ready for pip package

MANIFEST.in

@@ -1 +1 @@
-include README.md LICENSE
+include README.md LICENSE filtus/man/* filtus/man/pictures/* filtus/data/* filtus/testfiles/*

filtus/Filter.py

@@ -464,7 +464,7 @@ def getPos(v): return int(getPosStr(v))
     reader = VariantFileReader.VariantFileReader()
 
     def test_comphetTrio():
-        test = "example_files\\multiallelic_tests.vcf"; ch_fa_mo=[0,1,2]
+        test = "testfiles\\multiallelic_tests.vcf"; ch_fa_mo=[0,1,2]
         vflist = reader.readVCFlike(test, sep="\t", chromCol="CHROM", posCol="POS", geneCol="Gene_INFO", splitAsInfo="INFO", keep00=1)
         VFch, VFfa, VFmo = [vflist[i] for i in ch_fa_mo] 
         res = trioRecessiveFilter(VFch, VFfa, VFmo, "Recessive")

filtus/Filtus.py

@@ -30,15 +30,29 @@
 import FiltusUtils
 import InputDialog
 
+
+try:
+    SCRIPT_DIR = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
+except NameError:
+    # For py2exe
+    try:
+        sys.stdout = open("filtus.log", 'w')
+    except Exception:
+        pass
+
+    if hasattr(sys, 'executable'):
+        SCRIPT_DIR = os.path.abspath(os.path.join(os.path.dirname(sys.executable), '..'))
+    else:
+        print "Can't get script path"
+
+
 # module FiltusQC is imported in a try clause - to check availability of numpy and matplotlib.
 try:
     import FiltusQC
     PLOT_error = None
 except ImportError as e:
-    print 'plot import error'
+    print e
     PLOT_error = e
-
-SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
 
 class FiltusGUI(object):
     def __init__(self, parent):
@@ -660,10 +674,10 @@ def main():
     #root.mainloop() # moved to bottom of file
 
     printVF = FiltusAnalysis._printVF
-    test_csv = ["example_files\\test%d.csv" %i for i in (1,2)]
-    test_vcf = "example_files\\vcf_test.vcf"
+    test_csv = ["testfiles\\test%d.csv" %i for i in (1,2)]
+    test_vcf = "testfiles\\vcf_test.vcf"
     controltrio = "C:\\testfiles\\trioControl\\hg002_hg003_hg004.hg19_multianno.hgmd.header.txt"
-    test_trio = "example_files\\trioHG002_22X.vcf"
+    test_trio = "testfiles\\trioHG002_22X.vcf"
 
     def test_version():
         '''checks that the correct version number is used when saving output files'''
@@ -800,7 +814,7 @@ def test_advancedload():
         print "Testing advanced load........",
         filtus.clearAll()
         filtus.advLoad = FiltusWidgets.AdvancedLoad(filtus)
-        filtus.advLoad.dirEntry.setvalue("example_files")
+        filtus.advLoad.dirEntry.setvalue("testfiles")
         filtus.advLoad.endswithEntry.setvalue(".vcf")
         filtus.advLoad.endswithVar.set(1)
         filtus.advLoad_prompt()

filtus/FiltusAnalysis.py

@@ -1126,7 +1126,7 @@ def _printVF(VF, truncate=10):
     reader = VariantFileReader.VariantFileReader()
 
     def test_denovo():
-        test = "example_files\\trio1000.vcf"; frqCol="1000g2014oct_all"; ch_fa_mo=[0,1,2]
+        test = "testfiles\\trioHG002_22X.vcf"; frqCol="1000g2014oct_all"; ch_fa_mo=[0,1,2]
         vflist = reader.readVCFlike(test, sep="\t", chromCol="VCF_CHR", posCol="VCF_POS", geneCol="Gene.refGene", formatCol="VCF_FORMAT",splitAsInfo="", keep00=1)
         VFch, VFfa, VFmo = [vflist[i] for i in ch_fa_mo] 
         dn = DeNovoComputer()

filtus/VariantFileReader.py

@@ -196,7 +196,7 @@ def process(line):
 
 if __name__ == "__main__":
     reader = VariantFileReader()
-    testfile = "example_files\\test_file.csv"
+    testfile = "testfiles\\test_file.csv"
     vflist = reader.readVCFlike(testfile, sep=",", chromCol="CHROM", posCol="POS", geneCol="Gene", splitAsInfo="INFO", keep00=1)
     assert vflist[0].length == 425
     vflist = reader.readVCFlike(testfile, sep=",", chromCol="CHROM", posCol="POS", geneCol="Gene", splitAsInfo="INFO", keep00=1, prefilter=("contain", "splic"))

setup.py

@@ -40,7 +40,8 @@
     },
     'package_data': {
         'filtus': [
-            'man/*/*',
+            'man/pictures/*.png',
+            'man/*.html',
             'data/*',
             'testfiles/*'
         ]