[med-svn] [fastaq] 01/03: Imported Upstream version 3.9.0

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository fastaq.

commit b7d2572be8eeca7f500a8dd461f3792a0afc705e
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Wed Oct 14 19:32:21 2015 +0000

    Imported Upstream version 3.9.0
---
 pyfastaq/common.py                                 |  2 +-
 pyfastaq/tasks.py                                  | 23 ++++++++++++++++++++++
 .../data/tasks_test_length_offsets_from_fai.fa     |  6 ++++++
 .../data/tasks_test_length_offsets_from_fai.fa.fai |  3 +++
 pyfastaq/tests/tasks_test.py                       |  8 ++++++++
 setup.py                                           |  2 +-
 6 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/pyfastaq/common.py b/pyfastaq/common.py
index f19280d..9b9d5ab 100644
--- a/pyfastaq/common.py
+++ b/pyfastaq/common.py
@@ -1 +1 @@
-version = '3.8.0'
+version = '3.9.0'
diff --git a/pyfastaq/tasks.py b/pyfastaq/tasks.py
index 9518176..41755c6 100644
--- a/pyfastaq/tasks.py
+++ b/pyfastaq/tasks.py
@@ -680,6 +680,29 @@ def lengths_from_fai(fai_file, d):
     utils.close(f)
 
 
+def length_offsets_from_fai(fai_file):
+    '''Returns a dictionary of positions of the start of each sequence, as
+       if all the sequences were catted into one sequence.
+       eg if file has three sequences, seq1 10bp, seq2 30bp, seq3 20bp, then
+       the output would be: {'seq1': 0, 'seq2': 10, 'seq3': 40}'''
+    positions = {}
+    total_length = 0
+    f = utils.open_file_read(fai_file)
+
+    for line in f:
+        try:
+            (name, length) = line.rstrip().split()[:2]
+            length = int(length)
+        except:
+            raise Error('Error reading the following line of fai file ' + fai_file + '\n' + line)
+
+        positions[name] = total_length
+        total_length += length
+
+    utils.close(f)
+    return positions
+
+
 def split_by_base_count(infile, outfiles_prefix, max_bases, max_seqs=None):
     '''Splits a fasta/q file into separate files, file size determined by number of bases.
 
diff --git a/pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa b/pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa
new file mode 100644
index 0000000..7ba49bf
--- /dev/null
+++ b/pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa
@@ -0,0 +1,6 @@
+>seq1
+ACGCTCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGA
+>seq2
+A
+>seq3
+ACGTGTT
diff --git a/pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa.fai b/pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa.fai
new file mode 100644
index 0000000..c1c0e22
--- /dev/null
+++ b/pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa.fai
@@ -0,0 +1,3 @@
+seq1	42	6	42	43
+seq2	1	55	1	2
+seq3	7	63	7	8
diff --git a/pyfastaq/tests/tasks_test.py b/pyfastaq/tests/tasks_test.py
index 7527160..0bae920 100644
--- a/pyfastaq/tests/tasks_test.py
+++ b/pyfastaq/tests/tasks_test.py
@@ -435,6 +435,14 @@ class TestLengthsFromFai(unittest.TestCase):
             self.assertEqual(int(i), d[i])
 
 
+class TestLengthOffsetsFromFai(unittest.TestCase):
+    def test_length_offsets_from_fai(self):
+        '''Test length_offsets_from_fai'''
+        got = tasks.length_offsets_from_fai(os.path.join(data_dir, 'tasks_test_length_offsets_from_fai.fa.fai'))
+        expected = {'seq1': 0, 'seq2': 42, 'seq3': 43}
+        self.assertEqual(expected, got)
+
+
 class TestSplit(unittest.TestCase):
     def test_split_by_base_count(self):
         '''Check that fasta/q files get split by base count correctly'''
diff --git a/setup.py b/setup.py
index 03a237d..eca24c8 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='pyfastaq',
-    version='3.8.0',
+    version='3.9.0',
     description='Script to manipulate FASTA and FASTQ files, plus API for developers',
     packages = find_packages(),
     author='Martin Hunt',

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