From e7456e0e1d0504f3a1ec8a9b41377aba51be544a Mon Sep 17 00:00:00 2001 From: Marcelo Gobelli Date: Tue, 9 Jul 2019 06:23:54 -0700 Subject: [PATCH 1/5] initial commit --- .../20190613-fastas/chrMchr1-1.fasta.eg | 2 +- .../20190613-fastas/chrMchr1-2.fasta.eg | 2 +- .../20190613-fastas/chrMchr1_1_ONLY.fasta.eg | 1 + .../20190613-fastas/chrMchr1_2_ONLY.fasta.eg | 1 + .../nguyen_nc_2018/20190613-fastas/days.txt | 7 ++++ .../nguyen_nc_2018/20190613-fastas/files.py | 10 +++++ .../20190613-fastas/new_days.txt | 8 ++++ .../20190613-fastas/test_four.py | 15 +++++++ .../20190613-fastas/test_one.py | 39 +++++++++++++++++++ .../20190613-fastas/test_three.py | 10 +++++ .../20190613-fastas/test_two.py | 11 ++++++ data/gen/nguyen_nc_2018/test_two.py | 11 ++++++ days.txt | 7 ++++ files.py | 10 +++++ 14 files changed, 132 insertions(+), 2 deletions(-) create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/days.txt create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/files.py create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/new_days.txt create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/test_four.py create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/test_one.py create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/test_three.py create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/test_two.py create mode 100644 data/gen/nguyen_nc_2018/test_two.py create mode 100644 days.txt create mode 100644 files.py diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg index 4d8fb37..f87dbee 100644 --- a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg @@ -14,4 +14,4 @@ ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC -ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC +ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg index c883058..0adb649 100644 --- a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg @@ -14,4 +14,4 @@ ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG -GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg new file mode 100644 index 0000000..e6098ea --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg @@ -0,0 +1 @@ +>1 chrM:1-16571GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC>2 chr1:1-X \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg new file mode 100644 index 0000000..8d1dfac --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg @@ -0,0 +1 @@ +>1 chrM:1-16571CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGCGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT>2 chr1:1-X \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/days.txt b/data/gen/nguyen_nc_2018/20190613-fastas/days.txt new file mode 100644 index 0000000..36839d3 --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/days.txt @@ -0,0 +1,7 @@ +Monday +Tuesday +Wednesday +Thursday +Friday +Saturday +Sunday diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/files.py b/data/gen/nguyen_nc_2018/20190613-fastas/files.py new file mode 100644 index 0000000..7b98296 --- /dev/null +++ b/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) diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/new_days.txt b/data/gen/nguyen_nc_2018/20190613-fastas/new_days.txt new file mode 100644 index 0000000..1208999 --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/new_days.txt @@ -0,0 +1,8 @@ +days of week +Monday +Tuesday +Wednesday +Thursday +Friday +Saturday +Sunday diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/test_four.py b/data/gen/nguyen_nc_2018/20190613-fastas/test_four.py new file mode 100644 index 0000000..8309cd6 --- /dev/null +++ b/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 \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py b/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py new file mode 100644 index 0000000..266e65f --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py @@ -0,0 +1,39 @@ +import errno + +mylines = [] + +with open('chrMchr1-1.fasta.eg', 'r') as myfile: + for a_line in myfile: + mylines.append(a_line.rstrip('\n')) + if a_line == '>2 chr1:1-X\n': + break + +with