From a01a93cda4c052feae5059a82e8ab4b6eee68fb4 Mon Sep 17 00:00:00 2001
From: anegm98 <a.negm98.an@gmail.com>
Date: Tue, 26 May 2020 08:07:23 +0200
Subject: [PATCH] update sam file format

---
 README.md              |  6 +++---
 setup.py               |  2 +-
 src/reporter.py        | 13 +++++++------
 tests/test_reporter.py |  6 +++---
 4 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index a1554c2..d4b9555 100644
--- a/README.md
+++ b/README.md
@@ -65,7 +65,7 @@ how many sequence reads to be loaded into memory per iteration to be mapped
 ###  Output:
 
 - #### pseudo SAM file `-o` str()
-a file containing only read name, position, and read sequence per match
+a file containing only read name, reference name, position, and read sequence per match
 
 ## Getting started
 
@@ -75,7 +75,7 @@ a file containing only read name, position, and read sequence per match
 
 - In your command line environment:
 
-		pip install path/to/sternum-x.x.x-py2.py3-none-any.whl
+		pip install path/to/sternum-x.x.x-py3-none-any.whl
 
 ### Run an example
 
@@ -84,6 +84,6 @@ a file containing only read name, position, and read sequence per match
 		sternum -m method -r path/to/reference.fastx -s path/to/sequence.fastx -k kmerSize -p minPercentage -c minKcount -b batchSize -o path/to/myfirstmap
 
 - this file will be genrated:
-path/to/myfirstmap_\$m_\$sequenceID.pSAM
+path/to/myfirstmap_\$m_\$sequenceID.sam
 
 - you can try with files in [sternum/data](https://github.com/anegm98/Sternum/tree/master/data)
diff --git a/setup.py b/setup.py
index fc401eb..3e8a7b7 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name='sternum',
-    version='1.0.0',
+    version='1.0.1',
     package_dir={"": "src"},
     install_requires=[],
     setup_requires=[],
diff --git a/src/reporter.py b/src/reporter.py
index fc91c03..14af6e5 100644
--- a/src/reporter.py
+++ b/src/reporter.py
@@ -39,16 +39,17 @@ def report(self, filePrefix=""):
         """
         readName = list(self.sequence.keys())[0]
         readName = readName[: readName.find(".")]
-        file = open(filePrefix+readName+".pSAM", 'w')
+        file = open(filePrefix+readName+".sam", 'w')
         lines = []
         for readID in self.matching:
             for refID in self.matching[readID]:
                 for matchInst in self.matching[readID][refID]:
-                    line = readID + '\tNone'
-                    line += '\t' + str(matchInst[0][0] + 1)
-                    line += ' ' + str(matchInst[1] + 1)
-                    line += '\tNone' + '\tNone' + '\tNone'
-                    line += '\t' + self.sequence[readID] + '\n'
+                    line = readID + '\t0'
+                    line += '\t' + refID
+                    line += '\t' + str(matchInst[1] + 1)
+                    line += '\t255' + '\t*' + '\t*' + '\t0'
+                    line += '\t' + self.sequence[readID]
+                    line += '\t*' + '\n'
                     lines.append(line)
         lines[-1] = lines[-1].rstrip('\n')
         file.writelines(lines)
diff --git a/tests/test_reporter.py b/tests/test_reporter.py
index f9b2bb1..599f828 100644
--- a/tests/test_reporter.py
+++ b/tests/test_reporter.py
@@ -12,12 +12,12 @@ def test_file_maker(self):
         """
         sternum = initiate_case(-1)
         reporter(sternum)
-        file = open("ERR1293055.pSAM")
+        file = open("ERR1293055.sam")
         line = file.readline()
         file.close()
-        self.assertIn("ERR1293055.19\tNone\t14 728\tNone\tNone\tNone\
+        self.assertIn("ERR1293055.19\t0\tKR233687.2.1\t728\t255\t*\t*\t0\
 \tCTGGCGGAGAAGTGAGAAAT", line)
-        os.remove("ERR1293055.pSAM")
+        os.remove("ERR1293055.sam")
 
 
 if __name__ == '__main__':