Mercurial > repos > iuc > circos

annotate process-cytogenetic-bands.py @ 3:fd59d783248a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
author iuc
date Mon, 02 Dec 2019 08:14:29 -0500
parents 014a21767ac4
children c4bde687c846
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 #!/usr/bin/env python
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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2 import sys
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3
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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4 # band hs1 p36.32 p36.32 2200000 5100000 gpos25
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5 # band hs1 p36.31 p36.31 5100000 6900000 gneg
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6 # band hs1 p36.23 p36.23 6900000 8800000 gpos25
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7 COLS = (
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8 "chrom",
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9 "chromStart",
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10 "chromEnd",
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11 "name",
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12 "score",
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13 "strand",
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14 "thickStart",
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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15 "thickEnd",
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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16 "itemRgb",
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17 )
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18
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19 colormap = {}
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20 # Process optional cytogenetic bands
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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21 # band
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22 # ID
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23 # parentChr
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24 # parentChr
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25 # START
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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26 # END COLOR
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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27 with open(sys.argv[1], "r") as handle:
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28 for line in handle:
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29 if line.startswith("#"):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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30 continue
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31
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32 lineData = dict(zip(COLS, line.split()))
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33 color = lineData.get("itemRgb", "gpos50")
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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34
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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35 if color not in colormap:
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36 # Color MUST be an RGB triplet
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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37 if color.count(",") != 2:
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38 continue
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39 tmp = color.replace(",", "")
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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40 # Try interpreting it, without `,`s as an integer. If it fails this
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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41 # test there are non-numerical values and they might try and send
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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42 # us an `eval()` or a colour name. We do not currently support
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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43 # colour names just in case.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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44 try:
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45 int(tmp)
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46 except ValueError:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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47 # Does not look like an int
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48 continue
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49
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50 colormap[color] = "gx-karyotype-%s" % len(colormap.keys())
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51
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52 sys.stderr.write(
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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53 "{colorName} = {color}\n".format(colorName=colormap[color], color=color)
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54 )
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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55
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56 sys.stdout.write(
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57 "band {chrom} {name} {name} {chromStart} {chromEnd} {color}\n".format(
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58 # Can access name because requiring >bed3
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59 name=lineData["name"],
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60 chrom=lineData["chrom"],
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61 chromStart=lineData["chromStart"],
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62 chromEnd=lineData["chromEnd"],
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63 # 255,0,0 is a valid colour specifier
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64 color=colormap[color],
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65 )
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66 )
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67
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68
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69 # chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
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70 # chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
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71 # chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
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72 # name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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73 # score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
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74 # strand - Defines the strand - either '+' or '-'.
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75 # thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
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76 # thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
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77 # itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
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78 # blockCount - The number of blocks (exons) in the BED line.
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79 # blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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80 # blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.