add python-examples

python-examples/Marrus_claudanielis.txt

+Dive	Date	Lat	Lon	Depth	Notes
+Tiburon 596	19-Jul-03	36 36.12 N	122 22.48 W	1190	holotype
+JSL II 1411	16-Sep-86	39 56.4 N	70 14.3 W	518	paratype
+JSL II 930	18-Aug-84	40 05.03 N	69 03.01 W	686	Youngbluth (1989)
+Ventana 1575	11-Mar-99	36 42.24 N	122 02.52 W	767	
+Ventana 1777	16-Jun-00	36 42.60 N	122 02.70 W	934	
+Ventana 2243	9-Sep-02	36 42.48 N	122 03.84 W	1001	
+Tiburon 515	24-Nov-02	36 42.00 N	122 01.98 W	1156	
+Tiburon 531	13-Mar-03	24 19.02 N	109 12.18 W	1144	
+Tiburon 547	31-Mar-03	24 14.04 N	109 40.02 W	1126	
+JSL II 3457	26-Sep-03	40 17.77 N	68 06.68 W	862	Francesc Pages (pers.comm)
\ No newline at end of file

python-examples/Sobell_if1.py

+#!/usr/local/bin/python3
+my_in=input('Enter your name: ')
+if ( my_in != '' ) :
+  print( 'Thank you, '+my_in )
+print( 'Programming running, with or without your input' )

python-examples/Sobell_my_max.py

+#!/usr/local/bin/python3
+
+my_rand_list = [5, 6, 4, 1, 7, 3, 2, 0, 9, 8]
+largest = -1
+for item in my_rand_list:
+  if( item > largest ):
+    largest = item
+    print( largest )
+print
+print( 'largest number is ', largest )

python-examples/compositioncalc1.py

+#! /usr/bin/env python
+DNASeq = "ATGTCTCATTCAAAGCA"
+SeqLength = float(len(DNASeq))
+
+BaseList = "ACGT"
+for Base in BaseList:
+	Percent = 100 * DNASeq.count(Base) / SeqLength
+	print "%s: %4.1f" % (Base,Percent)

python-examples/compositioncalc2.py

+#!/usr/bin/env python	
+DNASeq = "ATGTCTCATTCAAAGCA"
+SeqLength = float(len(DNASeq))	
+
+BaseList = list(set(DNASeq))	
+for Base in BaseList:	
+	Percent = 100 * DNASeq.count(Base) / SeqLength	
+	print "%s: %4.1f" % (Base,Percent)

python-examples/dnacalc.py

+#! /usr/bin/env python
+
+DNASeq = "ATGAAC"
+print 'Sequence:', DNASeq 
+
+SeqLength = float(len(DNASeq))
+
+print "Sequence Length:", SeqLength
+
+NumberA = DNASeq.count('A')
+NumberC = DNASeq.count('C')
+NumberG = DNASeq.count('G')
+NumberT = DNASeq.count('T')
+
+print "A:", NumberA/SeqLength
+print "C:", NumberC/SeqLength
+print "G:", NumberG/SeqLength
+print "T:", NumberT/SeqLength

