed = ();
+
+sub fetch {
+ my $fl = shift (@_);
+ if (! -e $fl) {
+ $ftp->get($fl) or push (@failed, "$fl");
+ }
+}
+
$ftp->login or die "Unable to log in to FTP server";
$ftp->cwd($dir) or die "Unable to change to $dir";
$ftp->binary or warn "Unable to set binary mode";
-for (@ARGV) {
- $ftp->get($_) or die "Unable to retrieve $_";
+
+if (@ARGV) {
+# file names on command line
+ for (@ARGV) {
+ fetch ($_)
+ }
+} else {
+# read file names from stdin
+ while (<> ) {
+ chomp;
+ $_ =~ s/\r$//;
+ print "$_\n";
+ fetch ($_)
+ }
+}
+
+if (@failed) {
+ my $errs = join ("\n", @failed);
+ print STDERR "\nFAILED TO DOWNLOAD:\n\n$errs\n";
+ exit 1;
}
diff --git a/gbf2xml b/gbf2xml
new file mode 100755
index 0000000..9653fdf
--- /dev/null
+++ b/gbf2xml
@@ -0,0 +1,515 @@
+#!/usr/bin/perl
+
+# ===========================================================================
+#
+# PUBLIC DOMAIN NOTICE
+# National Center for Biotechnology Information (NCBI)
+#
+# This software/database is a "United States Government Work" under the
+# terms of the United States Copyright Act. It was written as part of
+# the author's official duties as a United States Government employee and
+# thus cannot be copyrighted. This software/database is freely available
+# to the public for use. The National Library of Medicine and the U.S.
+# Government do not place any restriction on its use or reproduction.
+# We would, however, appreciate having the NCBI and the author cited in
+# any work or product based on this material.
+#
+# Although all reasonable efforts have been taken to ensure the accuracy
+# and reliability of the software and data, the NLM and the U.S.
+# Government do not and cannot warrant the performance or results that
+# may be obtained by using this software or data. The NLM and the U.S.
+# Government disclaim all warranties, express or implied, including
+# warranties of performance, merchantability or fitness for any particular
+# purpose.
+#
+# ===========================================================================
+#
+# File Name: gbf2xml
+#
+# Author: Jonathan Kans
+#
+# Version Creation Date: 6/8/17
+#
+# ==========================================================================
+
+use strict;
+use warnings;
+
+
+# Script to convert GenBank flatfiles to INSDSeq XML.
+#
+# Feature intervals that refer to 'far' locations, i.e., those not within
+# the cited record and which have an accession and colon, are suppressed.
+# Those rare features (e.g., trans-splicing between molecules) are lost.
+#
+# Keywords and References are currently not supported.
+
+
+# state variables for tracking current position in flatfile
+
+my $in_seq;
+my $in_feat;
+my $in_key;
+my $in_qual;
+my $in_def;
+my $in_tax;
+my $any_feat;
+my $any_qual;
+my $current_key;
+my $current_loc;
+my $current_qual;
+my $current_val;
+my $moltype;
+my $division;
+my $update_date;
+my $organism;
+my $source;
+my $taxonomy;
+my $topology;
+my $sequence;
+my $length;
+my $is_translation;
+my $curr_seq;
+my $locus;
+my $defline;
+my $accn;
+my $accndv;
+my $location_operator;
+my $is_comp;
+
