Andreas Tille pushed to branch master at Debian Med / plasmidid
Commits:
4d18b933 by Andreas Tille at 2020-06-26T22:38:51+02:00
Remove empty patch
- - - - -
a19e1546 by Andreas Tille at 2020-06-26T22:50:35+02:00
DEP3
- - - - -
84c790ee by Andreas Tille at 2020-06-26T22:55:01+02:00
Add missing comma
- - - - -
6a488173 by Andreas Tille at 2020-06-26T23:02:46+02:00
Fix spelling
- - - - -
1af39f1b by Andreas Tille at 2020-06-26T23:05:40+02:00
Upload to new
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/AdjustPythonPath.patch
- − debian/patches/config_files.patch
- debian/patches/fixTests.patch
- debian/patches/series
- + debian/patches/spelling.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,14 +1,7 @@
-plasmidid (1.6.3+dfsg-1) UNRELEASED; urgency=medium
+plasmidid (1.6.3+dfsg-1) unstable; urgency=medium
- [ Andreas Tille ]
* Initial release (Closes: #963758)
- [ Steffen Moeller ]
- * debhelper-compat 13 (routine-update)
- * Rules-Requires-Root: no (routine-update)
- * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
- Repository-Browse. (routine-update)
- * Employ help2man to create missing man page
* Tests fail, apparently because of prokka
https://github.com/BU-ISCIII/plasmidID/issues/12
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
- help2man
+ help2man,
ncbi-blast+ <!nocheck>,
bedtools <!nocheck>,
bowtie2 <!nocheck>,
=====================================
debian/patches/AdjustPythonPath.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-06-26 18:33:35 +0200
+Description: Fix Python3 path
+
Index: plasmidid/bin/download_plasmid_database.py
===================================================================
--- plasmidid.orig/bin/download_plasmid_database.py
@@ -8,13 +12,6 @@ Index: plasmidid/bin/download_plasmid_database.py
# Standard library imports
import os
-@@ -157,4 +157,4 @@ if __name__ == '__main__':
- main()
- except Exception as e:
- logger.exception(e)
-- raise
-\ No newline at end of file
-+ raise
Index: plasmidid/bin/mashclust.py
===================================================================
--- plasmidid.orig/bin/mashclust.py
@@ -25,13 +22,6 @@ Index: plasmidid/bin/mashclust.py
# Standard library imports
import os
-@@ -396,4 +396,4 @@ if __name__ == '__main__':
- main()
- except Exception as e:
- logger.exception(e)
-- raise
-\ No newline at end of file
-+ raise
Index: plasmidid/bin/summary_report_pid.py
===================================================================
--- plasmidid.orig/bin/summary_report_pid.py
@@ -42,10 +32,3 @@ Index: plasmidid/bin/summary_report_pid.py
# Standard library imports
import os
-@@ -465,4 +465,4 @@ if __name__ == '__main__':
- main()
- except Exception as e:
- logger.exception(e)
-- raise
-\ No newline at end of file
-+ raise
=====================================
debian/patches/config_files.patch deleted
=====================================
=====================================
debian/patches/fixTests.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-06-26 19:12:34 +0200
+Description: Drop .sh extension of the binary
+
Index: plasmidid/TEST_DATA/test.sh
===================================================================
--- plasmidid.orig/TEST_DATA/test.sh
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,3 @@
-config_files.patch
fixTests.patch
AdjustPythonPath.patch
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -0,0 +1,59 @@
+Author: Andreas Tille <[email protected]>
+Last-Update: Fri, 26 Jun 2020 23:02:03 +0200
+Description: Fix spelling
+
+--- a/README.md
++++ b/README.md
+@@ -137,15 +137,15 @@ usage : plasmidID <-1 R1> <-2 R2> <-d da
+ --no-trim Reads supplied will not be quality trimmed
+
+ Coverage and Clustering:
+- -C | --coverage-cutoff <int> minimun coverage percentage to select a
plasmid as scafold (0-100), default 80
+- -S | --coverage-summary <int> minimun coverage percentage to include
plasmids in summary image (0-100), default 90
++ -C | --coverage-cutoff <int> minimum coverage percentage to select a
plasmid as scafold (0-100), default 80
++ -S | --coverage-summary <int> minimum coverage percentage to include
plasmids in summary image (0-100), default 90
+ -f | --cluster <int> kmer identity to cluster plasmids into the same
representative sequence (0 means identical) (0-1), default 0.5
+ -k | --kmer <int> identity to filter plasmids from the database
with kmer approach (0-1), default 0.95
+
+ Contig local alignment
+- -i | --alignment-identity <int> minimun identity percentage aligned for
a contig to annotate, default 90
+- -l | --alignment-percentage <int> minimun length percentage
aligned for a contig to annotate, default 20
+- -L | --length-total <int> minimun alignment length to filter
blast analysis
++ -i | --alignment-identity <int> minimum identity percentage aligned for
a contig to annotate, default 90
++ -l | --alignment-percentage <int> minimum length percentage
aligned for a contig to annotate, default 20
++ -L | --length-total <int> minimum alignment length to filter
blast analysis
+ --extend-annotation <int> look for annotation over regions with
no homology found (base pairs), default 500bp
+
+ Draw images:
+@@ -175,7 +175,7 @@ Since v1.6, the more relevant output is
+ - length: length of the reference sequence
+ - species: species of the reference sequence
+ - description: rest of reference fasta header
+- - contig_name: number of the contigs that align the minimun required
for complete contig track
++ - contig_name: number of the contigs that align the minimum required
for complete contig track
+ - SAMPLE:
+ - Image of the reconstructed plasmid (click to open in new tab)
+ - MAPPING % (percentage): percentage of reference covered with
reads
+--- a/plasmidID
++++ b/plasmidID
+@@ -58,15 +58,15 @@ usage : $0 <-1 R1> <-2 R2> <-d database(
+ --no-trim Reads supplied will not be quality trimmed
+
+ Coverage and Clustering:
+- -C | --coverage-cutoff <int> minimun coverage percentage to select a
plasmid as scafold (0-100), default 80
+- -S | --coverage-summary <int> minimun coverage percentage to include
plasmids in summary image (0-100), default 90
++ -C | --coverage-cutoff <int> minimum coverage percentage to select a
plasmid as scafold (0-100), default 80
++ -S | --coverage-summary <int> minimum coverage percentage to include
plasmids in summary image (0-100), default 90
+ -f | --cluster <int> kmer identity to cluster plasmids into the same
representative sequence (0 means identical) (0-1), default 0.5
+ -k | --kmer <int> identity to filter plasmids from the database
with kmer approach (0-1), default 0.95
+
+ Contig local alignment
+- -i | --alignment-identity <int> minimun identity percentage aligned for
a contig to annotate, default 90
+- -l | --alignment-percentage <int> minimun length percentage
aligned for a contig to annotate, default 20
+- -L | --length-total <int> minimun alignment length to filter
blast analysis
++ -i | --alignment-identity <int> minimum identity percentage aligned for
a contig to annotate, default 90
++ -l | --alignment-percentage <int> minimum length percentage
aligned for a contig to annotate, default 20
++ -L | --length-total <int> minimum alignment length to filter
blast analysis
+ --extend-annotation <int> look for annotation over regions with
no homology found (base pairs), default 500bp
+
+ Draw images:
View it on GitLab:
https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9
--
View it on GitLab:
https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9
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