co_occurance.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "co-occurance.ipynb",
      "provenance": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "mAEY2jPptAd6"
      },
      "outputs": [],
      "source": [
        "import pandas as pd\n",
        "def co_occurance_matrix(input_text,top_words,window_size):\n",
        "    co_occur = pd.DataFrame(index=top_words, columns=top_words)\n",
        "\n",
        "    for row,nrow in zip(top_words,range(len(top_words))):\n",
        "        for colm,ncolm in zip(top_words,range(len(top_words))):        \n",
        "            count = 0\n",
        "            if row == colm: \n",
        "                co_occur.iloc[nrow,ncolm] = count\n",
        "            else: \n",
        "                for single_essay in input_text:\n",
        "                    essay_split = single_essay.split(\" \")\n",
        "                    max_len = len(essay_split)\n",
        "                    top_word_index = [index for index, split in enumerate(essay_split) if row in split]\n",
        "                    for index in top_word_index:\n",
        "                        if index == 0:\n",
        "                            count = count + essay_split[:window_size + 1].count(colm)\n",
        "                        elif index == (max_len -1): \n",
        "                            count = count + essay_split[-(window_size + 1):].count(colm)\n",
        "                        else:\n",
        "                            count = count + essay_split[index + 1 : (index + window_size + 1)].count(colm)\n",
        "                            if index < window_size: \n",
        "                                count = count + essay_split[: index].count(colm)\n",
        "                            else:\n",
        "                                count = count + essay_split[(index - window_size): index].count(colm)\n",
        "                co_occur.iloc[nrow,ncolm] = count\n",
        "\n",
        "    return co_occur"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "corpus=['Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their identit The study of human eye colour as a physical trait is based on the developmental biology, morphology, chemistry and genetic determinants of the structure known as the iris, which is part of the uveal tract of the eye (Forrester et al., 2008). The iris is a small connective tissue and muscular structure of around 12 mm in diameter with a central opening called the pupil (Figure 1). It controls the amount of light entering the eye which is focused by the lens onto the retina so as to provide the sense of vision. It contracts in bright light making the pupil smaller and dilates in dark conditions making the pupil larger, which together with the source of the incident light can influence the perception of an individual’s eye colour and iris pattern (Figure 2). In the brown iris there is an abundance of melanocytes and melanin in the anterior border layer and stroma whereas in the blue iris these layers contain very little melanin. As light traverses these relatively melanin-free layers, collagen fibrils of the iris scatter the short blue wavelengths to the surface, thus a blue iris is a consequence of structure not of major differences in chemical composition. Different shades of blue, and in irises with a limited amount of melanin, different shades of grey, green and hazel, are determined by the thickness and density of the iris itself and the extent of accumulation of white collagen fibres, as well as patches of tissue loss in the anterior border layer and stroma. A person’s eye color depends on how much of a pigment called melanin is stored in the front layers of the iris, the structure surrounding the pupil. Specialized cells called melanocytes produce the melanin, which is stored in intracellular compartment called melanosomes. People have roughly the same number of melanocytes, but the amount of melanin within melanosomes and the number of melanosomes within melanocytes both vary. Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. One gene, called OCA2, codes for a protein called P protein  , which is involved in melanosome maturation and affects the amount and quality of melanin stored in the irisGenetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The transcript encoded by the OCA2 locus is divided into 24 coding exons covering approximately 345 kb (Lee et al., 1995). The gene encodes a 838 amino acid open reading frame producing a 110 kD protein that contains 12 transmembrane spanning regions. In the first whole genome based microsatellite screen (Zhu et al., 2004) it was estimated that one interval on chromosome 15 containing the OCA2 locus could account for 74% of variance of eye colour. People with green eyes have a moderate amount of melanin and moderate number of melanosomes, while people with brown eyes have high amount of melanin stored within many melanosomes. People with green eyes have a moderate amount of melanin and moderate number of melanosomes, while people with brown eyes have high amount of melanin stored within many melanosomes. Eye color ranges depending on how much melanin is stored in these compartments. In people with blue eyes a minimal amount of melanin is found within a small number of melanosomes The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their Experimental evidence in support of a regulatory role for the conserved region within intron 86 of HERC2 on OCA2 gene expression has been provided by Eiberg et al. (Eiberg et al., 2008), who tested the effects of this region using a transcriptional reporter assay by transfection of tissue culture cell lines that included the human OCA2 immediate promoter elements in the template. Reporter constructs were prepared for brown and blue associated rs12913832 SNP alleles which were both found to be active using Caco2 human colon carcinoma cells. However, in contrast to an activation