open('chrMchr1_1_ONLY.fasta.eg', 'w') as writer: + #for a in writer('chrMchr1-1.fasta.eg'): + writer.writelines(mylines) + print(*mylines, sep = "\n") + + # line = myfile.readline + # while line != '': + # print(line, end='') + # line = myfile.readline() + +mylines1 = [] + +with open('chrMchr1-2.fasta.eg', 'r') as myfile: + for a_line in myfile: + mylines1.append(a_line.rstrip('\n')) + if a_line == '>2 chr1:1-X\n': + break + +with open('chrMchr1_2_ONLY.fasta.eg', 'w') as writer: + #for a in writer('chrMchr1-1.fasta.eg'): + writer.writelines(mylines1) + print(*mylines1) + +#print(mylines, end='') + + +# new_path = '/Users/marcelo/Documents/deena_project/mitolin/data/gen/nguyen_nc_2018/20190613-fastas/pinga.fasta.eg' +# new_file = open(new_path, 'w') +# new_file.writelines(myfile) \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/test_three.py b/data/gen/nguyen_nc_2018/20190613-fastas/test_three.py new file mode 100644 index 0000000..0c8407f --- /dev/null +++ b/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='') + diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/test_two.py b/data/gen/nguyen_nc_2018/20190613-fastas/test_two.py new file mode 100644 index 0000000..eb3d4eb --- /dev/null +++ b/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) + diff --git a/data/gen/nguyen_nc_2018/test_two.py b/data/gen/nguyen_nc_2018/test_two.py new file mode 100644 index 0000000..c6a1dad --- /dev/null +++ b/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 \ No newline at end of file diff --git a/days.txt b/days.txt new file mode 100644 index 0000000..36839d3 --- /dev/null +++ b/days.txt @@ -0,0 +1,7 @@ +Monday +Tuesday +Wednesday +Thursday +Friday +Saturday +Sunday diff --git a/files.py b/files.py new file mode 100644 index 0000000..5e07687 --- /dev/null +++ b/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) From 8609637884b702e2e0a899dc6f1fa405d3a24c45 Mon Sep 17 00:00:00 2001 From: Marcelo Gobelli Date: Tue, 16 Jul 2019 06:00:34 -0700 Subject: [PATCH 2/5] changing order of code --- .../20190613-fastas/chrMchr1_1_ONLY.fasta.eg | 11 +++++++- .../20190613-fastas/chrMchr1_2_ONLY.fasta.eg | 11 +++++++- .../20190613-fastas/test_one.py | 27 +++++-------------- 3 files changed, 26 insertions(+), 23 deletions(-) diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg index e6098ea..f8aab2d 100644 --- a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_1_ONLY.fasta.eg @@ -1 +1,10 @@ ->1 chrM:1-16571GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC>2 chr1:1-X \ No newline at end of file +>1 chrM:1-16571 +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT +CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC +GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT +ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA +ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC +ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg index 8d1dfac..276d7ac 100644 --- a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1_2_ONLY.fasta.eg @@ -1 +1,10 @@ ->1 chrM:1-16571CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGCGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT>2 chr1:1-X \ No newline at end of file +>1 chrM:1-16571 +CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC +GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT +ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA +ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC +ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py b/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py index 266e65f..e07605b 100644 --- a/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py +++ b/data/gen/nguyen_nc_2018/20190613-fastas/test_one.py @@ -4,36 +4,21 @@ with open('chrMchr1-1.fasta.eg', 'r') as myfile: for a_line in myfile: - mylines.append(a_line.rstrip('\n')) 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: - #for a in writer('chrMchr1-1.fasta.eg'): - writer.writelines(mylines) - print(*mylines, sep = "\n") - - # line = myfile.readline - # while line != '': - # print(line, end='') - # line = myfile.readline() + writer.writelines("%s\n" % i for i in mylines) -mylines1 = [] +mylines = [] with open('chrMchr1-2.fasta.eg', 'r') as myfile: for a_line in myfile: - mylines1.append(a_line.rstrip('\n')) 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: - #for a in writer('chrMchr1-1.fasta.eg'): - writer.writelines(mylines1) - print(*mylines1) - -#print(mylines, end='') - - -# new_path = '/Users/marcelo/Documents/deena_project/mitolin/data/gen/nguyen_nc_2018/20190613-fastas/pinga.fasta.eg' -# new_file = open(new_path, 'w') -# new_file.writelines(myfile) \ No newline at end of file + writer.writelines("%s\n" % i for i in mylines) + \ No newline at end of file From 41292c66c8cac817415e2e426c2df9eb2b9547e1 Mon Sep 17 00:00:00 2001 From: Marcelo Gobelli Date: Sun, 28 Jul 2019 21:14:51 -0700 Subject: [PATCH 3/5] squashing commits --- .../20190613-fastas/1457-1sttry.dict | 94 ------------------- .../20190613-fastas/chrMchr1-1.fasta.eg | 17 ++++ .../20190613-fastas/chrMchr1-2.fasta.eg | 17 ++++ .../20190613-fastas/chrMchr1New-1.fasta.eg | 10 ++ .../20190613-fastas/chrMchr1New-2.fasta.eg | 10 ++ .../20190613-fastas/mitolin_split.py | 17 ++++ 6 files changed, 71 insertions(+), 94 deletions(-) delete mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/1457-1sttry.dict create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-1.fasta.eg create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-2.fasta.eg create mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/mitolin_split.py diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/1457-1sttry.dict b/data/gen/nguyen_nc_2018/20190613-fastas/1457-1sttry.dict deleted file mode 100644 index 9bf4851..0000000 --- a/data/gen/nguyen_nc_2018/20190613-fastas/1457-1sttry.dict +++ /dev/null @@ -1,94 +0,0 @@ -@HD VN:1.6 -@SQ SN:1 LN:16597 M5:d344d23f7264de3d23dadcaf5b9cbf5c -@SQ SN:2 LN:249250837 M5:3c8c004dd58004cb5a1e9f13ca06bf27 -@SQ SN:3 LN:243199547 M5:dce3277c058b918256bd22a2ab8229b5 -@SQ SN:4 LN:198022568 M5:4db4a7cae5d566c92bcb666999fd4fc1 -@SQ SN:5 LN:191154355 M5:2abd76b47fa06ad82e4c4f11cf0b4a5b -@SQ SN:6 LN:180915553 M5:39696d62533336b9cafd7a9a79ffb70a -@SQ SN:7 LN:171115147 M5:51963a028510b73dc48712f37a1519e7 -@SQ SN:8 LN:159138683 M5:434f9e6f1c9843f20159a2cc6081caa4 -@SQ SN:9 LN:146364139 M5:6d40af280c45bb377d411d92c11d144f -@SQ SN:10 LN:141213625 M5:e1c0437af4a79dd34039eedf74664a46 -@SQ SN:11 LN:135534939 M5:4252d9a58777ebe7fc6a541137877a5d -@SQ SN:12 LN:135006811 M5:d06620941ad531a982702830d9344bbc -@SQ SN:13 LN:133852046 M5:3e3f08f9f256069e31506688458836b7 -@SQ SN:14 LN:115169930 M5:6b3f8959ffa80516b873c9bf866feec3 -@SQ SN:15 LN:107349671 M5:3eedd9234d70b92407eb89c29cf2eb3c -@SQ SN:16 LN:102531522 M5:dd06cdf343083923e12529e618ffd301 -@SQ SN:17 LN:90354875 M5:60131d4196a0752b4714e69bb2e5115d -@SQ SN:18 LN:81195329 M5:0e8649b7fe38a06af01b8974326b14c2 -@SQ SN:19 LN:78077248 M5:1ce6188df592af201e3b98fd4b3299b6 -@SQ SN:20 LN:59129084 M5:4aa1b98e74a98d375e977bf3eccc73e8 -@SQ SN:21 LN:63025630 M5:87badda7f9a5e3bc0c33d30b6e4a7dfe -@SQ SN:22 LN:48129969 M5:738d907b14ee8b544dac9be9bc6ac655 -@SQ SN:23 LN:51304734 M5:0b0f4ced583963190c26a6e1d022f2fd -@SQ SN:24 LN:155270652 M5:1d59cbbb51b109881c4a9e67ebc0df69 -@SQ SN:25 LN:59373566 M5:1e86411d73e6f00a10590f976be01623 -@SQ SN:26 LN:106433 M5:d75b436f50a8214ee9c2a51d30b2c2cc -@SQ SN:27 LN:547496 M5:325ba9e808f669dfeee210fdd7b470ac -@SQ SN:28 LN:590426 M5:fa24f81b680df26bcfb6d69b784fbe36 -@SQ SN:29 LN:189789 M5:dbb6e8ece0b5de29da56601613007c2a -@SQ SN:30 LN:191469 M5:6ac8f815bf8e845bb3031b73f812c012 -@SQ SN:31 LN:4622290 M5:fe71bc63420d666884f37a3ad79f3317 -@SQ SN:32 LN:4795371 M5:18c17e1641ef04873b15f40f6c8659a4 -@SQ SN:33 LN:4610396 M5:2a3c677c426a10e137883ae1ffb8da3f -@SQ SN:34 LN:4683263 M5:9d51d4152174461cd6715c7ddc588dc8 -@SQ SN:35 LN:4833398 M5:efed415dd8742349cb7aaca054675b9a -@SQ SN:36 LN:4611984 M5:094d037050cad692b57ea12c4fef790f -@SQ SN:37 LN:4928567 M5:3b6d666200e72bcc036bf88a4d7e0749 -@SQ SN:38 LN:182896 M5:5d9ec007868d517e73543b005ba48535 -@SQ SN:39 LN:38914 