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updated doc
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@rajanbit
rajanbit committed May 15, 2024
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107 changes: 75 additions & 32 deletions docs/SeqPlotter_tutorial.ipynb
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"seq_logo(data, \"DNA\")"
]
},
{
"cell_type": "markdown",
"id": "63ae3225-6451-4867-8ae3-cb566b00943c",
"metadata": {},
"source": [
"### 1.25 Generate random nucleotide sequence\n",
"```\n",
"# Generating random sequences with given length and GC content \n",
">>> DNA.generate_random_seq(lenght, GC_frequency, count)\n",
"```\n",
"**Output:** append random sequences object of given length and GC content to the DNA object"
]
},
{
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"id": "1a3faf2f-34d5-4f8d-ba23-7e6964e8d1bc",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"seqID\tseq\n",
"random_seq1:\t[ATACAAATCACAAGTATTCAATACAATAGACGTATGTAAGACTGATTGTTAATTCAGTAAATAGACGTGA]\n",
"random_seq2:\t[TTCTTGTGTCATTATTTACACAGGAAATATGTAACCCAACACATAGATTTACAAACTATACTGGTAACAT]\n",
"random_seq3:\t[CGTTTAGTGTTGCATGATGCGATCATTACATTTCTTATACAGTTGATATCAACAAATGCTACACTGACAA]\n",
"random_seq4:\t[TAATGAGGTGAGCTTTAGATATAAAGGCTTCTTATAGCATACCATTGCAAAAGATCGCCATTATATAATG]\n",
"random_seq5:\t[TTCATTCAGAAATCAATATACAAACATTATTGAAATACCTCATTTTGTGTTTTGAAATCTAGTCAGGTAT]\n"
]
}
],
"source": [
"# Clearing records \n",
"DNA.clear()\n",
"\n",
"# Generating 10 random sequences with 70 bp length and 30% GC content \n",
"new_data = DNA.generate_random_seq(70, 0.3, 10)\n",
"\n",
"# Printing first 5 random sequences\n",
"DNA.head()"
]
},
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"35"
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" 'V': 7.701922950367426}"
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"3.87"
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"outputs": [
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"'G'"
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"outputs": [
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"'VGGEA'"
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"4"
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"'MLPFWKRLLYAAVIAGALVGADAQFWKTAGTAGSIQDSVKHYNRNEPKFPIDDSYDIVDSAGVARGDLPPKNCTAGYAGCVPKCIAEKGNRGLPGPLGPTGLKGEMGFPGMEGPSGDKGQKGDPGPYGQRGDKGERGSPGLHGQAGVPGVQGPAGNPGAPGINGKDGCDGQDGIPGLEGLSGMPGPRGYAGQLGSKGEKGEPAKENGDYA'"
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"[4 rows x 84 columns]"
]
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"execution_count": 46,
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},
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"outputs": [
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"seq4 3.832661 6.474332"
]
},
"execution_count": 47,
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"metadata": {},
"outputs": [
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.18"
"version": "3.8.19"
}
},
"nbformat": 4,
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