based model, a repression of Overall, the pattern of the genetic correlations corresponded well with what can be expected considering morphological differences during development. One such difference is the timing of formation. For instance, crypts are patch like atrophies in the two top cell layers in the iris, the anterior border layer and underlying stroma. They are formed sometime between the third and eight month of gestation and the principal distribution and depth of these atrophies are present at birth A person’s eye color depends on how much of a pigment called melanin is stored in the front layers of the iris, the structure surrounding the pupil. Specialized cells called melanocytes produce the melanin, which is stored in intracellular compartment called melanosomes. People have roughly the same number of melanocytes, but the amount of melanin within melanosomes and the number of melanosomes within melanocytes both vary. Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The transcript encoded by the OCA2 locus is divided into 24 coding exons covering approximately 345 kb (Lee et al., 1995). The gene encodes a 838 amino acid open reading frame producing a 110 kD protein that contains 12 transmembrane spanning regions. In the first whole genome based microsatellite screen (Zhu et al., 2004) it was estimated that one interval on chromosome 15 containing the OCA2 locus could account for 74% of variance of eye colour. People with green eyes have a moderate amount of melanin and moderate number of melanosomes, while people with brown eyes have high amount of melanin stored within many melanosomes. People with green eyes have a moderate amount of melanin and moderate number of melanosomes, while people with brown eyes have high amount of melanin stored within many melanosomes. Eye color ranges depending on how much melanin is stored in these compartments. In people with blue eyes a minimal amount of melanin is found within a small number of melanosomes The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their Experimental evidence in support of a regulatory role for the conserved region within intron 86 of HERC2 on OCA2 gene expression has been provided by Eiberg et al. (Eiberg et al., 2008), who tested the effects of this region using a transcriptional reporter assay by transfection of tissue culture cell lines that included the human OCA2 immediate promoter elements in the template. Reporter constructs were prepared for brown and blue associated rs12913832 SNP alleles which were both found to be active using Caco2 human colon carcinoma cells. However, in contrast to an activation based model, a repression of Overall, the pattern of the genetic correlations corresponded well with what can be expected considering morphological differences during development. One such difference is the timing of formation. For instance, crypts are patch like atrophies in the two top cell layers in the iris, the anterior border layer and underlying stroma. They are formed sometime between the third and eight month of gestation and the principal distribution and depth of these atrophies are present at birth Given that it potentially can be as many as 2700 genes involved in the formation of the iris, it is desirable to find the most likely candidates. Therefore, we performed an extensive literature search of the 449 genes that currently are listed by NEIBank as eye disease genes (this list can be obtained from the second author upon request). The Medline database was searched by entering the word ‘iris’ as well as the name of all disease genes listed. A total of 119 of the genes received at least one hit and a reading of the abstract for these studies revealed that 42 of them (Table 2) are associated with iris abnormalities Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. A number of other genes play smaller roles in eye color. The roles of the genes ASIP, IRF4, SLC24A4, SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1 are thought to combine with those of OCA2 and HERC2.Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The transcript encoded by the OCA2 locus is divided into 24 coding exons covering approximately 345 kb (Lee et al., 1995). The gene encodes a 838 amino acid open reading frame producing a 110 kD protein that contains 12 transmembrane spanning regions. In the first whole genome based microsatellite screen (Zhu et al., 2004) it was estimated that one interval on chromosome 15 containing the OCA2 locus could account for 74% of variance of eye colour. Due to the number of genes involved in eye color, the inheritance pattern is complex. Although a child’s eye color can generally be predicted by looking at the color of the parents’ eyes, the polymorphisms that can arise mean a child may well have an unexpected eye color. The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their identit A child’s eye color depends on the pairing of genes passed on from each parent, which is thought to involve at least three gene pairs.Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Given that it potentially can be as many as 2700 genes involved in the formation of the iris, it is desirable to find the most likely candidates. Therefore, we performed an extensive literature search of the 449 genes that currently are listed by NEIBank as eye disease genes (this list can be obtained from the second author upon request). The Medline database was searched by entering the word ‘iris’ as well as the name of all disease genes listed. A total of 119 of the genes received at least one hit and a reading of the abstract for these studies revealed that 42 of them (Table 2) are associated with iris abnormalities Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Several genetic conditions affect the eyes, with two examples being ocular albinism and oculocutaneous albinism.Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The transcript encoded by the OCA2 locus is divided into 24 coding exons covering approximately 345 kb (Lee et al., 1995). The gene encodes a 838 amino acid open reading frame producing a 110 kD protein that contains 12 transmembrane spanning regions. In the first whole genome based microsatellite screen (Zhu et al., 2004) it was estimated that one interval on chromosome 15 containing the OCA2 locus could account for 74% of variance of eye colour. Both conditions are caused by mutations in genes that contribute to melanin production and storage The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their identit In the case of ocular albinism, severely reduced pigmentation of the iris results in very light-colored eyes and vision problems. Oculocutaneous albinism also affects pigmentation of the iris, but the problem involves the skin and hair as well. People born with this condition tend to have very fair skin, white or almost white hair in addition to having very light-colored irises. Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. A person’s eye color depends on how much of a pigment called melanin is stored in the front layers of the iris, the structure surrounding the pupil. Specialized cells called melanocytes produce the melanin, which is stored in intracellular compartment called melanosomes. People have roughly the same number of melanocytes, but the amount of melanin within melanosomes and the number of melanosomes within melanocytes both vary. Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The transcript encoded by the OCA2 locus is divided into 24 coding exons covering approximately 345 kb (Lee et al., 1995). The gene encodes a 838 amino acid open reading frame producing a 110 kD protein that contains 12 transmembrane spanning regions. In the first whole genome based microsatellite screen (Zhu et al., 2004) it was estimated that one interval on chromosome 15 containing the OCA2 locus could account for 74% of variance of eye colour. People with green eyes have a moderate amount of melanin and moderate number of melanosomes, while people with brown eyes have high amount of melanin stored within many melanosomes. People with green eyes have a moderate amount of melanin and moderate number of melanosomes, while people with brown eyes have high amount of melanin stored within many melanosomes. Eye color ranges depending on how much melanin is stored in these compartments. In people with blue eyes a minimal amount of melanin is found within a small number of melanosomes The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their Experimental evidence in support of a regulatory role for the conserved region within intron 86 of HERC2 on OCA2 gene expression has been provided by Eiberg et al. (Eiberg et al., 2008), who tested the effects of this region using a transcriptional reporter assay by transfection of tissue culture cell lines that included the human OCA2 immediate promoter elements in the template. Reporter constructs were prepared for brown and blue associated rs12913832 SNP alleles which were both found to be active using Caco2 human colon carcinoma cells. However, in contrast to an activation based model, a repression of Overall, the pattern of the genetic correlations corresponded well with what can be expected considering morphological differences during development. One such difference is the timing of formation. For instance, crypts are patch like atrophies in the two top cell layers in the iris, the anterior border layer and underlying stroma. They are formed sometime between the third and eight month of gestation and the principal distribution and depth of these atrophies are present at birth Given that it potentially can be as many as 2700 genes involved in the formation of the iris, it is desirable to find the most likely candidates. Therefore, we performed an extensive literature search of the 449 genes that currently are listed by NEIBank as eye disease genes (this list can be obtained from the second author upon request). The Medline database was searched by entering the word ‘iris’ as well as the name of all disease genes listed. A total of 119 of the genes received at least one hit and a reading of the abstract for these studies revealed that 42 of them (Table 2) are associated with iris abnormalities Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The transcript encoded by the OCA2 locus is divided into 24 coding exons covering approximately 345 kb (Lee et al., 1995). The gene encodes a 838 amino acid open reading frame producing a 110 kD protein that contains 12 transmembrane spanning regions. In the first whole genome based microsatellite screen (Zhu et al., 2004) it was estimated that one interval on chromosome 15 containing the OCA2 locus could account for 74% of variance of eye colour. The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003), and is probably the most complex tissue structure that is readily available on the outside of the human body. Iris tissue forms complex patterns that contain many distinct features (Figure 2B), which are currently used as biomarkers for a wide variety of different purposes. For example, the tissue patterns that are present in the human iris can serve as a reliable basis for automatic personal identification. An increasing number of banks use the iris as a mean of identification rather than pin codes. At least 1 million frequent travellers to the UK will be able to enter the country without presenting a passport or explicitly asserting their identit Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , for eye color the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , and TYRP1. for eye color the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) The other main gene involved is called HERC2. Intron 86 on this gene controls the expression of OCA2, activating it or deactivating it as required. At least one polymorphism in this intron reduces the expression and activity of OCA2,which reduces how much P protein  is produced Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. for