[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 567a970b095f1da61430fb8ffdcb421b26280d76
Author: Horea Christian chymera eu>
AuthorDate: Sun Sep 27 21:15:41 2020 +
Commit: Horea Christian gmail com>
CommitDate: Sun Sep 27 21:15:41 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=567a970b
sci-biology/full_lengther_next: removed unmaintained package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian chymera.eu>
.../full_lengther_next-0.6.2.ebuild| 39 --
sci-biology/full_lengther_next/metadata.xml| 12 ---
2 files changed, 51 deletions(-)
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
deleted file mode 100644
index c333d2990..0
--- a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Classify assembled transcripts and fix frameshifts in ORFs"
-HOMEPAGE="http://www.rubydoc.info/gems/full_lengther_next
- http://www.scbi.uma.es/site/scbi/downloads/313-full-lengthernext";
-# https://rubygems.org/gems/full_lengther_next/versions/0.0.8
-# http://www.rubydoc.info/gems/full_lengther_next
-#
https://www.omniref.com/ruby/gems/full_lengther_next/0.0.8/symbols/FullLengtherNext
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
- >=dev-ruby/hoe-2.8.0
- >=dev-ruby/rdoc-3.10
- dev-ruby/bundler"
- # >=dev-ruby/newgem-1.5.3
-RDEPEND="${DEPEND}
- sci-biology/bioruby
- >=sci-biology/bio-cd-hit-report-0.1.0
- >=sci-biology/scbi_blast-0.0.37
- >=sci-biology/scbi_fasta-0.1.7
- >=sci-biology/scbi_zcat-0.0.2
- >=sci-biology/scbi_mapreduce-0.0.29
- >=sci-biology/scbi_plot-0.0.6
- >=dev-ruby/xml-simple-1.0.12
- >=dev-ruby/gnuplot-2.3.0"
diff --git a/sci-biology/full_lengther_next/metadata.xml
b/sci-biology/full_lengther_next/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/full_lengther_next/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 7e131dda52252fc29eed23acaa32a7add89c2ad2 Author: David Seifert gentoo org> AuthorDate: Sat Sep 2 11:55:25 2017 + Commit: David Seifert gentoo org> CommitDate: Sat Sep 2 11:55:25 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e131dda sci-biology/full_lengther_next: Update USE_RUBY to fix breakages Package-Manager: Portage-2.3.8, Repoman-2.3.3 sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild index 262ffddf5..c333d2990 100644 --- a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild +++ b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild @@ -3,7 +3,7 @@ EAPI=6 -USE_RUBY="ruby21" +USE_RUBY="ruby22 ruby23 ruby24" RUBY_FAKEGEM_TASK_DOC="" RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 2d80fd5e11977e2747dba7ac7737358599f08ac1 Author: Justin Lecher gentoo org> AuthorDate: Sun Mar 26 08:56:59 2017 + Commit: Justin Lecher gentoo org> CommitDate: Sun Mar 26 08:56:59 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d80fd5e sci-biology/full_lengther_next: Drop obsolete ruby version Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher gentoo.org> sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild | 10 ++ 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild index 5e2cb404d..262ffddf5 100644 --- a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild +++ b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild @@ -1,8 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 -USE_RUBY="ruby20 ruby21" +EAPI=6 + +USE_RUBY="ruby21" RUBY_FAKEGEM_TASK_DOC="" RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt" @@ -21,7 +22,8 @@ SLOT="0" KEYWORDS="~amd64" IUSE="" -DEPEND=">=dev-ruby/hoe-2.8.0 +DEPEND=" + >=dev-ruby/hoe-2.8.0 >=dev-ruby/rdoc-3.10 dev-ruby/bundler" # >=dev-ruby/newgem-1.5.3
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 268b423672eb86dd87e9db1029a21447f1dae3b4
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat May 7 14:36:25 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat May 7 14:36:25 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=268b4236
sci-biology/full_lengther_next: version bump
Package-Manager: portage-2.2.28
.../{full_lengther_next-0.6.1.ebuild => full_lengther_next-0.6.2.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.1.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
similarity index 100%
rename from sci-biology/full_lengther_next/full_lengther_next-0.6.1.ebuild
rename to sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 3629be6ae68b81f8f11f010edec9d57772d3cf59
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue May 3 16:39:23 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue May 3 16:39:23 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3629be6a
sci-biology/full_lengther_next: version bump
