Extract chromosome M data

data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg

@@ -14,4 +14,4 @@ ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
 AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
 ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG
 GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC
-ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC
+ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC

data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg

@@ -14,4 +14,4 @@ ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
 ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
 AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
 ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG
-GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC
+GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC

data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-1.fasta.eg

@@ -0,0 +1,10 @@
+>1 chrM:1-16571
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT
+CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
+GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT
+ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
+ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
+ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG
+GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC
+ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC

data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-2.fasta.eg

@@ -0,0 +1,10 @@
+>1 chrM:1-16571
+CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
+GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT
+ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
+ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
+ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG
+GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC
+ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT

data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg

@@ -0,0 +1,10 @@
+>1 chrM:1-16571
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT
+CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
+GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT
+ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
+ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
+ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG
+GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC
+ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC

data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg

@@ -0,0 +1,10 @@
+>1 chrM:1-16571
+CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
+GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT
+ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
+ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
+ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG
+GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC
+ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT

data/gen/nguyen_nc_2018/20190613-fastas/days.txt

@@ -0,0 +1,7 @@
+Monday
+Tuesday
+Wednesday
+Thursday
+Friday
+Saturday
+Sunday

data/gen/nguyen_nc_2018/20190613-fastas/files.py

@@ -0,0 +1,10 @@
+title = "days of week\n"
+path = '/Users/marcelo/Documents/deena_project/mitolin/data/gen/nguyen_nc_2018/20190613-fastas/days.txt'
+days_file = open(path, 'r')
+days = days_file.read()
+new_path = '/Users/marcelo/Documents/deena_project/mitolin/data/gen/nguyen_nc_2018/20190613-fastas/new_days.txt'
+new_days = open(new_path, 'w')
+new_days.write(title)
+print(title)
+new_days.write(days)
+print(days)

data/gen/nguyen_nc_2018/20190613-fastas/mitolin_split.py

@@ -0,0 +1,17 @@
+import errno
+import glob
+
+files = glob.glob('*.fasta.eg')
+x = 1
+
+for file in files:
+	with open(file, 'r') as myfile:
+		mylines = []
+		for a_line in myfile:
+			if a_line == '>2 chr1:1-X\n':
+				break
+			mylines.append(a_line.rstrip('\n')) 
+
+	with open("chrMchr1New-"+str(x)+".fasta.eg", 'w') as writer:
+ 		writer.writelines("%s\n" % i for i in mylines)
+ 		x += 1

data/gen/nguyen_nc_2018/20190613-fastas/new_days.txt

@@ -0,0 +1,8 @@
+days of week
+Monday
+Tuesday
+Wednesday
+Thursday
+Friday
+Saturday
+Sunday

data/gen/nguyen_nc_2018/20190613-fastas/test_four.py

@@ -0,0 +1,15 @@
+
+
+with open('chrMchr1-1.fasta.eg') as f:
+	with open('chrMchr1-2.fasta.eg') as g:
+		content = f.readlines()
+		content = g.readlines()
+# you may also want to remove whitespace characters like `\n` at the end of each line
+content = [x.strip() for x in content] 
+print(content)
+
+# with open('chrMchr1-1.fasta.eg', 'r') as myfile:
+# 	for a_line in myfile:
+# 		mylines.append(a_line)
+# 		if a_line == '>2 chr1:1-X\n':
+# 			break

data/gen/nguyen_nc_2018/20190613-fastas/test_one.py

@@ -0,0 +1,24 @@
+import errno
+
+mylines = []
+
+with open('chrMchr1-1.fasta.eg', 'r') as myfile:
+	for a_line in myfile:
+		if a_line == '>2 chr1:1-X\n':
+			break
+		mylines.append(a_line.rstrip('\n')) 
+
+with open('chrMchr1_1_ONLY.fasta.eg', 'w') as writer:
+	writer.writelines("%s\n" % i for i in mylines)
+
+mylines = []
+
+with open('chrMchr1-2.fasta.eg', 'r') as myfile:
+	for a_line in myfile:
+		if a_line == '>2 chr1:1-X\n':
+			break
+		mylines.append(a_line.rstrip('\n'))
+
+with open('chrMchr1_2_ONLY.fasta.eg', 'w') as writer:
+	writer.writelines("%s\n" % i for i in mylines)
+

data/gen/nguyen_nc_2018/20190613-fastas/test_three.py

@@ -0,0 +1,10 @@
+import errno
+
+mylines = []
+
+with open('chrMchr1-1.fasta.eg', 'rt') as a:
+	with open('chrMchr1-2.fasta.eg', 'rt') as b:
+		for a_line in zip(a, b):
+			mylines.append(a_line)
+print(mylines, end='')
+

data/gen/nguyen_nc_2018/20190613-fastas/test_two.py

@@ -0,0 +1,11 @@
+import os
+file_content = []
+path = '/Users/marcelo/Documents/deena_project/mitolin/data/gen/nguyen_nc_2018/20190613-fastas'
+
+for file in os.listdir(path):
+	#print(i)
+	if file.endswith(".eg"):
+		with open(os.path.join(path, file), "r") as fd:
+			file_content.append(fd.read)
+		print(file)
+

data/gen/nguyen_nc_2018/test_two.py

@@ -0,0 +1,11 @@
+
+import errno
+path = '/Users/marcelo/Documents/deena_project/mitolin/data/gen/nguyen_nc_2018/20190613-fastas'
+files = glob.glob(path)
+for name in files:
+    try:
+        with open(name) as f:
+            pass # do what you want
+    except IOError as exc:
+        if exc.errno != errno.EISDIR:
+            raise

days.txt

@@ -0,0 +1,7 @@
+Monday
+Tuesday
+Wednesday
+Thursday
+Friday
+Saturday
+Sunday

files.py

@@ -0,0 +1,10 @@
+title = "days of week\n"
+path = '/Users/marcelo/Documents/deena_project/days.txt'
+days_file = open(path, 'r')
+days = days_file.read()
+new_path = 'Users/marcelo/Documents/deena_project/new_days.txt'
+new_days = open(new_path, 'w')
+new_days.write(title)
+print(title)
+new_days.write(days)
+print(days)