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Convert to Functions Exercise #6

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dafd0c7
Convert to Functions Exercise
samordil Jan 30, 2022
441d090
Updated Exercise
samordil Feb 1, 2022
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881 changes: 881 additions & 0 deletions Data/genenames.txt
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1,790 changes: 893 additions & 897 deletions Data/humchrx.txt
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21 changes: 21 additions & 0 deletions Data/sampledna.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
GAAAATGGAGCTGTCTTGGCATGTAGTCTTTATTGCCCTGCTAAGTTTTTCATGCTGGGG
GTCAGACTGGGAGTCTGATAGAAATTTCATTTCCACCGCTGGTCCTCTAACCAATGACTT
GCTGCACAACCTGAGTGGTCTCCTGGGAGACCAGAGTTCTAACTTTGTAGCAGGGGACAA
AGACATGTATGTTTGTCACCAGCCACTGCCCACTTTCCTGCCAGAATACTTCAGCAGTCT
CCATGCCAGTCAGATCACCCATTATAAGGTATTTCTGTCATGGGCACAGCTCCTCCCAGC
AGGAAGCACCCAGAATCCAGACGAGAAAACAGTGCAGTGCTACCGGCGACTCCTCAAGGC
CCTCAAGACTGCACGGCTTCAGCCCATGGTCATCCTGCACCACCAGACCCTCCCTGCCAG
CACCCTCCGGAGAACCGAAGCCTTTGCTGACCTCTTCGCCGACTATGCCACATTCGCCTT
CCACTCCTTCGGGGACCTAGTTGGGATCTGGTTCACCTTCAGTGACTTGGAGGAAGTGAT
CAAGGAGCTTCCCCACCAGGAATCAAGAGCGTCACAACTCCAGACCCTCAGTGATGCCCA
CAGAAAAGCCTATGAGATTTACCACGAAAGCTATGCTTTTCAGGGCGGAAAACTCTCTGT
TGTCCTGCGAGCTGAAGATATCCCGGAGCTCCTGCTAGAACCACCCATATCTGCGCTTGC
CCAGGACACGGTCGATTTCCTCTCTCTTGATTTGTCTTATGAATGCCAAAATGAGGCAAG
TCTGCGGCAGAAGCTGAGTAAATTGCAGACCATTGAGCCAAAAGTGAAAGTTTTCATCTT
CAACCTAAAACTCCCAGACTGCCCCTCCACCATGAAGAACCCAGCCAGTCTGCTCTTCAG
CCTTTTTGAAGCCATAAATAAAGACCAAGTGCTCACCATTGGGTTTGATATTAATGAGTT
TCTGAGTTGTTCATCAAGTTCCAAGAAAAGCATGTCTTGTTCTCTGACTGGCAGCCTGGC
CCTTCAGCCTGACCAGCAGCAGGACCACGAGACCACGGACTCCTCTCCTGCCTCTGCCTA
TCAGAGAATCTGGGAAGCATTTGCCAATCAGTCCAGGGCGGAAAGGGATGCCTTCCTGCA
GGATACTTTCCCTGAAGGCTTCCTCTGGGGTGCCTCCACAGGAGCCTTTAACGTGGAAGG
AGGCTGGGCCGAGGGTGGGAGAGGGGTGAGCATCTGGGATCCACGCAGGCCCCTGAACAC
Empty file removed Data/untitled.txt
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4 changes: 2 additions & 2 deletions Notebooks/00.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -167,7 +167,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.8"
"version": "3.9.7"
}
},
"nbformat": 4,
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4 changes: 2 additions & 2 deletions Notebooks/01.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1295,7 +1295,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -1309,7 +1309,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.8"
"version": "3.9.7"
}
},
"nbformat": 4,
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75 changes: 54 additions & 21 deletions Notebooks/02.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -747,7 +747,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 8,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -780,39 +780,53 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\u001b[0;31mDocstring:\u001b[0m\n",
"S.count(sub[, start[, end]]) -> int\n",
"\n",
"Return the number of non-overlapping occurrences of substring sub in\n",
"string S[start:end]. Optional arguments start and end are\n",
"interpreted as in slice notation.\n",
"\u001b[0;31mType:\u001b[0m builtin_function_or_method\n"
]
},
"metadata": {},
"output_type": "display_data"
"name": "stdout",
"output_type": "stream",
"text": [
"Object `trna.count()` not found.\n",
"AAGGGCTTAGCTTAATTAAAGTGGCTGATTTGCGTTCAGTTGATGCAGAGTGGGGTTTTGCAGTCCTTA\n"
]
}
],
"source": [
"?trna.count()"
"#?trna.count()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 24,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"43.47826086956522\n",
"56.52173913043478\n"
]
}
],
"source": [
"A_count=trna.count('A')\n",
"C_count=trna.count('C')\n",
"G_count=trna.count('G')\n",
"T_count=trna.count('T')"
"T_count=trna.count('T')\n",
"\n",
"length_trna = len(trna)\n",
"\n",
"# GC Content %\n",
"total_gc_content = G_count + C_count\n",
"percentage_gc = (total_gc_content / length_trna) * 100\n",
"print(percentage_gc)\n",
"\n",
"# AT Content %\n",
"total_AT_content = T_count + A_count \n",
"percentage_AT = (total_AT_content / length_trna) * 100\n",
"print(percentage_AT)\n"
]
},
{
Expand Down Expand Up @@ -1056,6 +1070,25 @@
"2. The above amino acid is a bacterial restriction enzyme that recognizes \"TCCGGA\". Find the first restriction site in the following sequence: AAAAATCCCGAGGCGGCTATATAGGGCTCCGGAGGCGTAATATAAAA"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<list_reverseiterator object at 0x7f30400a38b0>\n"
]
}
],
"source": [
"a = list('ATCG')\n",
"\n",
"print(reversed(a))"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -1066,7 +1099,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -1080,7 +1113,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.8"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
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