+# subroutine to clear state variables for each flatfile
+# start in in_feat state to gracefully handle missing FEATURES/FH line
+
+sub clearflags {
+ $in_seq = 0;
+ $in_feat = 0;
+ $in_key = 0;
+ $in_qual = 0;
+ $in_def = 0;
+ $in_tax = 0;
+ $any_feat = 0;
+ $any_qual = 0;
+ $current_key = "";
+ $current_loc = "";
+ $current_qual = "";
+ $current_val = "";
+ $moltype = "";
+ $division = "";
+ $update_date = "";
+ $organism = "";
+ $source = "";
+ $taxonomy = "";
+ $topology = "";
+ $sequence = "";
+ $length = 0;
+ $is_translation = 0;
+ $curr_seq = "";
+ $locus = "";
+ $defline = "";
+ $accn = "";
+ $accndv = "";
+ $location_operator = "";
+ $is_comp = 0;
+}
+
+# recursive subroutine for parsing flatfile representation of feature location
+
+sub parseloc {
+ my $subloc = shift (@_);
+ my @working = ();
+
+ if ( $subloc =~ /^(join|order)\((.+)\)$/ ) {
+ $location_operator = $1;
+ my $temploc = $2;
+ my @items = split (',', $temploc);
+ foreach my $thisloc (@items ) {
+ if ( $thisloc !~ /^.*:.*$/ ) {
+ push (@working, parseloc ($thisloc));
+ }
+ }
+
+ } elsif ( $subloc =~ /^complement\((.+)\)$/ ) {
+ $is_comp = 1;
+ my $comploc = $1;
+ my @items = parseloc ($comploc);
+ my @rev = reverse (@items);
+ foreach my $thisloc (@rev ) {
+ if ( $thisloc =~ /^([^.]+)\.\.([^.]+)$/ ) {
+ $thisloc = "$2..$1";
+ }
+
+ if ( $thisloc =~ /^>([^.]+)\.\.([^.]+)$/ ) {
+ $thisloc = "<$1..$2";
+ }
+ if ( $thisloc =~ /^([^.]+)\.\.<([^.]+)$/ ) {
+ $thisloc = "$1..>$2";
+ }
+
+ if ( $thisloc !~ /^.*:.*$/ ) {
+ push (@working, parseloc ($thisloc));
+ }
+ }
+
+ } elsif ( $subloc !~ /^.*:.*$/ ) {
+ push (@working, $subloc);
+ }
+
+ return @working;
+}
+
+#subroutine to print next feature key / location / qualifier line
+
+sub flushline {
+ if ( $in_key == 1 ) {
+
+ if ( $any_qual == 1 ) {
+ print " </INSDFeature_quals>\n";
+ $any_qual = 0;
+ }
+
+ if ( $any_feat == 1 ) {
+ print " </INSDFeature>\n";
+ }
+ $any_feat = 1;
+
+ print " <INSDFeature>\n";
+
+ #print feature key and intervals
+ print " <INSDFeature_key>$current_key</INSDFeature_key>\n";
+
+ my $clean_loc = $current_loc;
+ $clean_loc =~ s/</</g;
+ $clean_loc =~ s/>/>/g;
+ print " <INSDFeature_location>$clean_loc</INSDFeature_location>\n";
+
+ print " <INSDFeature_intervals>\n";
+
+ # parse join() order() complement() ###..### location
+ $location_operator = 0;
+ $is_comp = 0;
+ my @theloc = parseloc ($current_loc);
+
+ # convert number (dot) (dot) number to number (tab) number
+ my $numivals = 0;
+ my $prime5 = 0;
+ my $prime3 = 0;
+ foreach my $thisloc (@theloc ) {
+ $numivals++;
+ print " <INSDInterval>\n";
+ if ( $thisloc =~ /^([^.]+)\.\.([^.]+)$/ ) {
+ my $fr = $1;
+ my $to = $2;
+ if ( $thisloc =~ /^</ ) {
+ $prime5 = 1;
+ }
+ if ( $thisloc =~ /\.\.>/ ) {
+ $prime3 = 1;
+ }
+ $fr =~ s/[<>]//;
+ $to =~ s/[<>]//;
+ print " <INSDInterval_from>$fr</INSDInterval_from>\n";
+ print " <INSDInterval_to>$to</INSDInterval_to>\n";
+ if ( $is_comp ) {
+ print " <INSDInterval_iscomp value=\"true\"/>\n";
+ }
+ print " <INSDInterval_accession>$accndv</INSDInterval_accession>\n";
+ } elsif ( $thisloc =~ /^(.+)\^(.+)$/ ) {
+ my $fr = $1;
+ my $to = $2;
+ $fr =~ s/[<>]//;
