[med-svn] [Git][med-team/transtermhp][master] 13 commits: Add python3 support
Nilesh Patra
gitlab at salsa.debian.org
Thu Aug 20 13:36:30 BST 2020
Nilesh Patra pushed to branch master at Debian Med / transtermhp
Commits:
5a9744be by Nilesh Patra at 2020-08-20T17:43:23+05:30
Add python3 support
- - - - -
2360dd7b by Nilesh Patra at 2020-08-20T17:45:03+05:30
Add autopkgtests
- - - - -
0a8d0bad by Nilesh Patra at 2020-08-20T17:45:20+05:30
Install relevant examples
- - - - -
885ae24f by Nilesh Patra at 2020-08-20T17:52:38+05:30
Add patch description
- - - - -
d0e074b7 by Nilesh Patra at 2020-08-20T17:53:09+05:30
Fix with cme
- - - - -
e3e10c45 by Nilesh Patra at 2020-08-20T17:54:58+05:30
Update changelog
- - - - -
ca2be496 by Nilesh Patra at 2020-08-20T17:56:38+05:30
routine-update: Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
472d560d by Nilesh Patra at 2020-08-20T17:56:39+05:30
routine-update: Add salsa-ci file
- - - - -
4e70a847 by Nilesh Patra at 2020-08-20T17:56:39+05:30
routine-update: Rules-Requires-Root: no
- - - - -
87c85268 by Nilesh Patra at 2020-08-20T17:56:46+05:30
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
f808ac49 by Nilesh Patra at 2020-08-20T17:56:47+05:30
Set field Upstream-Contact in debian/copyright.
Changes-By: lintian-brush
- - - - -
702de422 by Nilesh Patra at 2020-08-20T17:56:54+05:30
Remove obsolete field Contact from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
beebc37e by Nilesh Patra at 2020-08-20T18:04:36+05:30
Update to secure URLs
- - - - -
15 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/2to3.patch
- debian/patches/series
- + debian/salsa-ci.yml
- + debian/tests/README
- + debian/tests/control
- + debian/tests/data/infile.fasta
- + debian/tests/run-unit-test
- + debian/transtermhp.examples
- debian/transtermhp.install
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,26 @@
+transtermhp (2.09-5) UNRELEASED; urgency=medium
+
+ [ Steffen Moeller ]
+ * d/u/metadata: yamllint
+ * Update metadata with ref to conda
+
+ [ Nilesh Patra ]
+ * Add python3 support
+ * Add autopkgtests
+ * Install relevant examples
+ * Add patch description
+ * Fix with cme
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+ update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Use secure URI in Homepage field.
+ * Set field Upstream-Contact in debian/copyright.
+ * Remove obsolete field Contact from debian/upstream/metadata (already present
+ in machine-readable debian/copyright).
+
+ -- Nilesh Patra <npatra974 at gmail.com> Thu, 20 Aug 2020 17:54:42 +0530
+
transtermhp (2.09-4) unstable; urgency=medium
[ Steffen Möller ]
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -5,11 +5,12 @@ Uploaders: Alexandre Mestiashvili <mestia at debian.org>,
Fabian Klötzl <kloetzl at evolbio.mpg.de>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11)
-Standards-Version: 4.1.4
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/transtermhp
Vcs-Git: https://salsa.debian.org/med-team/transtermhp.git
-Homepage: http://transterm.cbcb.umd.edu/
+Homepage: https://transterm.cbcb.umd.edu/
+Rules-Requires-Root: no
Package: transtermhp
Architecture: any
=====================================
debian/copyright
=====================================
@@ -1,9 +1,10 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: transterm_hp
-Source: http://transterm.cbcb.umd.edu/index.php
+Source: https://transterm.cbcb.umd.edu/index.php
Files-Excluded:
2ndscore
transterm
+Upstream-Contact: Carl Kingsford <carlk at umiacs.umd.edu>
Files: *
Copyright: Carl Kingsford carlk at umiacs.umd.edu
@@ -33,7 +34,7 @@ License: GPL-2.0+
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
+ along with this program. If not, see <https://www.gnu.org/licenses/>
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,115 @@
+Author: Nilesh Patra <npatra974 at gmail.com>
+Description: Remove python-2 relevant code, use python3 support.
+Last Changed: August 20, 2020
+--- a/make_expterm.py
++++ b/make_expterm.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ import sys
+
+@@ -73,11 +73,11 @@
+ j = int((tail - min_tail[at])/dy)
+
+ if i == 0 or j == 0:
+- print >> sys.stderr, at, i, j, hp, tail, min_hp[at], min_tail[at], dx, dy
++ print(at, i, j, hp, tail, min_hp[at], min_tail[at], dx, dy, file=sys.stderr)
+
+ if not (0 <= i < num_bins and 0 <= j < num_bins):
+- print >> sys.stderr, "WARNING: out of range values:", i, j, at, hp, tail
+- print >> sys.stderr, "Ranges=", min_hp[at], max_hp[at], min_tail[at], max_tail[at]
++ print("WARNING: out of range values:", i, j, at, hp, tail, file=sys.stderr)
++ print("Ranges=", min_hp[at], max_hp[at], min_tail[at], max_tail[at], file=sys.stderr)
+ continue
+
+ D[at][i][j] += 1
+@@ -90,12 +90,12 @@
+ def warn_if_out_of_range(value, rng, title):
+ if value <= rng[0] or value >= rng[1]:
+ if title not in warned:
+- print >> sys.stderr, "@" * 60
+- print >> sys.stderr, """WARNING: random %s generated with energy lower than supplied range.
