[med-svn] [kraken] 01/01: Slighly more robust method to obtain taxid of fasta files to at least enable reading the provided data examples of autopkgtest

[Andreas Tille]

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tille pushed a commit to branch master
in repository kraken.

commit 7aadb7559d5264bfc577593a7bed71f92d0d75ed
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 7 13:44:48 2018 +0100

    Slighly more robust method to obtain taxid of fasta files to at least enable reading the provided data examples of autopkgtest
---
 debian/changelog                       |  8 ++++++++
 debian/patches/fix_reading_fasta.patch | 17 +++++++++++++++++
 debian/patches/series                  |  1 +
 3 files changed, 26 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index c106a40..50245fb 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+kraken (1.1-2) UNRELEASED; 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 13:41:39 +0100
+
 kraken (1.1-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/fix_reading_fasta.patch b/debian/patches/fix_reading_fasta.patch
new file mode 100644
index 0000000..e81e415
--- /dev/null
+++ b/debian/patches/fix_reading_fasta.patch
@@ -0,0 +1,17 @@
+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
+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);
diff --git a/debian/patches/series b/debian/patches/series
index e264766..95b845c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 use_jellyfish1.patch
 kraken_tmp_dir.patch
+fix_reading_fasta.patch

-- 
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