+ $to =~ s/[<>]//;
+ print " <INSDInterval_from>$fr</INSDInterval_from>\n";
+ print " <INSDInterval_to>$to</INSDInterval_to>\n";
+ if ( $is_comp ) {
+ print " <INSDInterval_iscomp value=\"true\"/>\n";
+ }
+ print " <INSDInterval_interbp value=\"true\"/>\n";
+ print " <INSDInterval_accession>$accndv</INSDInterval_accession>\n";
+ } elsif ( $thisloc =~ /^([^.]+)$/ ) {
+ my $pt = $1;
+ $pt =~ s/[<>]//;
+ print " <INSDInterval_point>$pt</INSDInterval_point>\n";
+ print " <INSDInterval_accession>$accndv</INSDInterval_accession>\n";
+ }
+ print " </INSDInterval>\n";
+ }
+
+ print " </INSDFeature_intervals>\n";
+
+ if ( $numivals > 1 ) {
+ print " <INSDFeature_operator>$location_operator</INSDFeature_operator>\n";
+ }
+ if ( $prime5 ) {
+ print " <INSDFeature_partial5 value=\"true\"/>\n";
+ }
+ if ( $prime3 ) {
+ print " <INSDFeature_partial3 value=\"true\"/>\n";
+ }
+
+ } elsif ( $in_qual == 1 ) {
+
+ if ( $any_qual == 0 ) {
+ print " <INSDFeature_quals>\n";
+ }
+ $any_qual = 1;
+
+ if ( $current_val eq "" ) {
+ print " <INSDQualifier>\n";
+ print " <INSDQualifier_name>$current_qual</INSDQualifier_name>\n";
+ print " </INSDQualifier>\n";
+ } else {
+ print " <INSDQualifier>\n";
+ print " <INSDQualifier_name>$current_qual</INSDQualifier_name>\n";
+ my $clean_val = $current_val;
+ $clean_val =~ s/</</g;
+ $clean_val =~ s/>/>/g;
+ print " <INSDQualifier_value>$clean_val</INSDQualifier_value>\n";
+ print " </INSDQualifier>\n";
+ }
+ }
+}
+
+# initialize flags and lists at start of program
+
+clearflags ();
+
+print "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
+print "<!DOCTYPE INSDSet PUBLIC \"-//NCBI//INSD INSDSeq/EN\" \"https://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd\">\n";
+print "<INSDSet>\n";
+
+# main loop reads one line at a time
+
+while (<> ) {
+ chomp;
+ $_ =~ s/\r$//;
+
+ # first check for extra definition or taxonomy lines, otherwise clear continuation flags
+ if ( $in_def ) {
+ if ( /^ {12}(.*)$/ ) {
+ $defline = $defline . " " . $1;
+ } else {
+ $in_def = 0;
+ }
+ } elsif ( $in_tax ) {
+ if ( /^ {12}(.*)$/ ) {
+ if ( $taxonomy eq "" ) {
+ $taxonomy = $1;
+ } else {
+ $taxonomy = $taxonomy . " " . $1;
+ }
+ } else {
+ $in_tax = 0;
+ }
+ }
+
+ if ( $in_def == 1 || $in_tax == 1 ) {
+
+ # continuation lines taken care of above
+
+ } elsif ( /^LOCUS\s+(\S*).*$/ ) {
+
+ # record locus
+ $locus = $1;
+ if ( / (\d+) bp / || / (\d+) aa / ) {
+ $length = $1;
+ }
+
+ if ( /^.*\s(\S+\s+\S+\s+\S+\s+\d+-\S+-\d+)$/ ) {
+ my $tail = $1;
+ if ( $tail =~ /^(\S*)\s+(\S*)\s+(\S*)\s+(\d*-\S*-\d*)$/ ) {
+ $moltype = $1;
+ $topology = $2;
+ $division = $3;
+ $update_date = $4;
+ $moltype = uc $moltype;
+ }
+ }
+
+ print " <INSDSeq>\n";
+
+ print " <INSDSeq_locus>$locus</INSDSeq_locus>\n";
+ print " <INSDSeq_length>$length</INSDSeq_length>\n";
+
+ if ( $moltype ne "" ) {
+ print " <INSDSeq_moltype>$moltype</INSDSeq_moltype>\n";
+ }
+ if ( $topology ne "" ) {
+ print " <INSDSeq_topology>$topology</INSDSeq_topology>\n";
+ }
+ if ( $division ne "" ) {
+ print " <INSDSeq_division>$division</INSDSeq_division>\n";
+ }
+ if ( $update_date ne "" ) {