++ print("@" * 60, file=sys.stderr)
++ print("""WARNING: random %s generated with energy lower than supplied range.
+ Such examples are ignored. I suggest you re-run calibrate.sh after changing
+- the lowerbound in the range variable therein.""" % (title)
+- print >> sys.stderr, "Range = ", rng, "Seen = ", value
+- print >> sys.stderr, "@" * 60
++ the lowerbound in the range variable therein.""" % (title), file=sys.stderr)
++ print("Range = ", rng, "Seen = ", value, file=sys.stderr)
++ print("@" * 60, file=sys.stderr)
+ warned[title] = True
+ return True
+ return False
+@@ -105,8 +105,8 @@
+ """Write out the matrix (transposed)"""
+ for j in range(len(A)):
+ for i in range(len(A)):
+- print A[i][j],
+- print
++ print(A[i][j], end=' ')
++ print()
+
+
+ def main():
+@@ -118,14 +118,14 @@
+ #tail_range = (float(sys.argv[6]), float(sys.argv[7]))
+
+ # print the header
+- print seqlen, num_bins # hp_range[0], hp_range[1], tail_range[0], tail_range[1]
++ print(seqlen, num_bins) # hp_range[0], hp_range[1], tail_range[0], tail_range[1]
+
+ set_ranges_from_file(infile, num_bins)
+ D = hist2d_from_file(infile, num_bins) #, hp_range, tail_range)
+
+ # for every at value, compute and print the matrix
+ for at in sorted(D):
+- print at, min_hp[at], max_hp[at], min_tail[at], max_tail[at]
++ print(at, min_hp[at], max_hp[at], min_tail[at], max_tail[at])
+ print_matrix(D[at])
+
+ if __name__ == '__main__': main()
+--- a/random_fasta.py
++++ b/random_fasta.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ # generate a FASTA file with length random characters
+ import random, sys
+@@ -11,7 +11,7 @@
+
+ def random_fasta(fasta, length, at):
+ fasta = open(fasta, 'w')
+- print >> fasta, ">random uniform length=", length
++ print(">random uniform length=", length, file=fasta)
+
+ for i in range(1,length+1):
+ fasta.write(random_base(at))
+@@ -26,7 +26,7 @@
+ i += random.randint(5, 500)
+ j = i + random.randint(200, 2000)
+ if(j < length):
+- print >> coords, "UNK", i, j, "random"
++ print("UNK", i, j, "random", file=coords)
+ i = j
+ coords.close()
+
+--- a/calibrate.sh
++++ b/calibrate.sh
+@@ -52,11 +52,11 @@
+ MAKE_EXPTERM=`findprog make_expterm.py`
+
+ #==============================
+-# Ensure python is avialable
++# Ensure python3 is avialable
+ #==============================
+
+-if [ ! -x "`which python`" ] ; then
+- echo "`basename $0`: python must be installed to run calibration scripts" > /dev/stderr
++if [ ! -x "`which python3`" ] ; then
++ echo "`basename $0`: python3 must be installed to run calibration scripts" > /dev/stderr
+ exit 3
+ fi
+