eye color the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) The other main gene involved is called HERC2. Intron 86 on this gene controls the expression of OCA2, activating it or deactivating it as required. At least one polymorphism in this intron reduces the expression and activity of OCA2,which reduces how much P protein  is produced Several other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5, SLC45A2 , TPCN2 , TYR , and TYRP1. for eye color the effects of these genes likely combine with those of OCA2 and HERC2 to produce a continuum of eye colors in different people. Genetics plays an important role in determining eye color, with up to 150 genes involved and two genes, OCA2 and HERC2 for eye color The inheritance of iris color is largely determined by two genes as well for eye color, EYCL1 (also called the gey gene) and EYCL3 (also called the bey2 gene) two major genes are responsible for eye color: HERC2 and OCA2. inally, two major genes are responsible for eye color: HERC2 and OCA2. inally, two major genes are responsible for eye color: HERC2 and OCA2. two major genes are responsible for eye color: HERC2 and OCA2.t wo major genes are responsible for eye color: HERC2 , two major genes are responsible for eye color: HERC2 MC1R contains eye color regions that increase the probability of obtaining green eye,MC1R contains eye color regions that increase the probability of obtaining green eye MC1R contains eye color regions that increase the probability of obtaining green eye everal other genes play smaller roles in determining eye color. Some of these genes are also involved in skin and hair coloring. Genes with reported roles in eye color include ASIP, IRF4, SLC24A4, for eye color SLC24A5 ']\n",
        "words = ['OCA2','HERC2','EYCL1','gey','EYCL3','bey2','SLC24A5','SLC45A2','TPCN2','MC1R','TYR','TYRP1','eye']\n",
        "smallword=['OCA2','SLC24A5','SLC45A2 ','IRF4']\n",
        "phen=['light skin']\n",
        "window_size = 100\n",
        "\n",
        "result = co_occurance_matrix(corpus,words,window_size)\n",
        "result"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 457
        },
        "id": "B-9aXJGjtC5y",
        "outputId": "7053ca60-1401-41b8-effd-27bbe686b602"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "        OCA2 HERC2 EYCL1  gey EYCL3 bey2 SLC24A5 SLC45A2 TPCN2 MC1R TYR TYRP1  \\\n",
              "OCA2       0   134    28   27    27   27       1      43    44    9  41     5   \n",
              "HERC2    100     0    22   24    23   23       3      35    35   13  31     3   \n",
              "EYCL1     20    20     0   12    12   12       0       9     9    1   5     0   \n",
              "gey       19    22    12    0    12   12       0       9     9    2   7     0   \n",
              "EYCL3     19    21    12   12     0   12       0       9     9    2   7     0   \n",
              "bey2      19    21    12   12    12    0       0       9     9    2   7     0   \n",
              "SLC24A5   37    34     9    9     9    9       0      16    16    2  15     2   \n",
              "SLC45A2   37    29     9    9     9    9       0       0    16    0  15     2   \n",
              "TPCN2     37    29     9    9     9    9       0      16     0    0  15     2   \n",
              "MC1R       1    19     2    3     3    3       3       0     0    0   0     0   \n",
              "TYR       65    49     9   13    13   13       0      27    27    0   0     3   \n",
              "TYRP1     31    23     4    6     6    6       0      12    12    0  11     0   \n",
              "eye      309   318    98  100   102  102      12     108   106   32  95     6   \n",
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    {
      "cell_type": "code",
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        "copy=result\n",
        "copy"
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      "execution_count": null,
      "outputs": [
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          "output_type": "execute_result",
          "data": {
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              "        OCA2 HERC2 EYCL1  gey EYCL3 bey2 SLC24A5 SLC45A2 TPCN2 MC1R TYR TYRP1  \\\n",
              "OCA2       0   134    28   27    27   27       1      43    44    9  41     5   \n",
              "HERC2    100     0    22   24    23   23       3      35    35   13  31     3   \n",
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              "EYCL3     19    21    12   12     0   12       0       9     9    2   7     0   \n",
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              "TPCN2     37    29     9    9     9    9       0      16     0    0  15     2   \n",
              "MC1R       1    19     2    3     3    3       3       0     0    0   0     0   \n",
              "TYR       65    49     9   13    13   13       0      27    27    0   0     3   \n",
              "TYRP1     31    23     4    6     6    6       0      12    12    0  11     0   \n",
              "eye      309   318    98  100   102  102      12     108   106   32  95     6   \n",
              "\n",
              "         eye  \n",
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              "      <td>120</td>\n",
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              "    <tr>\n",
              "      <th>SLC45A2</th>\n",
              "      <td>37</td>\n",
              "      <td>29</td>\n",
              "      <td>9</td>\n",
              "      <td>9</td>\n",
              "      <td>9</td>\n",
              "      <td>9</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>16</td>\n",
              "      <td>0</td>\n",
              "      <td>15</td>\n",
              "      <td>2</td>\n",
              "      <td>106</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>TPCN2</th>\n",
              "      <td>37</td>\n",
              "      <td>29</td>\n",
