[med-svn] [tophat] 01/01: fix tophat compatibility with recent samtools

[Fabian Klötzl]

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kloetzl-guest pushed a commit to branch master
in repository tophat.

commit a7b57930efd2d93fab3e62e044a6e8c3b850c3fe
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Wed Dec 6 15:35:05 2017 +0100

    fix tophat compatibility with recent samtools
---
 debian/changelog                                   |  1 +
 .../fix-compatibility-with-recent-samtools.patch   | 58 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 3 files changed, 60 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index b6d8265..66d78fd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -12,6 +12,7 @@ tophat (2.1.1+dfsg-5) UNRELEASED; urgency=medium
   [ Fabian Klötzl ]
   * remove convenience copy of samtools.
     Closes: #780816
+  * adapt tophat script to recent samtools version
 
   [ Andreas Tille ]
   * Remove unused license paragraph
diff --git a/debian/patches/fix-compatibility-with-recent-samtools.patch b/debian/patches/fix-compatibility-with-recent-samtools.patch
new file mode 100644
index 0000000..5e04ead
--- /dev/null
+++ b/debian/patches/fix-compatibility-with-recent-samtools.patch
@@ -0,0 +1,58 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Wed, 6 Dec 2017 15:32:12 +0100
+Subject: fix compatibility with recent samtools
+
+---
+ src/tophat.py | 10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/src/tophat.py b/src/tophat.py
+index 1eed276..4b8bbb1 100755
+--- a/src/tophat.py
++++ b/src/tophat.py
+@@ -182,7 +182,7 @@ use_BWT_FIFO = False # can only be set to True if use_zpacker is True and only w
+ unmapped_reads_fifo = None # if use_BWT_FIFO is True, this tricks bowtie into writing the
+                            # unmapped reads into a compressed file
+ 
+-samtools_path = "samtools_0.1.18"
++samtools_path = "samtools"
+ bowtie_path = None
+ fail_str = "\t[FAILED]\n"
+ gtf_juncs = None #file name with junctions extracted from given GFF file
+@@ -1162,7 +1162,7 @@ def nonzeroFile(filepath):
+          head_cmd = ["head", "-1"]
+          head = subprocess.Popen(head_cmd, stdin=samtools_view.stdout, stdout=subprocess.PIPE)
+ 
+-         samtools_view.stdout.close() # as per http://bugs.python.org/issue7678
++         # samtools_view.stdout.close() # as per http://bugs.python.org/issue7678
+          output = head.communicate()[0][:-1]
+ 
+          if len(output) > 0:
+@@ -1569,7 +1569,7 @@ def get_samtools_version():
+ def check_samtools():
+     #th_log("Checking for Samtools")
+     global samtools_path
+-    samtools_path=prog_path("samtools_0.1.18")
++    samtools_path=prog_path("samtools")
+     #samtools_version_str, samtools_version_arr = get_samtools_version()
+     #if samtools_version_str == None:
+     if not samtools_path:
+@@ -2744,16 +2744,16 @@ def compile_reports(params, sam_header_filename, ref_fasta, mappings, readfiles,
+ 
+         if params.report_params.sort_bam:
+             pids = [0 for i in range(num_bam_parts)]
+-            sorted_bam_parts = ["%s%d_sorted" % (alignments_output_filename, i) for i in range(num_bam_parts)]
++            sorted_bam_parts = ["%s%d_sorted.bam" % (alignments_output_filename, i) for i in range(num_bam_parts)]
+             #left_um_parts = ["%s%s%d_sorted" % (alignments_output_filename, i) for i in range(num_bam_parts)]
+             #right_um_parts = ["%s%d_sorted" % (alignments_output_filename, i) for i in range(num_bam_parts)]
+             for i in range(num_bam_parts):
+                     bamsort_cmd = [samtools_path,
+                                    "sort",
+                                    bam_parts[i],
++                                   "-o",
+                                    sorted_bam_parts[i]]
+ 
+-                    sorted_bam_parts[i] += ".bam"
+                     print >> run_log, " ".join(bamsort_cmd)
+ 
+                     if i + 1 < num_bam_parts:
diff --git a/debian/patches/series b/debian/patches/series
index 32c87aa..da7befd 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ remove_3rd_party_code.patch
 fix_includes_path.patch
 fix-gcc6.patch
 remove-convenience-copy-of-samtools.patch
+fix-compatibility-with-recent-samtools.patch

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