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
hardening.patch
0002-read_seq-return-NULL-instead-of-false.patch
0003-Don-t-overwrite-CXXFLAGS.patch
+2to3.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/tests/README
=====================================
@@ -0,0 +1,5 @@
+Tests for transtermhp
+====================
+
+The data for tests has been referenced from:
+ http://crispr.otago.ac.nz/newTTDB/
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @, python3
+Restrictions: allow-stderr
+
=====================================
debian/tests/data/infile.fasta
=====================================
@@ -0,0 +1,38 @@
+>9258
+GGCGGUCGGAGGGACUCACCCUCUGACCUCUCCA
+>9361
+UGGCCACCACCUGGAAUUCAGAAUGGGGCGCCCAGAACGCACCAGGGCCUGGGGUUGGGAUUCCCGAGUGGGAGCCCUUGGGGCGCUGGGAAUGCGGAGGCCGGGGCUGCUUUGGCUCCUGUCAGAGCCCUUCGGCCAUCCCUGACCUAGAACCUGACGUGAGUGGACCCCAGACCUCCCGCUCUCCAGGUGUUUCCAGACUGUUCCCUGAGAGCGGAGCCCAGCCCCUGCCCCUCCCCACAGGACGCACUCCCUAUUUAUGUUUGCACUAGAGGUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUGACCAAUUAACUUAUUUAUUCGGGAGGUUGGGGUGUCCCAGGGGACCCAGCGUAGGGACAGCCUUGGCUCUGGCGUGUUUUCUGUGAAAACGGAGCCGAGCCGUGGGCUGCUCCCCCUUGGCCUCCUGGCCUCCGUGCCUCCCUUCGCUUAUGUUUUGAAGAAAUAUUUAUCUGAUCAAGUUGUCUGAAUAAUGCUGAUUUGGUGACAGGCUGUCGCUACAUCGCUGAACCUCUGCUCCCCAGGGGAGUUUUGUCUGUAACCGCCCUACUGGUCAGUGGCGAGAAAUAAAAUGUGCUUAGAAAAG
+>9365
+GGAGACUGGACAUUCAUCUUCACCUGGCUCAAAUCUUUUAGUAGCCACUCCUCCACACCCCCCUCCCCUAUUUAUUUCUGGUUUAGAAAGGGAAUUAGGGCCUCCGGGCCAGGCCCCAAGCUUGGAACUUUAAACAACAACACUUAAAACCUAGGAUGUGAAGAUGUAUGGCCUGAACAAUGGGGCACUGGCUACCACAUAGAGUUCAGACUAGGGCUCCCAGAACUCACUGGGAGUCUGAAAUCUGGAUUCCUGAGUGCAGCCUAGGACACCUGGAAUGUGCAAGUCAGGGAAUCCUUGGUUCUGGUCAGAACAUCUCUUGAGAAGAUCUCACUUAGAACUUGACACAAGUGGACCUCAGGUCUCCCUUUCUUCAGAUGUCUCCAGACUCUCCUGAGAUGGAGAGCCCAGCCCCUCUUGUCUCCCACAGGGCCAGUUCUUUCUAUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUGAUAAACCUAUUUAUUCAGGAGGUUAGUGUGUCCUGGGAGAGCCAGCAGAGGGGCUGCCUUGGCUUAGACAUGUUUUCUAUGAAAACGGAGCUGAACUAUAGGCUGUUCCCACCGGCCUCCAGGCCUCUGUGCCUUCUUUUGCAUAAUUUUGUUUUAAUUUAUCUGAUCAAGUUGUCUAAAUAAUGCUGAUUUGGUGACCUACUGUCGCUAUGUCGCUGAACCUCUGCUCCCCAGGGGAGUUGUCUUUGUAAUCGCCCAACUGAUCAGUGGCGAAAAAUAAAGUGUGCUUGGAAGUG
+>9371
+GGGGGAUGCAUGCAGAUCAUUCACCACCCAGCCCAUCGCCCUCCCUGUCCUGCCAUUCCCAUUGGGCCUCCUCGUCCCCGAAAGGAAGGGGGACGAGCCGGGUCUCUAAGUCAUCACCCCGAACAACAACACUUAGAACUUGAGAUGCAAGGAUGUGUGACUCAGACCAGACCGGGGGCACUGACCACCGCAGCCUGGAAUCCAAACUGGGGCUUGCAGAACCCACUGGGUCUCCAGAUGCAAAUGGGGACACCUGAAAUGUGGAGGUCUCCUUGAGCCUCCGGCUCACUUCCGAAGAUCUGAGGAGUCCUCACCCAGAACUUGGCAUGACCUCCGACCUCCCUUGCACCGAAAGUUUCUAGACCCUCCCCUAAGAGAUGAAGCCCCCCGCCACGUGGCACUAGUCAGCCCUCUAUUUAUGUUUGCACUGAGAAUUAUUUAUUAUUUAUUAUUUAUAUAUUUAUUUAUUUCCUGGUGAAUGUAUUUAUUCAGGAGGUCGGGGAACCUGGGGGAUCCAGUGUUGGGGGUUGCCUGAGCUCAGACAUGUUUUCUAUGAAAAUGGAGCUGGAAUGUAGGCUGCUCCCACCCCGCUUCCUGGCCUCCUUACCUCCCUGUGCUUGUGGAUUUAUCGAUCGAGUUGUCUGGAUAAUGCUGAUUUGGCGACAGACUGUUGCUAUCUCGCUGAACCUCUGCUCCCCAGGGGAGUUGUGCCUGUAAUCGUCCUACUGGUCAGUGGCGAAAAAUAAAGUUUGCUUAGAAAAG