Package-Manager: portage-2.2.28
.../{full_lengther_next-0.6.0.ebuild => full_lengther_next-0.6.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.6.1.ebuild
similarity index 100%
rename from sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
rename to sci-biology/full_lengther_next/full_lengther_next-0.6.1.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 38be5e9dfc05edf1648b9e6a4818d94117dc6d6b
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Apr 27 18:09:55 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Apr 27 18:09:55 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=38be5e9d
sci-biology/full_lengther_next: version bump; added more new DEPSs
Package-Manager: portage-2.2.28
sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild | 4
1 file changed, 4 insertions(+)
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
index 64d300a..4348fcf 100644
--- a/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
+++ b/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
@@ -23,11 +23,15 @@ KEYWORDS="~amd64"
IUSE=""
DEPEND=">=dev-ruby/hoe-2.8.0
+ >=dev-ruby/rdoc-3.10
dev-ruby/bundler"
+ # >=dev-ruby/newgem-1.5.3
RDEPEND="${DEPEND}
sci-biology/bioruby
+ >=sci-biology/bio-cd-hit-report-0.1.0
>=sci-biology/scbi_blast-0.0.37
>=sci-biology/scbi_fasta-0.1.7
+ >=sci-biology/scbi_zcat-0.0.2
>=sci-biology/scbi_mapreduce-0.0.29
>=sci-biology/scbi_plot-0.0.6
>=dev-ruby/xml-simple-1.0.12
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/files/, sci-biology/full_lengther_next/
commit: 85fe7624385b5d424a1d250106a55c4aad74217f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 26 12:07:50 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 26 12:07:50 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=85fe7624
sci-biology/full_lengther_next: version bump
Package-Manager: portage-2.2.28
.../full_lengther_next/files/download_fln_dbs.rb | 260 -
5.7.ebuild => full_lengther_next-0.6.0.ebuild} | 7 +-
2 files changed, 1 insertion(+), 266 deletions(-)
diff --git a/sci-biology/full_lengther_next/files/download_fln_dbs.rb
b/sci-biology/full_lengther_next/files/download_fln_dbs.rb
deleted file mode 100644
index 90eacbb..000
--- a/sci-biology/full_lengther_next/files/download_fln_dbs.rb
+++ /dev/null
@@ -1,260 +0,0 @@
-#!/usr/bin/env ruby
-
-# 15-2-2011 Noe Fernandez-Pozo
-# Script to download Full-LengtherNext databases.
-# Once in UniProtKB/Swiss-Prot, a protein entry is removed from
UniProtKB/TrEMBL.
-
-require 'net/ftp'
-require 'open-uri'
-
-class FtpClient
-
-def initialize
-end
-
-def connect(server)
- @server=server
-end
-
-def login
-
-end
-
-def chdir(dir)
- @dir=dir
-end
-
-def getbinaryfile(file,output_file)
- if !File.exists?(output_file) &&
!File.exists?(output_file.gsub('.gz',''))
- puts " - Downloading"
- cmd="wget #{@server}/#{@dir}/#{file} -O #{output_file}"
- system(cmd)
-else
- puts "File #{output_file}, or #{output_file.gsub('.gz','')} already
exists. Skip download"
-end
-
-end
-
-def close
-end
-
-end
-### Functions
-
-def download_ncrna(formatted_db_path)
-
- if !File.exists?(File.join(formatted_db_path, "nc_rna_db"))
- Dir.mkdir(File.join(formatted_db_path, "nc_rna_db"))
- end
-
- puts "Downloading ncRNA database"
- open(File.join(formatted_db_path, "nc_rna_db/ncrna_fln_100.fasta.zip"),
"wb") do |my_file|
- my_file.print
open('http://www.scbi.uma.es/downloads/FLNDB/ncrna_fln_100.fasta.zip').read
- end
- puts "\nncRNA database downloaded"
-
-
ncrna_zip=File.join(formatted_db_path,'nc_rna_db','ncrna_fln_100.fasta.zip')
- ncrna_out_dir=File.join(formatted_db_path,'nc_rna_db')
- system("unzip", ncrna_zip, "-d", ncrna_out_dir)
- system("rm", ncrna_zip)
-
- puts "\nncRNA database decompressed"
-
-
ncrna_fasta=File.join(formatted_db_path,'nc_rna_db','ncrna_fln_100.fasta')
- system("makeblastdb", "-in", ncrna_fasta, "-dbtype", "nucl",
"-parse_seqids")
-
- puts "\nncRNA database completed"
-end
-
-def conecta_uniprot(my_array, formatted_db_path)
-
- #$ftp = Net::FTP.new()
- $ftp = FtpClient.new()
-
- if !File.exists?(formatted_db_path)
- Dir.mkdir(formatted_db_path)
- end
-
- $ftp.connect('ftp://ftp.uniprot.org')
-
- $ftp.login
-
- puts "connected to UniProt"
-
- my_array.each do |db_group|
- puts "Downloading #{db_group}"
- download_uniprot(db_group, formatted_db_path)
- end
-
-
varsplic_out=File.join(formatted_db_path,'uniprot_sprot_varsplic.fasta.gz')
-
$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/complete")
- $ftp.getbinaryfile("uniprot_sprot_varsplic.fasta.gz", varsplic_out)
-
- puts "isoform files downloaded"
-
- $ftp.close
-
-end
