[med-svn] [qcumber] 01/01: check whether reference file is a valid fasta file

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 56a71c870c2d3903805b78fe77b8969f49f07c6a
Author: Andreas Tille <tille at debian.org>
Date:   Thu Feb 23 16:02:01 2017 +0100

    check whether reference file is a valid fasta file
---
 debian/changelog                 |  6 ++++++
 debian/patches/check_fasta.patch | 38 ++++++++++++++++++++++++++++++++++++++
 debian/patches/series            |  1 +
 3 files changed, 45 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 0167d28..e523759 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+qcumber (1.0.5+dfsg-2) UNRELEASED; urgency=medium
+
+  * Check reference file for valid fasta
+
+ -- Andreas Tille <tille at debian.org>  Thu, 23 Feb 2017 14:59:46 +0100
+
 qcumber (1.0.5+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #855211)
diff --git a/debian/patches/check_fasta.patch b/debian/patches/check_fasta.patch
new file mode 100644
index 0000000..cd807ee
--- /dev/null
+++ b/debian/patches/check_fasta.patch
@@ -0,0 +1,38 @@
+--- a/QCumber.py
++++ b/QCumber.py
+@@ -29,6 +29,24 @@ r1_pattern = parameter["Pattern"]["R1"]
+ r2_pattern = parameter["Pattern"]["R2"]
+ lane_pattern = parameter["Pattern"]["lane"]
+ 
++from sys import stderr
++from Bio import SeqIO
++
++def check_fasta(fastafile, filetype='File'):
++	seq_record = SeqIO.parse(fastafile, "fasta")
++	try:
++		for seq in seq_record:
++			break # break after first sequence
++	except FileNotFoundError as err:
++		print("%s %s does not exist" % (filetype, fastafile), file=stderr)
++		return False
++	try:
++		s=str(seq) # we somehow need to touch the sequence element to trigger an error or not
++		return True
++	except:
++		print('%s %s does not contain valid fasta data' % (filetype, fastafile), file=stderr)
++		return False
++
+ def get_illumina_reads(  output, tmp):
+ 	## Add readsets to sample
+ 	readsets = []
+@@ -271,8 +289,8 @@ def main(arguments):
+ 		if not arguments["reference"]:
+ 			sys.exit("Mapping needs a reference.")
+ 		else:
+-			if not os.path.exists(arguments["reference"]):
+-				sys.exit("Reference does not exist.")
++			if not check_fasta(arguments["reference"],"Reference"):
++				sys.exit(1)
+ 
+ 	if not arguments["nokraken"]:
+ 		if not os.path.exists(arguments["db"]):
diff --git a/debian/patches/series b/debian/patches/series
index 56c9d55..e06dd47 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 set_absolute_path_to_tex_template.patch
 adapt_config.patch
+check_fasta.patch

-- 
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