+>9544
+GGGAGGACGAACAUCCAUCCUUCCCAAACCCCUCCCCCGCCCCAAUCCCUUUAUUAUCCCCUCCUUCAGACACCCUCAUCCUCUUCUGGCUCAAAAAGAGAAUUGGGGACUUAGGGCCAGACCCCAAGCUUAGAACUUUAAGCAACGCCACCACCACUUCGAAGCCUGGGGUUCAGGAAUGUGUGGCCUGCACAGUGAAGUGCUGGCAACCACUGAGAAUUUAAACUGGGGCCUCCAGCACUCACUGGGGCCUACAGCUUCCAUCCCUGAACUCAGUCUGUGACAUCUGGAAUCUGGAGACCAGGGAGCCUUUGGUUCUGGCCGGAACGCUGCAAGACUUGAGAAGACAUCACCUAGAAGUUGACACAAGUGGACCUCGGGCCUUCCUCUCUCCAGAUGUUUCCAGACUUCCUUGAGACAUGGAGCCUGGCCCUCCCCAUGGAGCCAGCCCCCUCUAUUUAUGUUUGUACUUGUGAUUAUUUAUUAUUUAUUAUUUAUUUAUUUAUUUACCGAUUAAUGUAUUUAUUUGGGAGGUCGGGGGAUCCCAGGGGACCCAAUGUGGGAGCUGCCUUGGCUCAGACAUGUUUUCUGUGAAAACGGAGCUGAACAAUAGGCUGUUCCCACAUAGCCUCCUGGCCUCUGUGCCUUCUUUUGAUUAUGUUUUUUAAAAUAUUUAUCUGAUUAAGUUGUCCGAACAAUGCAGAUUUGGUGACUGACUGUCACUCAUUGCUGAGCCUCUGCUCCCCAGGGGAGUUGUGUCUGUAAUCGCCCUACUAUUCAGUGGCGAGAAAUAAAGUUUGCUUAGAAAAG
+>9598
+GGGAGGACGAACAUCCAACCUUCCCAAACGCCUCCCCUGCCCCAAUCCCUUUAUUACCCCCUCCUUCAGACACCCUCAACCUCUUCUGGCUCAAAAAGAGAAUUGGGGGCUUAGGGUCGGAACCCAAGCUUAGAACUUUAAGCAACAACACCACCACUUCGAAACCUGGGAUUCAGGAAUGUGUGGCCUGCACAGUGAAGUGCUGGCAACCACUAAGAAUUCAAACUGGGGCCUCCAGAACUCACUGGGGCCUACAGCUUUGAUCCCUGACAUCUGGAAUCUGGAGACCAGGGAGCCUUUGAUUCUGGCCAGAAUUCUGCAGGACUUGAGAAGACCUCACCUAGAAAUUGACACAAGUGGACCUUAGGCCUUCCUCUCUCCAGAUGUUUCCAGACUUCCUUGAGACACGGAGCCCAGCCCUCCCCAUGGAGCCAGCUCCCUCUAUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACAGAUGAAUGUAUUUAUUUGGGAGGUCGGGGUAUCCUGGGGGACCCAAUGUAGGAGCUGCCUUGGCUCAGACAUGUUUUCUGUGAAAACGGAGCUGAACAAUAGGCUGUUCCCAUGUAGCCCCCUGGCCUCUGUGCCUUCUUUUGAUUAUGUUUUUUAAAAUAUUUAUCUGAUUAAGUUGUCUAAACAAUGCUGAUUUGGUGACCAACUGUCACUCAUUGCUGAGCCUCUGCUCCCCAGGGGAGUUGUGUCUGUAAUCGCCCUACUAUUCAGUGGCGAGAAAUAAAGUUUGCUUAGAAAAG
+>9606
+GGGAGGACGAACAUCCAACCUUCCCAAACGCCUCCCCUGCCCCAAUCCCUUUAUUACCCCCUCCUUCAGACACCCUCAACCUCUUCUGGCUCAAAAAGAGAAUUGGGGGCUUAGGGUCGGAACCCAAGCUUAGAACUUUAAGCAACAAGACCACCACUUCGAAACCUGGGAUUCAGGAAUGUGUGGCCUGCACAGUGAAGUGCUGGCAACCACUAAGAAUUCAAACUGGGGCCUCCAGAACUCACUGGGGCCUACAGCUUUGAUCCCUGACAUCUGGAAUCUGGAGACCAGGGAGCCUUUGGUUCUGGCCAGAAUGCUGCAGGACUUGAGAAGACCUCACCUAGAAAUUGACACAAGUGGACCUUAGGCCUUCCUCUCUCCAGAUGUUUCCAGACUUCCUUGAGACACGGAGCCCAGCCCUCCCCAUGGAGCCAGCUCCCUCUAUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACAGAUGAAUGUAUUUAUUUGGGAGACCGGGGUAUCCUGGGGGACCCAAUGUAGGAGCUGCCUUGGCUCAGACAUGUUUUCCGUGAAAACGGAGCUGAACAAUAGGCUGUUCCCAUGUAGCCCCCUGGCCUCUGUGCCUUCUUUUGAUUAUGUUUUUUAAAAUAUUUAUCUGAUUAAGUUGUCUAAACAAUGCUGAUUUGGUGACCAACUGUCACUCAUUGCUGAGCCUCUGCUCCCCAGGGGAGUUGUGUCUGUAAUCGCCCUACUAUUCAGUGGCGAGAAAUAAAGUUUGCUUAGAAAAG