M5:d92206d1bb4c3b4019c43c0875c06dc0 -@SQ SN:40 LN:37175 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b -@SQ SN:41 LN:90085 M5:868e7784040da90d900d2d1b667a1383 -@SQ SN:42 LN:169874 M5:569af3b73522fab4b40995ae4944e78e -@SQ SN:43 LN:187035 M5:75e4c8d17cd4addf3917d1703cacaf25 -@SQ SN:44 LN:36148 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 -@SQ SN:45 LN:40103 M5:06cbf126247d89664a4faebad130fe9c -@SQ SN:46 LN:1680828 M5:d89517b400226d3b56e753972a7cad67 -@SQ SN:47 LN:37498 M5:96358c325fe0e70bee73436e8bb14dbd -@SQ SN:48 LN:81310 M5:efc49c871536fa8d79cb0a06fa739722 -@SQ SN:49 LN:174588 M5:6c04a968f1904e1d29c2ce6dee8cefe2 -@SQ SN:50 LN:41001 M5:43f69e423533e948bfae5ce1d45bd3f1 -@SQ SN:51 LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7 -@SQ SN:52 LN:92689 M5:aa81be49bf3fe63a79bdc6a6f279abf6 -@SQ SN:53 LN:159169 M5:f40598e2a5a6b26e84a3775e0d1e2c81 -@SQ SN:54 LN:27682 M5:851106a74238044126131ce2a8e5847c -@SQ SN:55 LN:166566 M5:7daaa45c66b288847b9b32b964e623d3 -@SQ SN:56 LN:186858 M5:b0cd691f6d9cbb6269b41c9cab43eae6 -@SQ SN:57 LN:164239 M5:9d424fdcc98866650b58f004080a992a -@SQ SN:58 LN:137718 M5:46c2032c37f2ed899eb41c0473319a69 -@SQ SN:59 LN:172545 M5:5eb3b418480ae67a997957c909375a73 -@SQ SN:60 LN:172294 M5:99ff70078697f160ac5ba548f0e60f78 -@SQ SN:61 LN:172149 M5:6d243e18dea1945fb7f2517615b8f52e -@SQ SN:62 LN:161147 M5:1d708b54644c26c7e01c2dad5426d38c -@SQ SN:63 LN:179198 M5:f977edd13bac459cb2ed4a5457dba1b3 -@SQ SN:64 LN:161802 M5:fc35de963c57bf7648429e6454f1c9db -@SQ SN:65 LN:155397 M5:3238fb74ea87ae857f9c7508d315babb -@SQ SN:66 LN:186861 M5:6fe9abac455169f50470f5a6b01d0f59 -@SQ SN:67 LN:180455 M5:399dfa03bf32022ab52a846f7ca35b30 -@SQ SN:68 LN:179693 M5:d5b2fc04f6b41b212a4198a07f450e20 -@SQ SN:69 LN:211173 M5:63945c3e6962f28ffd469719a747e73c -@SQ SN:70 LN:15008 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 -@SQ SN:71 LN:128374 M5:a4aead23f8053f2655e468bcc6ecdceb -@SQ SN:72 LN:129120 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f -@SQ SN:73 LN:19913 M5:d0f40ec87de311d8e715b52e4c7062e1 -@SQ SN:74 LN:43691 M5:b4eb71ee878d3706246b7c1dbef69299 -@SQ SN:75 LN:27386 M5:ba8882ce3a1efa2080e5d29b956568a4 -@SQ SN:76 LN:40652 M5:3e06b6741061ad93a8587531307057d8 -@SQ SN:77 LN:45941 M5:7fed60298a8d62ff808b74b6ce820001 -@SQ SN:78 LN:40531 M5:93f998536b61a56fd0ff47322a911d4b -@SQ SN:79 LN:34474 M5:118a25ca210cfbcdfb6c2ebb249f9680 -@SQ SN:80 LN:41934 M5:fdcd739913efa1fdc64b6c0cd7016779 -@SQ SN:81 LN:45867 M5:e0c82e7751df73f4f6d0ed30cdc853c0 -@SQ SN:82 LN:39939 M5:131b1efc3270cc838686b54e7c34b17b -@SQ SN:83 LN:33824 M5:99795f15702caec4fa1c4e15f8a29c07 -@SQ SN:84 LN:41933 M5:445a86173da9f237d7bcf41c6cb8cc62 -@SQ SN:85 LN:42152 M5:ef4258cdc5a45c206cea8fc3e1d858cf -@SQ SN:86 LN:43523 M5:2f8694fc47576bc81b5fe9e7de0ba49e -@SQ SN:87 LN:43341 M5:cc34279a7e353136741c9fce79bc4396 -@SQ SN:88 LN:39929 M5:0996b4475f353ca98bacb756ac479140 -@SQ SN:89 LN:36651 M5:89bc61960f37d94abf0df2d481ada0ec -@SQ SN:90 LN:38154 M5:e4afcd31912af9d9c2546acf1cb23af2 -@SQ SN:91 LN:36422 M5:7de00226bb7df1c57276ca6baabafd15 -@SQ SN:92 LN:39786 M5:5a8e43bec9be36c7b49c84d585107776 -@SQ SN:93 LN:38502 M5:1d78abec37c15fe29a275eb08d5af236 diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg new file mode 100644 index 0000000..f87dbee --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg @@ -0,0 +1,17 @@ +>1 chrM:1-16571 +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT +CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC +GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT +ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA +ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC +ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC +>2 chr1:1-X +ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA +ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC +ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg new file mode 100644 index 0000000..0adb649 --- /dev/null +++ b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg @@ -0,0 +1,17 @@ +>1 chrM:1-16571 +CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC +GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT +ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA +ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC +ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT +>2 chr1:1-X +GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT +ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA +ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG +GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC \ No newline at end of file diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-1.