[med-svn] [fastaq] 02/03: Imported Upstream version 3.11.0

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
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commit e83fffbce611f881bbb5f63af44e71a99dc936c0
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon Nov 30 19:09:05 2015 +0000

    Imported Upstream version 3.11.0
---
 pyfastaq/common.py                                             |  2 +-
 pyfastaq/runners/interleave.py                                 | 10 +++++++++-
 pyfastaq/tasks.py                                              |  9 ++++++++-
 .../tests/data/sequences_test_deinterleaved_no_suffixes_1.fa   |  4 ++++
 .../tests/data/sequences_test_deinterleaved_no_suffixes_2.fa   |  4 ++++
 .../tests/data/sequences_test_interleaved_with_suffixes.fa     |  8 ++++++++
 pyfastaq/tests/tasks_test.py                                   |  5 +++++
 setup.py                                                       |  2 +-
 8 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/pyfastaq/common.py b/pyfastaq/common.py
index b951f1c..aa6eaf2 100644
--- a/pyfastaq/common.py
+++ b/pyfastaq/common.py
@@ -1 +1 @@
-version = '3.10.1'
+version = '3.11.0'
diff --git a/pyfastaq/runners/interleave.py b/pyfastaq/runners/interleave.py
index 60f2782..4732820 100644
--- a/pyfastaq/runners/interleave.py
+++ b/pyfastaq/runners/interleave.py
@@ -5,8 +5,16 @@ def run(description):
     parser = argparse.ArgumentParser(
         description = description,
         usage = 'fastaq interleave <infile_1> <infile_2> <outfile>')
+    parser.add_argument('--suffix1', help='Suffix to add to all names from infile_1 (if suffix not already present)')
+    parser.add_argument('--suffix2', help='Suffix to add to all names from infile_2 (if suffix not already present)')
     parser.add_argument('infile_1', help='Name of first input file')
     parser.add_argument('infile_2', help='Name of second input file')
     parser.add_argument('outfile', help='Name of output file of interleaved reads')
     options = parser.parse_args()
-    tasks.interleave(options.infile_1, options.infile_2, options.outfile)
+    tasks.interleave(
+        options.infile_1,
+        options.infile_2,
+        options.outfile,
+        suffix1=options.suffix1,
+        suffix2=options.suffix2
+    )
diff --git a/pyfastaq/tasks.py b/pyfastaq/tasks.py
index e5e1b42..0085b83 100644
--- a/pyfastaq/tasks.py
+++ b/pyfastaq/tasks.py
@@ -354,7 +354,9 @@ def get_seqs_flanking_gaps(infile, outfile, left, right):
     utils.close(fout)
 
 
-def interleave(infile_1, infile_2, outfile):
+def interleave(infile_1, infile_2, outfile, suffix1=None, suffix2=None):
+    '''Makes interleaved file from two sequence files. If used, will append suffix1 onto end 
+    of every sequence name in infile_1, unless it already ends with suffix1. Similar for sufffix2.'''
     seq_reader_1 = sequences.file_reader(infile_1)
     seq_reader_2 = sequences.file_reader(infile_2)
     f_out = utils.open_file_write(outfile)
@@ -366,6 +368,11 @@ def interleave(infile_1, infile_2, outfile):
             utils.close(f_out)
             raise Error('Error getting mate for sequence', seq_1.id, ' ... cannot continue')
 
+        if suffix1 is not None and not seq_1.id.endswith(suffix1):
+            seq_1.id += suffix1
+        if suffix2 is not None and not seq_2.id.endswith(suffix2):
+            seq_2.id += suffix2
+
         print(seq_1, file=f_out)
         print(seq_2, file=f_out)
 
diff --git a/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa
new file mode 100644
index 0000000..d79df33
--- /dev/null
+++ b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa
@@ -0,0 +1,4 @@
+>1/1
+ACGTA
+>2
+A
diff --git a/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa
new file mode 100644
index 0000000..dfe47cd
--- /dev/null
+++ b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa
@@ -0,0 +1,4 @@
+>1
+ACGTA
+>2/2
+C
diff --git a/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa b/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa
new file mode 100644
index 0000000..3692716
--- /dev/null
+++ b/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa
@@ -0,0 +1,8 @@
+>1/1
+ACGTA
+>1/2
+ACGTA
+>2/1
+A
+>2/2
+C
diff --git a/pyfastaq/tests/tasks_test.py b/pyfastaq/tests/tasks_test.py
index 3d157ea..e8688b9 100644
--- a/pyfastaq/tests/tasks_test.py
+++ b/pyfastaq/tests/tasks_test.py
@@ -224,6 +224,11 @@ class TestInterleave(unittest.TestCase):
                          tmp)
         self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_interleaved.fa'), tmp))
 
+        tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_no_suffixes_1.fa'),
+                         os.path.join(data_dir, 'sequences_test_deinterleaved_no_suffixes_2.fa'),
+                         tmp, suffix1='/1', suffix2='/2')
+        self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_interleaved_with_suffixes.fa'), tmp))
+
         with self.assertRaises(tasks.Error):
             tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_bad_1.fa'),
                              os.path.join(data_dir, 'sequences_test_deinterleaved_bad_2.fa'),
diff --git a/setup.py b/setup.py
index baa05ba..39fcf5c 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='pyfastaq',
-    version='3.10.1',
+    version='3.11.0',
     description='Script to manipulate FASTA and FASTQ files, plus API for developers',
     packages = find_packages(),
     author='Martin Hunt',

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