diff _modules/SeqStats.py @ 0:69e8f12c8b31 draft

"planemo upload"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/_modules/SeqStats.py	Fri Mar 11 15:06:20 2022 +0000
@@ -0,0 +1,93 @@
+##@file SeqStats.py
+#
+# Utility class to store results (statistics) for a sequence once all coverage results have been processed for it
+
+class SeqStats:
+    def __init__(self,P_class, P_left, P_right, P_type, P_orient, ave_whole_cov, phage_plus_norm, phage_minus_norm, ArtcohesiveSeq,\
+                 P_seqcoh, Redundant, Mu_like, added_whole_coverage, Permuted, termini_coverage_norm_close, picMaxPlus_norm_close, \
+                 picMaxMinus_norm_close, gen_len, termini_coverage_close,ArtPackmode, termini, forward, reverse, ArtOrient, \
+                 picMaxPlus_close, picMaxMinus_close, picOUT_norm_forw, picOUT_norm_rev, picOUT_forw, picOUT_rev, \
+                 lost_perc, R1, R2, R3, picMaxPlus_host, picMaxMinus_host, drop_cov, added_paired_whole_coverage, P_concat):
+        self.P_class=P_class # TODO: some information about the meaning of these fields would be welcome.
+        self.P_left=P_left
+        self.P_right=P_right
+        self.P_type=P_type
+        self.P_orient=P_orient
+        self.ave_whole_cov=ave_whole_cov
+        self.phage_plus_norm=phage_plus_norm
+        self.phage_minus_norm=phage_minus_norm
+        self.ArtcohesiveSeq=ArtcohesiveSeq
+        self.P_seqcoh=P_seqcoh
+        self.Redundant=Redundant
+        self.Mu_like=Mu_like
+        self.added_whole_coverage=added_whole_coverage
+        self.Permuted=Permuted
+        self.termini_coverage_norm_close=termini_coverage_norm_close
+        self.picMaxPlus_norm_close=picMaxPlus_norm_close
+        self.picMaxMinus_norm_close=picMaxMinus_norm_close
+        self.gen_len=gen_len
+        self.termini_coverage_close=termini_coverage_close
+        self.ArtPackmode=ArtPackmode
+        self.termini=termini
+        self.forward=forward
+        self.reverse=reverse
+        self.ArtOrient=ArtOrient
+        self.picMaxPlus_close=picMaxPlus_close
+        self.picMaxMinus_close=picMaxMinus_close
+        self.picOUT_norm_forw=picOUT_norm_forw
+        self.picOUT_norm_rev=picOUT_norm_rev
+        self.picOUT_forw=picOUT_forw
+        self.picOUT_rev=picOUT_rev
+        self.lost_perc=lost_perc
+        self.R1=R1
+        self.R2=R2
+        self.R3=R3
+        self.picMaxPlus_host=picMaxPlus_host
+        self.picMaxMinus_host=picMaxMinus_host
+        self.drop_cov=drop_cov
+        self.added_paired_whole_coverage=added_paired_whole_coverage
+        self.P_concat=P_concat
+
+    def toFile(self,ficname): #TODO: implement me
+        pass
+
+# types of the elements of the class
+# <type 'str'>
+# <type 'numpy.int64'>
+# <type 'numpy.int64'>
+# <type 'str'>
+# <type 'str'>
+# <type 'float'>
+# <class 'pandas.core.frame.DataFrame'>
+# <class 'pandas.core.frame.DataFrame'>
+# <type 'str'>
+# <type 'str'>
+# <type 'int'>
+# <type 'int'>
+# <type 'list'>
+# <type 'str'>
+# <type 'list'>
+# <type 'list'>
+# <type 'list'>
+# <type 'int'>
+# <type 'list'>
+# <type 'str'>
+# <type 'str'>
+# <type 'str'>
+# <type 'str'>
+# <type 'str'>
+# <type 'list'>
+# <type 'list'>
+# <type 'list'>
+# <type 'list'>
+# <type 'list'>
+# <type 'list'>
+# <type 'float'>
+# <type 'float'>
+# <type 'float'>
+# <type 'float'>
+# <type 'str'>
+# <type 'str'>
+# <type 'list'>
+# <type 'list'>
+# <type 'str'>