[med-svn] [Git][med-team/kraken][debian/jessie-backports-sloppy] 5 commits: Slighly more robust method to obtain taxid of fasta files to at least enable…

[Andreas Tille]

Andreas Tille pushed to branch debian/jessie-backports-sloppy at Debian Med / kraken


Commits:
7aadb755 by Andreas Tille at 2018-02-07T12:44:48Z
Slighly more robust method to obtain taxid of fasta files to at least enable reading the provided data examples of autopkgtest

- - - - -
d4d320a7 by Andreas Tille at 2018-02-07T12:59:23Z
Forwarded issue upstream

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5b70f5b5 by Andreas Tille at 2018-02-07T13:06:36Z
Upload to unstable

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cfa81f03 by Andreas Tille at 2018-02-07T13:18:13Z
Merge branch 'master' into debian/jessie-backports-sloppy

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5619acd2 by Andreas Tille at 2018-02-12T10:01:03Z
Upload to jessie-sloppy

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3 changed files:

- debian/changelog
- + debian/patches/fix_reading_fasta.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,17 @@
-kraken (1.1-1~bpo8+1) jessie-backports-sloppy; urgency=medium
+kraken (1.1-2~bpo8+1) jessie-backports-sloppy; urgency=medium
 
   * Rebuild for jessie-backports-sloppy.
   * Revert to debhelper 10 (latest version in Jessie)
 
- -- Andreas Tille <tille at debian.org>  Tue, 06 Feb 2018 14:44:02 +0100
+ -- Andreas Tille <tille at debian.org>  Mon, 12 Feb 2018 11:00:42 +0100
+
+kraken (1.1-2) unstable; urgency=medium
+
+  * Slighly more robust method to obtain taxid of fasta files to at least
+    enable reading the provided data examples of autopkgtest
+    Closes: #889623
+
+ -- Andreas Tille <tille at debian.org>  Wed, 07 Feb 2018 13:59:49 +0100
 
 kraken (1.1-1) unstable; urgency=medium
 


=====================================
debian/patches/fix_reading_fasta.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Slighly more robust method to obtain taxid of fasta files to at
+  least enable reading the provided data examples of autopkgtest
+Bug-Debian: https://bugs.debian.org/889623
+Forwarded: https://github.com/DerrickWood/kraken/issues/111
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 07 Feb 2018 13:41:39 +0100
+
+--- a/scripts/scan_fasta_file.pl
++++ b/scripts/scan_fasta_file.pl
+@@ -32,6 +32,8 @@ while (<>) {
+   # while (/.../g) needed because non-redundant DBs sometimes have multiple
+   #   sequence IDs in the header; extra sequence IDs are prefixed by
+   #   '\x01' characters (if downloaded in FASTA format from NCBI FTP directly).
++  s/^>gi\|/>/;
++  s/\| .*//;
+   while (/(?:^>|\x01)(\S+)/g) {
+     my $seqid = $1;
+     my $taxid = krakenlib::check_seqid($seqid);


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 use_jellyfish1.patch
 kraken_tmp_dir.patch
+fix_reading_fasta.patch



View it on GitLab: https://salsa.debian.org/med-team/kraken/compare/407ad4ca0d4e9983a53e07bacfbfec8196a47b2d...5619acd2061ad6dc63e222d50cfd3f7c293455fd

-- 
View it on GitLab: https://salsa.debian.org/med-team/kraken/compare/407ad4ca0d4e9983a53e07bacfbfec8196a47b2d...5619acd2061ad6dc63e222d50cfd3f7c293455fd
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