python-examples/dnacalc1.py

+#! /usr/bin/env python
+# This program takes a DNA sequence (without checking)
+# and shows its length and the nucleotide composition
+# This program is described in Chapter 8 of PCfB
+
+DNASeq = "ATGTCTCATTCAAAGCA"
+
+# gather user input for sequence
+# this overrides the definition of DNASeq above
+# DNASeq = raw_input("Enter a sequence: ")
+DNASeq = DNASeq.upper()  # convert to uppercase for .count() function
+DNASeq = DNASeq.replace(" ","") # remove spaces
+
+print 'Sequence:', DNASeq 
+
+# below are nested functions: first find the length, then make it float
+
+SeqLength = float(len(DNASeq)) 
+
+print "Sequence Length:", SeqLength
+
+NumberA = DNASeq.count('A')
+NumberC = DNASeq.count('C')
+NumberG = DNASeq.count('G')
+NumberT = DNASeq.count('T')
+
+# Old way to output the Numbers
+# print "A:", NumberA/SeqLength
+# print "C:", NumberC/SeqLength
+# print "G:", NumberG/SeqLength
+# print "T:", NumberT/SeqLength
+
+# Calculate percentage and output to 1 decimal
+print "A: %.1f" % (100 * NumberA / SeqLength)
+print "C: %.1f" % (100 * NumberC / SeqLength)
+print "G: %.1f" % (100 * NumberG / SeqLength)
+print "T: %.1f" % (100 * NumberT / SeqLength)
+
+#
+# End of Chapter 8
+
+# Beginning of Chapter 9
+#
+# Calculating primer melting points with different formulas by length
+
+TotalStrong = NumberG + NumberC
+TotalWeak = NumberA + NumberT
+
+if SeqLength >=  14:
+	#formula for sequences > 14 nucleotides long 
+	MeltTempLong = 64.9 + 41 * (TotalStrong - 16.4) / SeqLength 
+	print "Tm Long (>14): %.1f C" % (MeltTempLong)
+else:
+	#formula for sequences less than 14 nucleotides long
+	MeltTemp = (4 * TotalStrong) + (2 * TotalWeak)
+	print "Tm Short: %.1f C" % (MeltTemp)
+
+

python-examples/ex03.py

+#!/usr/bin/env python
+print( 'Good morning!' )
+# in python2, the above would be 
+#   print 'Good morning!'

python-examples/ex04.py

+#! /usr/bin/env python
+# Revision of "dnacalc.py" from Ch 8 of Haddock & Dunn
+# Converted from Python 2 to Python 3
+
+DNASeq = "ATGAAC"
+print ( 'Sequence:', DNASeq )
+
+SeqLength = len(DNASeq)
+
+print ( "Sequence Length:", SeqLength )
+
+NumberA = DNASeq.count('A')
+NumberC = DNASeq.count('C')
+NumberG = DNASeq.count('G')
+NumberT = DNASeq.count('T')
+
+print ( "A:", NumberA/SeqLength )
+print ( "C:", NumberC/SeqLength )
+print ( "G:", NumberG/SeqLength )
+print ( "T:", NumberT/SeqLength )

python-examples/ex05.py

+#! /usr/bin/env python
+# Revision of "dnacalc.py" from Ch 8 of Haddock & Dunn
+# Converted from Python 2 to Python 3
+# Converted ratio to percentage and used formatted output
+
+DNASeq = "ATGAAC"
+print ( 'Sequence:', DNASeq )
+
+SeqLength = len(DNASeq)
+
+print ( "Sequence Length:", SeqLength )
+
+NumberA = DNASeq.count('A')
+NumberC = DNASeq.count('C')
+NumberG = DNASeq.count('G')
+NumberT = DNASeq.count('T')
+
+print ( "A: %.1f%%" % (100*NumberA/SeqLength) )
+print ( "C: %.1f%%" % (100*NumberC/SeqLength) )
+print ( "G: %.1f%%" % (100*NumberG/SeqLength) )
+print ( "T: %.1f%%" % (100*NumberT/SeqLength) )