+>9615
+GGGGGUAGGACGUCCAUUCUUGCCCAAACCGACCCUUUGAUCACUCACUUCCUCUGACCCCUCACCCCCUUCAGGCUUAGAAAGAGAAUUAAGGGCUCAGGGCUGGGCCUCAAGCUUAGAACUUUAAACGACACUUAGAAACCUAAGAUCCAGGGAUGUGAGACCCCGAUGACAUGACACAGCACUGGCCACCACCAAGAAUUCAAACCAGGGCUUCCAGCACUCACUGGAGACCUCAGGUUUGGAUCCCUGAAUGCAACUUGGAAUUCUUGGAAUGUAGGGGUCAGGGAACCUUCAGUUCUGGCUAGAACACUUCAGAACAACCCUUGAGAAGAUCUCAACUAGAAUCUGACAUGAGUGGAUCUCACACCUCCCUUUCGUCAUAUGUUCCCAGACUCUCCUGAGAAGGAAAGCCCAGUGACUCCCACGUGGAGCCAGCUCUUCCUAUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUGAUGGAUGUAUUUAUUUGGGAAGUUGGGGUGUCCUGGAAGACCGAACGUAGGGGCUGCCUUGGCUCAGACGUGUUUUCUGUGAAAACGGAGCUGAACUCUAGGCUGUUCCCACCUGGCCUCCUGGCCUCUGUGCCUCCUUUUGCUUAUGUUUUUCAAAAAUAUUUAUCUGAUAGAGUUAUCUAAACAAUGCUGAUUUGGUGACUGACUGUCGCUACAUCGUGGAACCUCUGCUCCCCAGGGGAGUUAUGUCUGUAAUCGCCCUACUGGUCAGUGGCGAGAAAUAAAAUGUGCUUGAAAAAG
+>9685
+GGGGGCCGGACAUCCAUCCUUGCCCACCUCAACUCCUUUGUUAUCUGCUCCUUCUGACCCCCUCAUCCCCUUCUGGCUUAGAAAGAGAAUUAGGGGCUCAGGGCUGGGCCCCAAGCUUAGAACUUUAAAUAACAACACUUAGAAACCUAAGAUCCGGGGACCUGGACUUUGGAGCAUUGGCCACCAGCAAGAAUUCAAACUGGGGCUUCCAGCAUUCACUGGAGAUCUCAGGUUUGGGUCCCUCAACGCAACCUGGGACACCUGGAAUUCGGGGGUCAGGGAACCUUUCUGGCCAGACCCAGCCCCUCCCUCAUGGGGCCAGCUCCCUCUAUUUAUAUUUGCACUAGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUGAUGAAUAUAUUUAUUUGGGAGGUUGGGGUGUCCUGGGAGACCAAAUGAAGGGGCUGCCUUGACUCGGACAUGUUUUCUGUGAAAACGGAGCUGAACUCUAGGCUCUUCCCUCCUGGCCUCCUGGCCUCUGUGCCUCCUUUUGCUUAUAUAUUUUUAAAAAUAUUUAUCUGAUCGAGUUGUCUAAUUAAUGCUGAUUUGGUGACUGACUGUUGCUACAUCGCUGAACCUCUGCUCCCCAGGGGAGUUAUGUCUGUAACCGCCCUACUGUUCAGUGGCGAGAAAUAAAAUGUACCUAGAAAAG
+>9785
+GGGGGAUGGAUGCCCAUCCUUCCCCAACCCCCUCACCCACCUCGGUCCCUUUAUAAUCCAUUUCUUCAGACCCCUUCUUCCCCUCCUGGCUUAGAAUGGAAAUUAGGGGCUCAGGGGUGGGCCCAACUUUAUAAUUUUAAAUAACACUUAGAAGCCUGAGAUGCAGGGGUGUGUGACCUGGACAAUGGGGCACUGGCCGCCACCUAGAAUCCAAAGUUAGGCUUCCAGAACCCACUGGAUCCCUGAAUGUAAAUUGGGACACCCAGAACAUGGAAGCCAAAGAGUCUUUGGUUCUAUCCAGAACACUUGAGAACAUCCUGAGAAGACCUUACGUAGAAUUUGACAUGAGUAGACCUCAGAUCUCCCUCUCUCCAGAAGUUUCCAGACCCUUUCCUGAGAUAUGAAGCCCCUGCCUCUCCGCAUGAAUCGGGCCCCCUCUAUUUAUGUUUGUACUUGUAAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUGAUGAGAAUGUAUUUAUUCGGGAGGUCGGGGCCCUGGGGGACCAAGGUAAGGCUGCCUGUGCUUAGACAUGUUUUCUGUGAAAACGGAGCUGAACCAUAGGCUAUUCCCACUUGGCCUCCUGGCCUCUGUGCCUCCCUUUGCUUAUGUUUUUAAAAAAUAUUUAUCUGAUCAAGUUGUCUGAAUAAUGCUGAUUUGGUGACAGACUGUCGCUAUAUCGCUAAACCUCUGCUCCCCAGGGGAGCUGUGUCUGUAACCGCCCUACUGGUCAGUGGCGAGAAAUAAAGUUUGCUUUGAAAAG
+>9796