-
-def download_uniprot(uniprot_group, formatted_db_path)
-
-
sp_out=File.join(formatted_db_path,"uniprot_sprot_#{uniprot_group}.dat.gz")
-
tr_out=File.join(formatted_db_path,"uniprot_trembl_#{uniprot_group}.dat.gz")
-
$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions")
- puts " from
ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_#{uniprot_group}.dat.gz"
- puts " from
ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_#{uniprot_group}.dat.gz"
- $ftp.getbinaryfile("uniprot_sprot_#{uniprot_group}.dat.gz", sp_out)
- $ftp.getbinaryfile("uniprot_trembl_#{uniprot_group}.dat.gz", tr_out)
-
- puts "#{uniprot_group} files downloaded"
-
-end
-
-def filter_incomplete_seqs(file_name, isoform_hash, formatted_db_path)
-
- puts "filtering sequences from #{file_name}"
-
- # UniProtKB fragments with FT NON_CONS and FT NON_TER features.
- #
- # * FT NON_TER: The residue at an extremity of the sequence is not
the terminal residue. If applied to position 1, this signifies that the first
position is not the N-terminus of the complete molecule. If applied to the last
position, it means that this position is
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 4df929cb91f6716fb1702ad0c92689c44b4bbd89
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Mar 13 17:30:53 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Mar 13 17:30:53 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4df929cb
sci-biology/full_lengther_next: added more DEPENDencies, added more relevant
HOMEPAGE
Package-Manager: portage-2.2.26
.../full_lengther_next/full_lengther_next-0.5.7.ebuild | 12
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
index 52412c0..1f3476f 100644
--- a/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
+++ b/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
@@ -11,9 +11,10 @@ RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
inherit ruby-fakegem
DESCRIPTION="Classify assembled transcripts and fix frameshifts in ORFs"
-HOMEPAGE="http://www.scbi.uma.es/site/scbi/downloads/313-full-lengthernext";
+HOMEPAGE="http://www.rubydoc.info/gems/full_lengther_next
+ http://www.scbi.uma.es/site/scbi/downloads/313-full-lengthernext";
# https://rubygems.org/gems/full_lengther_next/versions/0.0.8
-# http://www.rubydoc.info/gems/full_lengther_next/0.0.8/frames
+# http://www.rubydoc.info/gems/full_lengther_next
#
https://www.omniref.com/ruby/gems/full_lengther_next/0.0.8/symbols/FullLengtherNext
LICENSE="MIT"
@@ -21,13 +22,16 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=">=dev-ruby/hoe-2.8.0"
+DEPEND=">=dev-ruby/hoe-2.8.0
+ dev-ruby/bundler"
RDEPEND="${DEPEND}
+ sci-biology/bioruby
>=sci-biology/scbi_blast-0.0.37
>=sci-biology/scbi_fasta-0.1.7
>=sci-biology/scbi_mapreduce-0.0.29
>=sci-biology/scbi_plot-0.0.6
- >=dev-ruby/xml-simple-1.0.12"
+ >=dev-ruby/xml-simple-1.0.12
+ >=dev-ruby/gnuplot-2.3.0"
#src_prepare(){
# cp "${FILESDIR}"/download_fln_dbs.rb all/full_lengther_next-0.0.8/bin
|| die
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 647b66f0280dbf78d736abbe107f3fd93996616f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Mar 13 00:13:19 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Mar 13 00:13:19 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=647b66f0
sci-biology/full_lengther_next: version bump
Package-Manager: portage-2.2.26
.../{full_lengther_next-0.5.6.ebuild => full_lengther_next-0.5.7.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.5.6.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
similarity index 100%
rename from sci-biology/full_lengther_next/full_lengther_next-0.5.6.ebuild
rename to sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/, sci-biology/full_lengther_next/files/
commit: e870de5e7451b02cb563d5567dcb7ddccced0eab
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Feb 10 14:50:27 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Feb 10 14:50:27 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e870de5e
sci-biology/full_lengther_next: version bump
Package-Manager: portage-2.2.26
.../full_lengther_next/files/download_fln_dbs.rb | 260 +
0.8.ebuild => full_lengther_next-0.5.6.ebuild} | 5 +
2 files changed, 265 insertions(+)
diff --git a/sci-biology/full_lengther_next/files/download_fln_dbs.rb
b/sci-biology/full_lengther_next/files/download_fln_dbs.rb
new file mode 100644
index 000..90eacbb
--- /dev/null
+++ b/sci-biology/full_lengther_next/files/download_fln_dbs.rb
@@ -0,0 +1,260 @@
+#!/usr/bin/env ruby
+
+# 15-2-2011 Noe Fernandez-Pozo
+# Script to download Full-LengtherNext databases.