+ print " <INSDSeq_update-date>$update_date</INSDSeq_update-date>\n";
+ }
+
+ } elsif ( /^DEFINITION\s*(.*).*$/ ) {
+
+ # record first line of definition line
+ $defline = $1;
+ # next line with leading spaces will be continuation of definition line
+ $in_def = 1;
+
+ } elsif ( /^ACCESSION\s*(\S*).*$/ ) {
+
+ # record accession
+ $accn = $1;
+
+ } elsif ( /^VERSION\s*(\S*).*$/ ) {
+
+ # record accession.version
+ $accndv = $1;
+
+ } elsif ( /^SOURCE\s*(.*)$/ ) {
+
+ # record source
+ $source = $1;
+
+ } elsif ( /^ {1,3}ORGANISM\s+(.*)$/ ) {
+
+ # record organism
+ if ( $organism eq "" ) {
+ $organism = $1;
+ if ( $organism =~ /^([^(]*) \(.*\)/ ) {
+ $organism = $1;
+ }
+ }
+ # next line with leading spaces will be start of taxonomy
+ $in_tax = 1;
+
+ } elsif ( /^FEATURES\s+.*$/ ) {
+
+ # beginning of feature table, flags already set up
+
+ # first print saved fields
+ $defline =~ s/\.$//;
+ $defline =~ s/</</g;
+ $defline =~ s/>/>/g;
+ if ( $defline ne "" ) {
+ print " <INSDSeq_definition>$defline</INSDSeq_definition>\n";
+ }
+ if ( $accn ne "" ) {
+ print " <INSDSeq_primary-accession>$accn</INSDSeq_primary-accession>\n";
+ }
+ if ( $accndv ne "" ) {
+ print " <INSDSeq_accession-version>$accndv</INSDSeq_accession-version>\n";
+ }
+
+ $in_feat = 1;
+
+ if ( $source ne "" ) {
+ print " <INSDSeq_source>$source</INSDSeq_source>\n";
+ }
+ if ( $organism ne "" ) {
+ print " <INSDSeq_organism>$organism</INSDSeq_organism>\n";
+ }
+ $taxonomy =~ s/\.$//;
+ if ( $taxonomy ne "" ) {
+ print " <INSDSeq_taxonomy>$taxonomy</INSDSeq_taxonomy>\n";
+ }
+
+ print " <INSDSeq_feature-table>\n";
+
+ } elsif ( /^ORIGIN\s*.*$/ ) {
+
+ # end of feature table, print final newline
+ flushline ();
+
+ if ( $any_qual == 1 ) {
+ print " </INSDFeature_quals>\n";
+ $any_qual = 0;
+ }
+
+ print " </INSDFeature>\n";
+
+ print " </INSDSeq_feature-table>\n";
+
+ $in_feat = 0;
+ $in_key = 0;
+ $in_qual = 0;
+ $is_translation = 0;
+ $in_seq = 1;
+
+ } elsif ( /^\/\/\.*/ ) {
+
+ # at end-of-record double slash
+ print " <INSDSeq_sequence>$sequence</INSDSeq_sequence>\n";
+ print " </INSDSeq>\n";
+ # reset variables for catenated flatfiles
+ clearflags ();
+
+ } elsif ( $in_seq == 1 ) {
+
+ if ( /^\s+\d+ (.*)$/ || /^\s+(.*)\s+\d+$/ ) {
+ # record sequence
+ $curr_seq = $1;
+ $curr_seq =~ s/ //g;
+ $curr_seq = lc $curr_seq;
+ if ( $sequence eq "" ) {
+ $sequence = $curr_seq;
+ } else {
+ $sequence = $sequence . $curr_seq;
+ }
+ }
+
+ } elsif ( $in_feat == 1 ) {
+
+ if ( /^ {1,10}(\w+)\s+(.*)$/ ) {
+ # new feature key and location
+ flushline ();
+
+ $in_key = 1;
+ $in_qual = 0;
+ $current_key = $1;
+ $current_loc = $2;
+
+ } elsif ( /^\s+\/(\w+)=(.*)$/ ) {
+ # new qualifier
+ flushline ();
+
+ $in_key = 0;
+ $in_qual = 1;
+ $current_qual = $1;
+ # remove leading double quote
+ my $val = $2;
+ $val =~ s/\"//g;
+ $current_val = $val;
+ if ( $current_qual =~ /(?:translation|transcription|peptide)/ ) {
+ $is_translation = 1;
+ } else {
+ $is_translation = 0;
+ }
+
+ } elsif ( /^\s+\/(\w+)$/ ) {
+ # new singleton qualifier - e.g., trans-splicing, pseudo
+ flushline ();
+
+ $in_key = 0;
+ $in_qual = 1;