+GGGGGGGUACGUCCGUCCUCGCCCACCUCAAUCCCUUUAUUAUCUGCUCCUUCAGAACCCUCUCAUCCCCUUCUGAGGUUUAGAAAGGGAAUGAAGGGCUCAGGGCCGGGCCCCAAACUCAGAACUUGAAACAACAACAACACUUAGAAACCUAGAAUGCAGGGAUGUGUGACCUGGACAACGGGGCACCGGUCACCACCAAGAAUUCAAACUGGGGCUUCCAGAACUCACUGGGGGCCUCAGAUUUGGAUCCCUGAAUGCAGCCUGGGACACCUGGAACGUGGGGGCCAGGAAACCUUUGGUUCUGGCCAGAACACUUCAGAACAUCCGUUGAGAAGAUCUCACCCAGAACUUGAUGAGAGUGGACCACAGGUCUCCCUUUUUUCAAAUGUUUCCAAACUCUCCCGAGUUGUAGAGCCCAGGCCCUCCGCCAUGGGGCCGGCUCCCUCUAUUUAUGUCUGCACUUGAGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUAAUGAAUGUAUUUAUUCAGGAGGUUGAGGUGUCCUGGGAGACCCAACAUAGGGGCUGCCUUGGCUCAGACAUGUUUUCUGUGAAAACGGAGCUGAACUGUAGGUUGUUCCCAUCUGGCCUCCUGGCCUCUGUGCUUCCUUUUGCUUAUGUUUUUAAACAAUAUUUAUCUGAUCAAGUUGUCUAAAUAAUGCUGAUUUGGUGACCAACUGUCGCUACAUCGCUGAACCUCUGCUCCCCAGGGGAGUUGUAUCUGUAAGCGCCCUACUGGUCAGUGGCGAUAAAUAAAGUAUGCUUAGAAAAG
+>9913
+GGGUGCAGGACAUGCAUCUUCUCCCACCUCAGUUACCUUAUUAUUUAAUCCUUCAGGCCCUUCUCAUCCCCUUCUGGUUUAGAAAGGGAAUUAUGGGCUCAGGGCUGGGCUCCAAGCAUCCAACUUUAAACAACAGCUACAUUUAGAAAUUAGGGAUGUAGGGAAGUGAGGCCUGGACAACGGGCCACCAACCACCAUCAAGGACUGGAACUGGAACUUCCAGAACUCCCUGGGGUCCACAAGCUUGGGUUCCCGGAUGCAACCUGGGACACCCAGAAUGUGAGGGCCAGGGCUCUUACCGGAACACUUCGCAACAUUCCUUGAGAAGAUCUCACCUAGAACUUGACAUGCGUGGACUUCAACUCUCCCUUCCUGCCAAUGUUUCCAGACUCCCCUGAGGUGGGAAGCCCAGCCCCAACCCCACUGGGCCAACUCCCUCUGUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUAAUGAAUGUAUUUAUUCAGGAGGUCAAGGUGUCCUGGGAGACACAAACUAAGGGCUGCCUUGGCUCAGAUGUGUUUUCUGUGAAAACGGAGCUGAACUGCAGGUUGCUCCCACCAUGCCUCCUCGCCUUUGUGCCUCCUUUUGCUUAUGUUUUUUAAAAAAUAUUUAUCUGAUCGAGUUGUCUAAAUGAUGCUGAUUUGGUGACUGAUUUGUCGCUACAUCACUGAACCUCCGCUCCCCAGGGGAGUCAUGCCUGUAACCGCCCUACUGGUCAGUGGCGAGAAAUAAAGUGUCCUGAGAAAAG
+>9986
+GGGGACUGACCAUCACUCCUCCCCCUCUCCCACCCCAGCCCCCUCACUCUGGGCGCCCUCAGCCCCUCUCAUCCUCCUCUAGCUUAGAAACAGAAAUGAGGGGCUCAGAAUCAGACCUCAGAACUUUUAACACCACCACUUAGAAACCUGGACCGUGGUGGUGUAGGCCUGCACAGUCAGGGCCCUGGCCACACCAAAGCAUUCAAACUGAGGCUUCCAGGACUCACUGGGGCCUUCAGAACUCCAUUCUCAGAUUGAGCCCGGAACAUCCGGAAUGUGGGGACCACGUAGCCGUGGGUUCAGGCCAGAACCUUCUAGAAGAGCCCUUGAGAGAAGUUGUCACCCAGACCUAGGCCUUCCUCUCCUCAGAUGUUUCUACACUCUUCUCUGCAAUGUGGAGCCCCGCCCCCCGCCGAGGGCAGGGCCCCUCUAUUUAUAGUUGCACUGGUGAUUAUUUAUUAUUUAUUUAAUAUUUAUUUAUUUGCCGAUGAAUGUAUUUAUUUGGAAGCUCAGCGCAUCCUGGGGUACCCAGCGUAGGAGCUGCCUUGGUUCUCACACGUUUUCCGUGAAAACAGAGCAGAACCAUGGGUCGAUCCCACCUGGCCUCCUGGCCCCUGUGCCUCCCUUCACUUAUGUUUUUAAGAAGAUAUUUAUCUGAUCAGGUUGUCUCACUAAUGCUGAUUUGGUGACUGACCCGUCGCUACAUCACCGAACCUCUGCUCCCUAAGGGAGUUGUGUUGGUAACCGCCCUACUGGUCAGUGGCGAGAAAUAAAGACUCCUUAAAAAAU
+>10090