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-1.fasta.eg new file mode 100644 index 0000000..f8aab2d --- /dev/null +++ b/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 diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-2.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1New-2.fasta.eg new file mode 100644 index 0000000..276d7ac --- /dev/null +++ b/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 diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/mitolin_split.py b/data/gen/nguyen_nc_2018/20190613-fastas/mitolin_split.py new file mode 100644 index 0000000..5017c4b --- /dev/null +++ b/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 From 4798f2b828721df29fff367339f0747e8ef5d69e Mon Sep 17 00:00:00 2001 From: Marcelo Gobelli Date: Sun, 28 Jul 2019 21:49:55 -0700 Subject: [PATCH 4/5] Delete chrMchr1-1.fasta.eg --- .../20190613-fastas/chrMchr1-1.fasta.eg | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg deleted file mode 100644 index f87dbee..0000000 --- a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-1.fasta.eg +++ /dev/null @@ -1,17 +0,0 @@ ->1 chrM:1-16571 -GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT -CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC -GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT -ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA -ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA -AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA -ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG -GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC -ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC ->2 chr1:1-X -ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA -ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA -AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA -ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG -GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC -ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC \ No newline at end of file From cdd29a27be26591469f41691f2e300089a00247a Mon Sep 17 00:00:00 2001 From: Marcelo Gobelli Date: Sun, 28 Jul 2019 21:50:05 -0700 Subject: [PATCH 5/5] Delete chrMchr1-2.fasta.eg --- .../20190613-fastas/chrMchr1-2.fasta.eg | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg diff --git a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg b/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg deleted file mode 100644 index 0adb649..0000000 --- a/data/gen/nguyen_nc_2018/20190613-fastas/chrMchr1-2.fasta.eg +++ /dev/null @@ -1,17 +0,0 @@ ->1 chrM:1-16571 -CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC -GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT -ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA -ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA -AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA -ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG -GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC -ATACTACTAATCTCATCAATACAACCCCACCCATCCTACCCAGCACACACACACCGCTGC -GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT ->2 chr1:1-X -GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT -ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA -ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA -AACCCCCCCCCCCCCCCCCCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA -ACAAAGAACCCTAACACCAGCCTAACCAGACCCATGTACTCTTTCAAATTTTATCTTTAG -GCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCC \ No newline at end of file