python-examples/ex06.py

+#! /usr/bin/env python
+## Revision of "dnacalc1.py" from Ch 8 of Haddock & Dunn
+## Original comments
+# This program takes a DNA sequence (without checking)
+# and shows its length and the nucleotide composition
+# This program is described in Chapter 8 of PCfB
+## Converted from Python 2 to Python 3
+## Modified formatted output to include percent symbol
+## Removed material from Ch 9 from the end of the script
+
+DNASeq = "ATGTCTCATTCAAAGCA"
+
+# gather user input for sequence
+# this overrides the definition of DNASeq above
+DNASeq = input("Enter a sequence: ")
+DNASeq = DNASeq.upper()  # convert to uppercase for .count() function
+DNASeq = DNASeq.replace(" ","") # remove spaces
+
+print ( 'Sequence:', DNASeq )
+
+SeqLength = len(DNASeq)
+
+print ( "Sequence Length:", SeqLength )
+
+NumberA = DNASeq.count('A')
+NumberC = DNASeq.count('C')
+NumberG = DNASeq.count('G')
+NumberT = DNASeq.count('T')
+
+# Old way to output the Numbers
+# print "A:", NumberA/SeqLength
+# print "C:", NumberC/SeqLength
+# print "G:", NumberG/SeqLength
+# print "T:", NumberT/SeqLength
+
+# Calculate percentage and output to 1 decimal
+print ( "A: %.1f%%" % (100 * NumberA / SeqLength) )
+print ( "C: %.1f%%" % (100 * NumberC / SeqLength) )
+print ( "G: %.1f%%" % (100 * NumberG / SeqLength) )
+print ( "T: %.1f%%" % (100 * NumberT / SeqLength) )

python-examples/ex07.py

+#! /usr/bin/env python
+## Revision of "dnacalc1.py" from Ch 9 of Haddock & Dunn
+## Original comments
+# This program takes a DNA sequence (without checking)
+# and shows its length and the nucleotide composition
+# This program is described in Chapter 8 of PCfB
+## Converted from Python 2 to Python 3
+## Modified formatted output to include percent symbol
+
+DNASeq = "ATGTCTCATTCAAAGCA"
+
+# gather user input for sequence
+# this overrides the definition of DNASeq above
+DNASeq = input("Enter a sequence: ")
+DNASeq = DNASeq.upper()  # convert to uppercase for .count() function
+DNASeq = DNASeq.replace(" ","") # remove spaces
+
+print ( 'Sequence:', DNASeq )
+
+SeqLength = len(DNASeq)
+
+print ( "Sequence Length:", SeqLength )
+
+NumberA = DNASeq.count('A')
+NumberC = DNASeq.count('C')
+NumberG = DNASeq.count('G')
+NumberT = DNASeq.count('T')
+
+# Old way to output the Numbers
+# print "A:", NumberA/SeqLength
+# print "C:", NumberC/SeqLength
+# print "G:", NumberG/SeqLength
+# print "T:", NumberT/SeqLength
+
+# Calculate percentage and output to 1 decimal
+print ( "A: %.1f%%" % (100 * NumberA / SeqLength) )
+print ( "C: %.1f%%" % (100 * NumberC / SeqLength) )
+print ( "G: %.1f%%" % (100 * NumberG / SeqLength) )
+print ( "T: %.1f%%" % (100 * NumberT / SeqLength) )
+
+#
+# End of Chapter 8
+
+# Beginning of Chapter 9
+#
+# Calculating primer melting points with different formulas by length
+
+TotalStrong = NumberG + NumberC
+TotalWeak = NumberA + NumberT
+
+if SeqLength >=  14:
+	#formula for sequences > 14 nucleotides long 
+	MeltTempLong = 64.9 + 41 * (TotalStrong - 16.4) / SeqLength 
+	print ( "Tm Long (>14): %.1f C" % (MeltTempLong) )
+else:
+	#formula for sequences less than 14 nucleotides long
+	MeltTemp = (4 * TotalStrong) + (2 * TotalWeak)
+	print ( "Tm Short: %.1f C" % (MeltTemp) )
+
+