+AGGGAAUGGGUGUUCAUCCAUUCUCUACCCAGCCCCCACUCUGACCCCUUUACUCUGACCCCUUUAUUGUCUACUCCUCAGAGCCCCCAGUCUGUAUCCUUCUAACUUAGAAAGGGGAUUAUGGCUCAGGGUCCAACUCUGUGCUCAGAGCUUUCAACAACUACUCAGAAACACAAGAUGCUGGGACAGUGACCUGGACUGUGGGCCUCUCAUGCACCACCAUCAAGGACUCAAAUGGGCUUUCCGAAUUCACUGGAGCCUCGAAUGUCCAUUCCUGAGUUCUGCAAAGGGAGAGUGGUCAGGUUGCCUCUGUCUCAGAAUGAGGCUGGAUAAGAUCUCAGGCCUUCCUACCUUCAGACCUUUCCAGAUUCUUCCCUGAGGUGCAAUGCACAGCCUUCCUCACAGAGCCAGCCCCCCUCUAUUUAUAUUUGCACUUAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUGCUUAUGAAUGUAUUUAUUUGGAAGGCCGGGGUGUCCUGGAGGACCCAGUGUGGGAAGCUGUCUUCAGACAGACAUGUUUUCUGUGAAAACGGAGCUGAGCUGUCCCCACCUGGCCUCUCUACCUUGUUGCCUCCUCUUUUGCUUAUGUUUAAAACAAAAUAUUUAUCUAACCCAAUUGUCUUAAUAACGCUGAUUUGGUGACCAGGCUGUCGCUACAUCACUGAACCUCUGCUCCCCACGGGAGCCGUGACUGUAAUCGCCCUACGGGUCAUUGAGAGAAAUAAAGAUCGCUUGGAAAAG
+>10116
+GGCGACUGGCGUGUUCAUCCGUUCUCUACCCAGCCCCUGUCCCCGACUCUGACCCCCAUUACUCUGACCCCUUUAUCGUCUACUCCUCAGAGCCCCCAAUCUGUGUCCUUCUAACUUAGAAAGGGAAUUGUGGCUCUGGGUCCAACUCCGGGCUCAGAAUUUCCAACAACUACGAUGCUCAGAAACACACGAGACGCUGAAGUAGUGGCCUGGAUUGCGGGCUGCUCAUGAGCCGCCACCGGCAAGGAUUCCAAUGGGCUUUCGGAACUCACUGGAUCCCGGAAUGUCGAUGCCUGAGUGGAUCGGGGGAGUGGAGGGGGGAGUGGAUCAGGCUGCCUCUGGCUCACAAGGCUGCUGAAGAUGUCUCAGGCCUCCCUUCCUUCCUUCCUUCCCUCCCUCAGAGCUUCCCAGACUGUUCCCUGAGGCACAGCGCCCAGCCUUCCUUACGGAACCCCCUCUAUUUAUAAUUGCACCUGUGACUAUUUAUUUAUUAUUUAUUAUUUAUUUAUUUGCUUAUGAAUGUAUUUAUUUGGAAGGCCGGGGCGUCCUGGAGGACCCAGCGUUGGGAAGCUGUCUUCAGGCCAACAUGUUUUCUGUGAAAACGGAGCUAAACUACCAGCUAUCCCCAUCUGGUCCCCCACCCCUGCCUCGUUGCCUCCCCCCUUUUCUUUUGCUUAUGUUUAAAACAAGAUAUUUAUCUAACCCAGUUGUCUUAAUAAUGCUGAUUUGGUGACCAGGCUGUCGCUACAUCACUGAACCUCUGCUCCCCACGGGAGCCGUGACUGUAAUCGCCCUACGGGUCAUUGAGAGAAAUAAAGUUCGCUUGGAAAAG
+>10141
+UAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUGAUGAUUGUAUUUAUUUGGAAGGUUAGAGUGUCCAGGGCCCAUCAGAGGAACAGUCCGGGGUCAGACAUGUUUUCUGUGAAAACAGAAUGAAAUGCAGACUGUUCCCACCUGGCCUCUCGGCCUCUGAACCUUCUUUUGCUUUUUAAAAAACAUACUAUUUAUCUAAUCCAGUAUCUUAAUAAUCUGAUUUGGUGACCAACUGUCGCUGCAUCGCUGAAACUCUGCUCCCCAGGGGAGUUGUCUGUAAUCGUCCUACUGGUCAGUGGCGAGAAAUAAAGACUGCUUAGAAAAG
+>13616
+GAGAAAAGGGAAGUAAUACCCCCAACCUCCAUACUCUUCUUCACUCCCUACUUAACUUUUAUCGGUCUUCUUCCUUGUCCCUAGAAGGGUCCUUUUCUGGAUCAGGAAAAUGGUUCCGCAGUCUGGGAAUUAGAGUUUAGAACAAUCUAGAAUAUGAUAAAGGACAUUGAGAAACCAAGGAUCAGAAGAAUGAGAAUAGCUGUAUAAAUUGGCUGCAUAUCGAGGACCAUGGAAAUAUGGGAUCCAGAGUAACAUAAAAAUCUAUUAAGAAAUCCGUGUGCUGAAACAAAUUUAGAACCUAGAUAAAAACUGCAACCUGGAGACCAAGGGUACAGUUCCUAACACACAGAACAAGGACUAGCCCUAAAAGCCUGACCUGAGGGAAAGGAUCCUCUUUACUCUAGACCCUCUUUACUCUUUACCACUCUCUGAGAUAUAUCUGAUUUAGACCCAAUGUUGAAAUCUAGUUCUUUCCUGUUCUAUUUAUUGUGAUGCAGGAGCCAUGCCUUUUGCUUUCCCCCUCCCCCGAAGCGGCUUCUGUUAUUUAUGAUUGGAUAAUAUGGUUAUUUAUUUAUUUAUUAUUUAUUUAUUUAUUCUUAAGUGUAUUUAUUGAGAAGGUUAUCAUUCAUGGGGGGACACAGAUGUUGAGGUUUCCCCCAGCUCAGGAGUAUUUUCUAUGAAAAUGGAGCUGAAGCAAGGGGUGCUUCUAUCCUGGCCCCUUGAUCACCCUCCCACCUGCCUAUUUUUAAAAAUUAUCUGAUUUUAUUACAUUGUUGAUUUAGUGGCUAUGCGUCGCUGUAUCUCUGAACCUGUGCUCCCCAGGGGAGUCGUGUCUGUAAGCGCCCUAUUUGUCAGUGGUGAGAAAUAAACUUUGCUUUGAAAAG