              "      <td>9</td>\n",
              "      <td>9</td>\n",
              "      <td>9</td>\n",
              "      <td>9</td>\n",
              "      <td>0</td>\n",
              "      <td>16</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>15</td>\n",
              "      <td>2</td>\n",
              "      <td>104</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>MC1R</th>\n",
              "      <td>1</td>\n",
              "      <td>19</td>\n",
              "      <td>2</td>\n",
              "      <td>3</td>\n",
              "      <td>3</td>\n",
              "      <td>3</td>\n",
              "      <td>3</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>45</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>TYR</th>\n",
              "      <td>65</td>\n",
              "      <td>49</td>\n",
              "      <td>9</td>\n",
              "      <td>13</td>\n",
              "      <td>13</td>\n",
              "      <td>13</td>\n",
              "      <td>0</td>\n",
              "      <td>27</td>\n",
              "      <td>27</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>3</td>\n",
              "      <td>163</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>TYRP1</th>\n",
              "      <td>31</td>\n",
              "      <td>23</td>\n",
              "      <td>4</td>\n",
              "      <td>6</td>\n",
              "      <td>6</td>\n",
              "      <td>6</td>\n",
              "      <td>0</td>\n",
              "      <td>12</td>\n",
              "      <td>12</td>\n",
              "      <td>0</td>\n",
              "      <td>11</td>\n",
              "      <td>0</td>\n",
              "      <td>70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>eye</th>\n",
              "      <td>309</td>\n",
              "      <td>318</td>\n",
              "      <td>98</td>\n",
              "      <td>100</td>\n",
              "      <td>102</td>\n",
              "      <td>102</td>\n",
              "      <td>12</td>\n",
              "      <td>108</td>\n",
              "      <td>106</td>\n",
              "      <td>32</td>\n",
              "      <td>95</td>\n",
              "      <td>6</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
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              "\n",
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              "\n",
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              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
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              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
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        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "copy.drop(columns=['OCA2','HERC2','EYCL1','gey','EYCL3','bey2','SLC24A5','SLC45A2','TPCN2','MC1R','TYR','TYRP1'], inplace= True)\n",
        "copy.drop(['eye'], inplace=True)\n",
        "copy"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 426
        },
        "id": "WG3-4MomtI0V",
        "outputId": "aafb346e-24a5-461a-e947-95acc664996c"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "         eye\n",
              "OCA2     393\n",
              "HERC2    330\n",
              "EYCL1     84\n",
              "gey       86\n",
              "EYCL3     88\n",
              "bey2      88\n",
              "SLC24A5  120\n",
              "SLC45A2  106\n",
              "TPCN2    104\n",
              "MC1R      45\n",
              "TYR      163\n",
              "TYRP1     70"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-1106e1c1-0fa3-4ec2-9bfd-5dec8b2a44b8\">\n",
              "    <div class=\"colab-df-container\">\n",
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              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>eye</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>OCA2</th>\n",
              "      <td>393</td>\n",
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              "    <tr>\n",
              "      <th>HERC2</th>\n",
              "      <td>330</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>EYCL1</th>\n",
              "      <td>84</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>gey</th>\n",
              "      <td>86</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>EYCL3</th>\n",
              "      <td>88</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>bey2</th>\n",
              "      <td>88</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SLC24A5</th>\n",
              "      <td>120</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SLC45A2</th>\n",
              "      <td>106</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>TPCN2</th>\n",
              "      <td>104</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>MC1R</th>\n",
              "      <td>45</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>TYR</th>\n",
              "      <td>163</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>TYRP1</th>\n",
              "      <td>70</td>\n",
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              "\n",
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              "\n",
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              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
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              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-1106e1c1-0fa3-4ec2-9bfd-5dec8b2a44b8 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-1106e1c1-0fa3-4ec2-9bfd-5dec8b2a44b8');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
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              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 4
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "copy.to_csv('eye color.csv')"
      ],
      "metadata": {
        "id": "tyvvX3CGtNTP"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}