+ $current_qual = $1;
+ $current_val = "";
+ $is_translation = 0;
+
+ } elsif ( /^\s+(.*)$/ ) {
+
+ if ( $in_key == 1 ) {
+ # continuation of feature location
+ $current_loc = $current_loc . $1;
+
+ } elsif ( $in_qual == 1 ) {
+ # continuation of qualifier
+ # remove trailing double quote
+ my $val = $1;
+ $val =~ s/\"//g;
+ if ( $is_translation == 1 ) {
+ $current_val = $current_val . $val;
+ } else {
+ $current_val = $current_val . " " . $val;
+ }
+ }
+ }
+ }
+}
+
+print "</INSDSet>\n";
+
diff --git a/xtract.go b/xtract.go
index 1ffcd35..ef609f1 100644
--- a/xtract.go
+++ b/xtract.go
@@ -71,7 +71,7 @@ import (
// VERSION AND HELP MESSAGE TEXT
-const xtractVersion = "6.70"
+const xtractVersion = "6.80"
const xtractHelp = `
Overview
@@ -334,7 +334,7 @@ Mammalian Sequence Download
ftp-ls ftp.ncbi.nlm.nih.gov ncbi-asn1 |
grep -e gbmam -e gbpri -e gbrod |
- xargs ftp-cp ftp.ncbi.nlm.nih.gov ncbi-asn1
+ ftp-cp ftp.ncbi.nlm.nih.gov ncbi-asn1
Human Subset Extraction
@@ -345,39 +345,17 @@ Human Subset Extraction
run-ncbi-converter asn2all -i "$fl" -a t -b -c -O 9606 -f s > ${fl%.aso.gz}.xml
done
-PubMed Fetch Script
-
- DownloadPubmed() {
- failed=""
- while read fl
- do
- if [ ! -f "$fl" ]
- then
- echo "$fl"
- ftp-cp ftp.ncbi.nlm.nih.gov "$1" "$fl"
- fi
- if [ ! -f "$fl" ]
- then
- failed="$failed\n$fl"
- fi
- done
- if [ -n "$failed" ]
- then
- echo -e "\nFAILED TO DOWNLOAD:\n$failed\n" >&2
- fi
- }
-
PubMed Download
ftp-ls ftp.ncbi.nlm.nih.gov pubmed/baseline |
grep -v ".md5" | grep "xml.gz" |
- DownloadPubmed pubmed/baseline
+ ftp-cp ftp.ncbi.nlm.nih.gov pubmed/baseline
PubMed Update
ftp-ls ftp.ncbi.nlm.nih.gov pubmed/updatefiles |
grep -v ".md5" | grep "xml.gz" |
- DownloadPubmed pubmed/updatefiles
+ ftp-cp ftp.ncbi.nlm.nih.gov pubmed/updatefiles
PubMed Unpacking
@@ -462,44 +440,23 @@ Reconstruct Release Files
done
rm -rf uids-???
-Aspera PubMed Fetch Script
-
- AsperaDownloadPubmed() {
- failed=""
- while read fl
- do
- if [ ! -f "$TARGET/$fl" ]
- then
- echo "$fl"
- "$ASPERA/ascp" -T -k 1 -l 50m -i "$ASPERA/asperaweb_id_dsa.openssh" \
- "anonftp at ftp.ncbi.nlm.nih.gov:/$1/$fl" "$TARGET"
- fi
- if [ ! -f "$TARGET/$fl" ]
- then
- failed="$failed\n$fl"
- fi
- done
- if [ -n "$failed" ]
- then
- echo -e "\nFAILED TO DOWNLOAD:\n$failed\n" >&2
- fi
- }
-
Aspera PubMed Download
- export ASPERA="$HOME/Applications/Aspera Connect.app/Contents/Resources"
- export TARGET="/Volumes/scientia/Release"
- ftp-ls ftp.ncbi.nlm.nih.gov pubmed/baseline |
+ asp-ls pubmed/baseline |
grep -v ".md5" | grep "xml.gz" |
- AsperaDownloadPubmed pubmed/baseline
+ asp-cp pubmed/baseline
Aspera PubMed Update
- export ASPERA="$HOME/Applications/Aspera Connect.app/Contents/Resources"
- export TARGET="/Volumes/scientia/Release"
- ftp-ls ftp.ncbi.nlm.nih.gov pubmed/baseline |
+ asp-ls pubmed/baseline |
grep -v ".md5" | grep "xml.gz" |
- AsperaDownloadPubmed pubmed/updatefiles
+ asp-cp pubmed/updatefiles
+
+Aspera Sequence Download
+
+ asp-ls ncbi-asn1 |
+ grep -e gbmam -e gbpri -e gbrod |
+ asp-cp ncbi-asn1
`
const xtractInternal = `
--
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