+>28377
+GGAAAUCCCCUCUUACCUGGUCCCAUUACUUUCCUUUUUUGUGCCCACUCCCCAAAUGCUGCCUCGUCGGGUCAAAACUGUAAACUG
+>42254
+CCUGAGAACGUGGCCGCCUUCCCCGCGGGGGCUCGCUCCAUCUAUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUGCCAGUGGAUAUAUUUAUUCAGGAGGUCGGGGAGACCCUACAUCGAAGCUGGCCUGGCUCGGACAUGUUUUCUGUGAAAACCGAGGUUGUUCCCAGCCAGUCUCUUGGUCUCCAGGCCUCCUUUGCAAGUGGUUUUAUUUAUCCGAUCAAAUUGUCUACGUUAAUGCUGAUUUGGUGACUAACUGUCGCUGCAUCGCUGAACCUCUGCUCCCCAGGGGAGUUGUGUCUGUAAUCGCCCUACUGGUCAGUGGCGAGAAAUAAAGUGUGCUUAGAAAAG
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,24 @@
+#!/bin/bash
+set -e
+
+pkg=transtermhp
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+export PATH=.:$PATH
+ls
+echo 'Test 1'
+./calibrate.sh expterm.dat
+echo 'PASS'
+
+echo 'Test 2'
+./mfold_rna.sh 2ndscore infile.fasta > test2.out
+echo 'PASS'
+
=====================================
debian/transtermhp.examples
=====================================
@@ -0,0 +1,6 @@
+debian/tests/data/*
+expterm.dat
+mfold_rna.sh
+calibrate.sh
+make_expterm.py
+random_fasta.py
=====================================
debian/transtermhp.install
=====================================
@@ -1,7 +1,3 @@
transterm usr/bin
2ndscore usr/bin
expterm.dat usr/share/transtermhp/
-calibrate.sh usr/share/doc/transtermhp/examples
-mfold_rna.sh usr/share/doc/transtermhp/examples
-make_expterm.py usr/share/doc/transtermhp/examples
-random_fasta.py usr/share/doc/transtermhp/examples
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,3 @@
-Contact: Carl Kingsford <carlk at umiacs.umd.edu>
Name: TransTermHP
Reference:
Author: >
@@ -11,10 +10,10 @@ Reference:
Volume: 8
Number: 2
Pages: R22
- URL: http://genomebiology.com/2007/8/2/R22/abstract
+ URL: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-2-r22
DOI: 10.1186/gb-2007-8-2-r22
PMID: 17313685
- eprint: http://genomebiology.com/content/pdf/gb-2007-8-2-r22.pdf
+ eprint: https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2007-8-2-r22
Registry:
- Name: OMICtools
Entry: OMICS_06165
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=3
opts=dversionmangle=s/[~\+]dfsg// \
- http://transterm.cbcb.umd.edu/transterm_hp_v(.*)\.zip
+ https://transterm.cbcb.umd.edu/transterm_hp_v(.*)\.zip
View it on GitLab: https://salsa.debian.org/med-team/transtermhp/-/compare/3d554c5826b4cf1ebc533f431fbdcc5e8a4f1e33...beebc37ec48db836ecf882695ed560d36723507d
--
View it on GitLab: https://salsa.debian.org/med-team/transtermhp/-/compare/3d554c5826b4cf1ebc533f431fbdcc5e8a4f1e33...beebc37ec48db836ecf882695ed560d36723507d
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