python-examples/ex08.py

+#!/usr/bin/env python
+## Revision of "proteincalc.py" from Ch 9 of Haddock & Dunn
+## Original comments
+# This program takes a protein sequence 
+# and determines its molecular weight
+# The look-up table is generated from a web page 
+# throught a series of regular expression replacements
+# This program is described in Chapter 9 of PCfB
+## Converted from Python 2 to Python 3
+
+AminoDict={
+'A':89.09,
+'R':174.20,
+'N':132.12,
+'D':133.10,
+'C':121.15,
+'Q':146.15,
+'E':147.13,
+'G':75.07,
+'H':155.16,
+'I':131.17,
+'L':131.17,
+'K':146.19,
+'M':149.21,
+'F':165.19,
+'P':115.13,
+'S':105.09,
+'T':119.12,
+'W':204.23,
+'Y':181.19,
+'V':117.15,
+'X':0.0,
+'-':0.0,
+'*':0.0 }
+
+#starting sequence string, on which to perform calculations
+ProteinSeq="FDILSATFTYGNR"
+
+MolWeight=0
+
+# step through each character in the ProteinSeq string, 
+# setting the AminoAcid variable to its value
+for AminoAcid in ProteinSeq:
+	# look up the value corresponding to the current amino acid
+	# add its value of the present amino acid to the running total
+	MolWeight = MolWeight + AminoDict[AminoAcid]
+
+# once the loop is completed, print protseq and the molecular weight
+print ( "Protein:", ProteinSeq )
+print ( "Molecular weight: %.1f" % (MolWeight) )

python-examples/ex09_log.txt

+[lij313@tux6 ~]$ python
+Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
+[GCC 7.3.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> ListofLists = [ [34.5, -120.6], [33.8, -122.7] ]
+>>> Dict = dict( ListofLists )
+>>> Dict
+{34.5: -120.6, 33.8: -122.7}
+>>> Dict[34.5]
+-120.6
+>>> Dict[M]=0
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+NameError: name 'M' is not defined
+>>> Dict['M']=0
+>>> Dict
+{34.5: -120.6, 33.8: -122.7, 'M': 0}
+>>> Dict['M']
+0
+>>> Dict['m']
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+KeyError: 'm'
+>>> Dict.keys()
+dict_keys([34.5, 33.8, 'M'])
+>>> Dict.values()
+dict_values([-120.6, -122.7, 0])
+>>> exit()
+[lij313@tux6 ~]$
\ No newline at end of file

python-examples/ex10.py

+#! /usr/bin/env python
+## Revision of "compositioncalc1.py" from Ch 9 of Haddock & Dunn
+## Converted from Python 2 to Python 3
+## Make output of program more like that of "dnacalc.py"
+DNASeq = "ATGTCTCATTCAAAGCA"
+print ( 'Sequence:', DNASeq )
+
+SeqLength = len(DNASeq)
+
+print ( "Sequence Length:", SeqLength )
+
+BaseList = "ACGT"
+for Base in BaseList:
+	Percent = 100 * DNASeq.count(Base) / SeqLength
+	print ( "%s: %4.1f%%" % (Base,Percent) )

python-examples/ex11_log.txt

+[lij313@tux6 ~]$ python
+Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
+[GCC 7.3.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> MyList=list( "abcde" )
+>>> MyList
+['a', 'b', 'c', 'd', 'e']
+>>> MyList[0:2]
+['a', 'b']
+>>> MyList[:3]
+['a', 'b', 'c']
+>>> MyList[3:]
+['d', 'e']
+>>> MyList[:]
+['a', 'b', 'c', 'd', 'e']
+>>> 
+>>> MyList[-2:]
+['d', 'e']
+>>> MyList[:-2]
+['a', 'b', 'c']
+>>> 
+>>> MyList[3]='x'
+>>> MyList
+['a', 'b', 'c', 'x', 'e']
+>>> exit()
+[lij313@tux6 ~]$ 
+
+[lij313@tux6 ~]$ python
+Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
+[GCC 7.3.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> range(0,10)
+range(0, 10)
+>>> X=range(0,10)
+>>> X
+range(0, 10)
+>>> X[:]
+range(0, 10)
+>>> for i in range(10,0,-1):
+...     print( i )
+... 
+10
+9
+8
+7
+6
+5
+4
+3
+2
+1
+>>> exit()
+[lij313@tux6 ~]$ 

