from EMAlgorithm import EMAlgorithm
from DatabaseReducer import DatabaseReducer

STAPHILOCCOCUS = "alignments/alignments_staphi"
SALMONELLA = "alignments/alignments_salmonella"
KLEBSIELLA = "alignments/alignments_klebsiella"

STAPHILOCCOCUS_NEW = "alignments/new/alignments_staphi"
SALMONELLA_NEW = "alignments/new/alignments_salmonella"
KLEBSIELLA_NEW = "alignments/new/alignments_klebsiella"

STAPHILOCCOCUS2 = "alignments/Ivan/outs/Staphi_x1.out"
SALMONELLA2 = "alignments/Ivan/outs/salmonella_x1.out"
KLEBSIELLA2 = "alignments/Ivan/outs/klebsiella_x1.fastq.out"

INPUT_FILE = KLEBSIELLA + "_x1.sam"

#DatabaseReducer().generate()
EM = EMAlgorithm().start(INPUT_FILE)



@@ -402,17 +402,21 @@
 LOCCOCUS
-2
+_TEST
  = %22alig
@@ -426,31 +426,24 @@
 nts/
-Ivan
+test
 /outs/
-S
+s
 taphi
-_x1.out
 %22%0ASA
@@ -446,25 +446,29 @@
 %22%0ASALMONELLA
-2
+_TEST
  = %22alignmen
@@ -466,28 +466,28 @@
 %22alignments/
-Ivan
+test
 /outs/salmon
@@ -494,15 +494,8 @@
 ella
-_x1.out
 %22%0AKL
@@ -506,9 +506,13 @@
 ELLA
-2
+_TEST
  = %22
@@ -526,12 +526,12 @@
 nts/
-Ivan
+test
 /out
@@ -546,21 +546,8 @@
 ella
-_x1.fastq.out
 %22%0A%0AI
@@ -568,16 +568,21 @@
 EBSIELLA
+_TEST
  + %22_x1.

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