Updated imports

cmseq/__init__.py

@@ -0,0 +1,2 @@
+from .cmseq import CMSEQ_DEFAULTS
+from .cmseq import BamFile

cmseq/breadth_depth.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python
 from __future__ import print_function
-from cmseq import CMSEQ_DEFAULTS
-from cmseq import BamFile
+
+from .cmseq import CMSEQ_DEFAULTS
+from .cmseq import BamFile
 
 import pandas as pd
 import numpy as np

cmseq/consensus.py

@@ -1,8 +1,4 @@
 #!/usr/bin/env python
-
-from cmseq import CMSEQ_DEFAULTS
-from cmseq import BamFile
-
 import pandas as pd
 import numpy as np
 import argparse
@@ -12,6 +8,9 @@
 from Bio.SeqRecord import SeqRecord
 from Bio.Alphabet import IUPAC
 
+from .cmseq import CMSEQ_DEFAULTS
+from .cmseq import BamFile
+
 def consensus_from_file():
 	parser = argparse.ArgumentParser(description="outputs the consensus in FASTA format. Non covered positions (or quality-trimmed positions) are reported as a dashes: -")
 	parser.add_argument('BAMFILE', help='The file on which to operate')

cmseq/poly.py

@@ -1,13 +1,12 @@
 #!/usr/bin/env python
-
-from cmseq import CMSEQ_DEFAULTS
-from cmseq import BamFile
-
 import pandas as pd
 import numpy as np
 import argparse
 import sys
 
+from .cmseq import CMSEQ_DEFAULTS
+from .cmseq import BamFile
+
 def poly_from_file():
 	parser = argparse.ArgumentParser(description="Reports the polymorpgic rate of each reference (polymorphic bases / total bases). Focuses only on covered regions (i.e. depth >= 1)")
 	parser.add_argument('BAMFILE', help='The file on which to operate')

cmseq/polymut.py

@@ -1,13 +1,12 @@
 #!/usr/bin/env python
-
-from cmseq import CMSEQ_DEFAULTS
-from cmseq import BamFile
-
 import pandas as pd
 import numpy as np
 import argparse
 import sys
 
+from .cmseq import CMSEQ_DEFAULTS
+from .cmseq import BamFile
+
 def polymut_from_file():
 	parser = argparse.ArgumentParser(description="Reports the polymorpgic rate of each reference (polymorphic bases / total bases). Focuses only on covered regions (i.e. depth >= 1)")
 	parser.add_argument('BAMFILE', help='The file on which to operate')

setup.py

@@ -3,7 +3,7 @@
 from io import open
 import os
 
-install_requires = ["numpy", "pysam", "pandas", "biopython", "bcbio-gff"]
+install_requires = ["numpy", "scipy", "pysam", "pandas", "biopython", "bcbio-gff"]
 setuptools.setup(
     name='CMSeq',
     version='1.0.0',