python-examples/ex12_log.txt

+[lij313@tux6 ~]$ python
+Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
+[GCC 7.3.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> X=list( "abcde" )
+>>> Y=X
+>>> Y
+['a', 'b', 'c', 'd', 'e']
+>>> X[2]='x'
+>>> X
+['a', 'b', 'x', 'd', 'e']
+>>> Y
+['a', 'b', 'x', 'd', 'e']
+>>> X=list( "fghij" )
+>>> X
+['f', 'g', 'h', 'i', 'j']
+>>> Y
+['a', 'b', 'x', 'd', 'e']
+>>> exit()
+[lij313@tux6 ~]$ 

python-examples/ex13_log.txt

+[lij313@tux6 ~]$ python
+Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
+[GCC 7.3.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> X=['a','b']
+>>> X[2]='c'
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+IndexError: list assignment index out of range
+>>> X.append('c')
+>>> X
+['a', 'b', 'c']
+>>> X.remove('b')
+>>> X
+['a', 'c']
+>>> Y=list("abbracadabra")
+>>>
+>>> Y
+['a', 'b', 'b', 'r', 'a', 'c', 'a', 'd', 'a', 'b', 'r', 'a']
+>>> Y.count('a')
+5
+>>> Y.index('r')
+3
+>>> 
+>>> 'd' in Y
+True
+>>> 'm' in Y
+False
+>>> exit()
+[lij313@tux6 ~]$ 
+

python-examples/ex14.py

+#!/usr/bin/env python	
+## Revision of "compositioncalc2.py" from Ch 9 of Haddock & Dunn
+## Converted from Python 2 to Python 3
+## Make output of program more like that of "dnacalc.py"
+DNASeq = "ATGTCTCATTCAAAGCA"
+print ( 'Sequence:', DNASeq )
+
+SeqLength = len(DNASeq)
+
+print ( "Sequence Length:", SeqLength )
+
+BaseList = list(set(DNASeq))	
+for Base in BaseList:	
+	Percent = 100 * DNASeq.count(Base) / SeqLength	
+	print ( "%s: %4.1f%%" % (Base,Percent) )

python-examples/ex14_log.txt

+[lij313@tux6 ~]$ python
+Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
+[GCC 7.3.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> S={'a','b','c'}
+>>> type(S)
+<class 'set'>
+>>> S
+{'b', 'a', 'c'}
+>>> T={'a','b','c','a'}
+>>> T
+{'b', 'a', 'c'}
+>>> exit()
+[lij313@tux6 ~]$ 
+
+
+[lij313@tux6 ~]$  diff compositioncalc2.py ex14.py
+1a2,4
+> ## Revision of "compositioncalc1.py" from Ch 9 of Haddock & Dunn
+> ## Converted from Python 2 to Python 3
+> ## Make output of program more like that of "dnacalc.py"
+3c6,10
+< SeqLength = float(len(DNASeq))	
+---
+> print ( 'Sequence:', DNASeq )
+> 
+> SeqLength = len(DNASeq)
+> 
+> print ( "Sequence Length:", SeqLength )
+8c15
+< 	print "%s: %4.1f" % (Base,Percent)
+---
+> 	print "%s: %4.1f%%" % (Base,Percent)
+[lij313@tux6 ~]$  diff ex10.py ex14.py
+1,2c1,2
+< #! /usr/bin/env python
+< ## Revision of "compositioncalc1.py" from Ch 9 of Haddock & Dunn
+---
+> #!/usr/bin/env python	
+> ## Revision of "compositioncalc2.py" from Ch 9 of Haddock & Dunn
+12,14c12,14
+< BaseList = "ACGT"
+< for Base in BaseList:
+< 	Percent = 100 * DNASeq.count(Base) / SeqLength
+---
+> BaseList = list(set(DNASeq))	
+> for Base in BaseList:	
+> 	Percent = 100 * DNASeq.count(Base) / SeqLength	
+[lij313@tux6 ~]$  
+
+[lij313@tux6 ~]$  chmod u+x ex14.py
+[lij313@tux6 ~]$  ./ex14.py
+Sequence: ATGTCTCATTCAAAGCA
+Sequence Length: 17
+G: 11.8%
+C: 23.5%
+A: 35.3%
+T: 29.4%
+[lij313@tux6 ~]$