[med-svn] [Git][med-team/spades][master] Refactored patch for bwa which()

[Lance Lin (@linqigang)]

Lance Lin pushed to branch master at Debian Med / spades


Commits:
28eac96c by Lance Lin at 2022-05-10T20:20:05+07:00
Refactored patch for bwa which()

- - - - -


2 changed files:

- debian/changelog
- debian/patches/0003_accept-system-bwa.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+spades (3.15.4+dfsg-2) UNRELEASED; urgency=medium
+
+  [ Lance Lin ]
+  * d/patches/0003_accept-system-bwa.patch - refactored 'which'
+  Closes: #1010788
+
+ -- Lance Lin <LQi254 at protonmail.com>  Tue, 10 May 2022 20:15:40 +0700
+
 spades (3.15.4+dfsg-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]


=====================================
debian/patches/0003_accept-system-bwa.patch
=====================================
@@ -54,31 +54,6 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
  
  
  def check_file_existence(input_filename, message="", log=None):
---- a/assembler/spades.py
-+++ b/assembler/spades.py
-@@ -163,6 +163,22 @@ def print_used_values(cfg, log):
-     print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", "  ")
-     log.info("")
- 
-+def which(program):
-+    def is_exe(fpath):
-+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
-+
-+    fpath, fname = os.path.split(program)
-+    if fpath:
-+        if is_exe(program):
-+            return program
-+    else:
-+        for path in os.environ["PATH"].split(os.pathsep):
-+            path = path.strip('"')
-+            exe_file = os.path.join(path, program)
-+            if is_exe(exe_file):
-+                return exe_file
-+
-+    return None
- 
- def create_logger():
-     log = logging.getLogger("spades")
 --- a/assembler/src/spades_pipeline/options_parser.py
 +++ b/assembler/src/spades_pipeline/options_parser.py
 @@ -992,7 +992,10 @@ def add_to_cfg(cfg, log, bin_home, spade
@@ -86,47 +61,24 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
          cfg["mismatch_corrector"] = empty_config()
          cfg["mismatch_corrector"].__dict__["skip-masked"] = None
 -        cfg["mismatch_corrector"].__dict__["bwa"] = os.path.join(bin_home, "spades-bwa")
-+        if which("bwa-spades"):
++        if support.which("bwa-spades"):
 +            cfg["mismatch_corrector"].__dict__["bwa"] = os.path.join(bin_home, "bwa-spades")
 +        else:
-+            cfg["mismatch_corrector"].__dict__["bwa"] = which("bwa")
++            cfg["mismatch_corrector"].__dict__["bwa"] = support.which("bwa")
          cfg["mismatch_corrector"].__dict__["threads"] = args.threads
          cfg["mismatch_corrector"].__dict__["output-dir"] = args.output_dir
      cfg["run_truseq_postprocessing"] = options_storage.run_truseq_postprocessing
 --- a/assembler/src/spades_pipeline/scripts/postprocessing_script.py
 +++ b/assembler/src/spades_pipeline/scripts/postprocessing_script.py
-@@ -45,6 +45,22 @@ def parse_args():
-                     action="store")
-     return parser.parse_args()
- 
-+def which(program):
-+    def is_exe(fpath):
-+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
-+
-+    fpath, fname = os.path.split(program)
-+    if fpath:
-+        if is_exe(program):
-+            return program
-+    else:
-+        for path in os.environ["PATH"].split(os.pathsep):
-+            path = path.strip('"')
-+            exe_file = os.path.join(path, program)
-+            if is_exe(exe_file):
-+                return exe_file
-+
-+    return None
- 
- def main():
-     args = parse_args()
 @@ -78,7 +94,10 @@ def main():
      #  run command
      if isfile(args.result_scaffolds_filename):
          shutil.move(args.result_scaffolds_filename, args.assembled_scaffolds_filename)
 -    alignment_bin = os.path.join(args.bin_home, "spades-bwa")
-+    if which("bwa-spades"):
-+        alignment_bin = which("bwa-spades")
++    if support.which("bwa-spades"):
++        alignment_bin = support.which("bwa-spades")
 +    else:
-+        alignment_bin = which("bwa")
++        alignment_bin = support.which("bwa")
      alignment_dir = os.path.join(args.output_dir, "alignment")
      sam_files = alignment.align_bwa(alignment_bin, args.assembled_scaffolds_filename,
                                      dataset_data, alignment_dir, log, args.threads)



View it on GitLab: https://salsa.debian.org/med-team/spades/-/commit/28eac96c2c84b580ae48da1085bb1df159f73bc8

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/-/commit/28eac96c2c84b580ae48da1085bb1df159f73bc8
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220510/b3a588fe/attachment-0001.htm>