+# Once in UniProtKB/Swiss-Prot, a protein entry is removed from
UniProtKB/TrEMBL.
+
+require 'net/ftp'
+require 'open-uri'
+
+class FtpClient
+
+def initialize
+end
+
+def connect(server)
+ @server=server
+end
+
+def login
+
+end
+
+def chdir(dir)
+ @dir=dir
+end
+
+def getbinaryfile(file,output_file)
+ if !File.exists?(output_file) &&
!File.exists?(output_file.gsub('.gz',''))
+ puts " - Downloading"
+ cmd="wget #{@server}/#{@dir}/#{file} -O #{output_file}"
+ system(cmd)
+else
+ puts "File #{output_file}, or #{output_file.gsub('.gz','')} already
exists. Skip download"
+end
+
+end
+
+def close
+end
+
+end
+### Functions
+
+def download_ncrna(formatted_db_path)
+
+ if !File.exists?(File.join(formatted_db_path, "nc_rna_db"))
+ Dir.mkdir(File.join(formatted_db_path, "nc_rna_db"))
+ end
+
+ puts "Downloading ncRNA database"
+ open(File.join(formatted_db_path, "nc_rna_db/ncrna_fln_100.fasta.zip"),
"wb") do |my_file|
+ my_file.print
open('http://www.scbi.uma.es/downloads/FLNDB/ncrna_fln_100.fasta.zip').read
+ end
+ puts "\nncRNA database downloaded"
+
+
ncrna_zip=File.join(formatted_db_path,'nc_rna_db','ncrna_fln_100.fasta.zip')
+ ncrna_out_dir=File.join(formatted_db_path,'nc_rna_db')
+ system("unzip", ncrna_zip, "-d", ncrna_out_dir)
+ system("rm", ncrna_zip)
+
+ puts "\nncRNA database decompressed"
+
+
ncrna_fasta=File.join(formatted_db_path,'nc_rna_db','ncrna_fln_100.fasta')
+ system("makeblastdb", "-in", ncrna_fasta, "-dbtype", "nucl",
"-parse_seqids")
+
+ puts "\nncRNA database completed"
+end
+
+def conecta_uniprot(my_array, formatted_db_path)
+
+ #$ftp = Net::FTP.new()
+ $ftp = FtpClient.new()
+
+ if !File.exists?(formatted_db_path)
+ Dir.mkdir(formatted_db_path)
+ end
+
+ $ftp.connect('ftp://ftp.uniprot.org')
+
+ $ftp.login
+
+ puts "connected to UniProt"
+
+ my_array.each do |db_group|
+ puts "Downloading #{db_group}"
+ download_uniprot(db_group, formatted_db_path)
+ end
+
+
varsplic_out=File.join(formatted_db_path,'uniprot_sprot_varsplic.fasta.gz')
+
$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/complete")
+ $ftp.getbinaryfile("uniprot_sprot_varsplic.fasta.gz", varsplic_out)
+
+ puts "isoform files downloaded"
+
+ $ftp.close
+
+end
+
+def download_uniprot(uniprot_group, formatted_db_path)
+
+
sp_out=File.join(formatted_db_path,"uniprot_sprot_#{uniprot_group}.dat.gz")
+
tr_out=File.join(formatted_db_path,"uniprot_trembl_#{uniprot_group}.dat.gz")
+
$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions")
+ puts " from
ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_#{uniprot_group}.dat.gz"
+ puts " from
ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_#{uniprot_group}.dat.gz"
+ $ftp.getbinaryfile("uniprot_sprot_#{uniprot_group}.dat.gz", sp_out)
+ $ftp.getbinaryfile("uniprot_trembl_#{uniprot_group}.dat.gz", tr_out)
+
+ puts "#{uniprot_group} files downloaded"
+
+end
+
+def filter_incomplete_seqs(file_name, isoform_hash, formatted_db_path)
+
+ puts "filtering sequences from #{file_name}"
+
+ # UniProtKB fragments with FT NON_CONS and FT NON_TER features.
+ #
+ # * FT NON_TER: The residue at an extremity of the sequence is not
the terminal residue. If applied to position 1, this signifies that the first
position is not the N-terminus of the complete molecule. If applied to the last
position, it means that this position is not the C-terminus o
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 2838a866558aaa6a54eb8b070f0a25fe18d9410d Author: Marius Brehler linux sungazer de> AuthorDate: Fri Dec 25 20:54:34 2015 + Commit: Marius Brehler linux sungazer de> CommitDate: Fri Dec 25 20:54:34 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2838a866 sci-biology/full_lengther_next: Fix header, remove ruby19 Package-Manager: portage-2.2.24 sci-biology/full_lengther_next/ChangeLog | 4 sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/sci-biology/full_lengther_next/ChangeLog b/sci-biology/full_lengther_next/ChangeLog index 641611d..6ae9e13 100644 --- a/sci-biology/full_lengther_next/ChangeLog +++ b/sci-biology/full_lengther_next/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ + 25 Dec 2015; Marius Brehler + full_lengther_next-0.0.8.ebuild: + sci-biology/full_lengther_next: Fix header, remove ruby19 + *full_lengther_next-0.0.8 (02 Dec 2015) 02 Dec 2015; Martin Mokrejs diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild b/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild index 77908a9..0465bc0 100644 --- a/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild +++ b/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Id$ EAPI=5 -USE_RUBY="ruby19 ruby20 ruby21" +USE_RUBY="ruby20 ruby21" RUBY_FAKEGEM_TASK_DOC="" RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
[gentoo-commits] proj/sci:master commit in: sci-biology/full_lengther_next/
commit: 4c9b70f59eea90bb9506dad00c536c7a89b6cf50
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Dec 2 22:21:09 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Dec 2 22:21:09 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4c9b70f5
sci-biology/full_lengther_next: new package
Package-Manager: portage-2.2.26
sci-biology/full_lengther_next/ChangeLog | 9 +++
.../full_lengther_next-0.0.8.ebuild| 30 ++
sci-biology/full_lengther_next/metadata.xml| 12 +
3 files changed, 51 insertions(+)
diff --git a/sci-biology/full_lengther_next/ChangeLog
b/sci-biology/full_lengther_next/ChangeLog
new file mode 100644
index 000..641611d
--- /dev/null
+++ b/sci-biology/full_lengther_next/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/full_lengther_next
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*full_lengther_next-0.0.8 (02 Dec 2015)
+
+ 02 Dec 2015; Martin Mokrejs
+ +full_lengther_next-0.0.8.ebuild, +metadata.xml:
+ sci-biology/full_lengther_next: new package
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild
new file mode 100644
index 000..77908a9
--- /dev/null
+++ b/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+USE_RUBY="ruby19 ruby20 ruby21"
+
+RUBY_FAKEGEM_TASK_DOC=""
+RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
+
+inherit ruby-fakegem
+
+DESCRIPTION="Classify assembled transcripts and fix frameshifts in ORFs"
+HOMEPAGE="http://www.scbi.uma.es/site/scbi/downloads/313-full-lengthernext";
+# https://rubygems.org/gems/full_lengther_next/versions/0.0.8
+# http://www.rubydoc.info/gems/full_lengther_next/0.0.8/frames
+#
https://www.omniref.com/ruby/gems/full_lengther_next/0.0.8/symbols/FullLengtherNext
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=dev-ruby/hoe-2.8.0"
+RDEPEND="${DEPEND}
+ >=sci-biology/scbi_blast-0.0.37
+ >=sci-biology/scbi_fasta-0.1.7
+ >=sci-biology/scbi_mapreduce-0.0.29
+ >=sci-biology/scbi_plot-0.0.6
+ >=dev-ruby/xml-simple-1.0.12"
diff --git a/sci-biology/full_lengther_next/metadata.xml
b/sci-biology/full_lengther_next/metadata.xml
new file mode 100644
index 000..5fa67e9
--- /dev/null
+++ b/sci-biology/full_lengther_next/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+trinityrnaseq/trinityrnaseq
+
+
