Mercurial > repos > cpt > cpt_fasta_charges
diff fasta_charges.py @ 1:054f96a0d0fb draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
|---|---|
| date | Mon, 05 Jun 2023 02:41:30 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_charges.py Mon Jun 05 02:41:30 2023 +0000 @@ -0,0 +1,362 @@ +#!/usr/bin/env python +import argparse +from Bio import SeqIO +import logging + +logging.basicConfig(level=logging.INFO) +log = logging.getLogger(name="charges") + +HTML_HEADER = "<html><head><title>Charges Report</title></head><body>" +HTML_FOOTER = "</body></html>" + +SVG_HEADER = '<svg width="%i" height="%i" xmlns="http://www.w3.org/2000/svg">\n' # % (calcWidth, calcHeight) +SVG_FOOTER = "</svg>" + +FULL_AA = [ + "H", + "S", + "Q", + "T", + "N", + "C", + "Y", + "A", + "V", + "I", + "L", + "M", + "P", + "F", + "W", + "G", + "E", + "R", + "D", + "K", +] + + +def charges_html(svg, fasta, aa, fgColor, bgColor, width=120): + colour_scheme = zip([x.upper() for x in aa], bgColor, fgColor) + copy_colour_scheme = zip([x.upper() for x in aa], bgColor, fgColor) + + # CSS and header styling + css = """<style type="text/css"> + .list li { list-style: none; margin:10px } + .info { float:left; width:20px } + pre { font-size:1.3em } + """ + info = '<h1>Charges</h1><h3>Legend</h3><ul class="list">' + for group in colour_scheme: + css += ".%s{ background: %s; color: %s}\n" % group + info += '<li><span class="%s" style="padding:5px">%s</span></li>\n' % ( + group[0], + group[0], + ) + css += "</style>" + info += "</ul>" + + # Pre-calculate, so we can use for testing 'in' + match_list = [group[0] for group in copy_colour_scheme] + + page = "" + # Parse sequences from fasta file + for record in SeqIO.parse(fasta, "fasta"): + page += "<pre><h3>>%s %s</h3>\n" % (record.id, record.description) + seq = list(str(record.seq).upper()) + + idx = 0 + for i in range(0, len(seq), width): + line_charges = [] + line_residues = seq[i : i + width] + line_numbers = [] + + for char in range(len(line_residues)): + if line_residues[char] in "KRkr": + line_charges.append("+") + elif line_residues[char] in "DEde": + line_charges.append("-") + else: + line_charges.append(" ") + + # Could be swapped out for math with i+char... + idx += 1 + if idx % 10 == 0: + line_numbers.append("%10s" % idx) + + # Replace with <span> + for m in match_list: + if line_residues[char].upper() in m: + line_residues[char] = '<span class="%s">%s</span>' % ( + m, + line_residues[char], + ) + + page += "".join(line_charges) + "\n" + page += "".join(line_residues) + "\n" + page += "".join(line_numbers) + "\n" + page += "\n" + page += "</pre>" + return HTML_HEADER + css + info + page + HTML_FOOTER + + +def charges_svg(svg, fasta, aa, fgColor, bgColor, width=120): + colour_scheme = zip([x.upper() for x in aa], bgColor, fgColor) + + svgWidth = 1100 + + # CSS and header styling + classList = [] + classes = '<style type="text/css">\n<![CDATA[\n' + + defClass = "" + for x in FULL_AA: + addAA = True + for y in aa: + if x in y: + addAA = False + if addAA: + defClass += x + + defBox = "#ffffff" + defText = "#000000" + + for group in colour_scheme: + classList.append(group[0]) + classes += "text.text_%s{fill: %s;}\n" % (group[0], group[2]) + classes += "rect.rect_%s{fill: %s; stroke: %s;}\n" % ( + group[0], + group[1], + group[1], + ) + # info += '<li><span class="%s" style="padding:5px">%s</span></li>\n' % (group[0], group[0]) + if defClass != "": + classes += "text.text_%s{fill: %s;}\n" % (defClass, defText) + classes += "rect.rect_%s{fill: %s; stroke: %s;}\n" % (defClass, defBox, defBox) + classList.append(defClass) + classes += "text.info_text{white-space: pre;}\n" + classes += "rect.rEven{fill: #fdfdfd; stroke: #fbfbfb;}\n" + classes += "rect.rOdd{fill: #f2f2fc; stroke: #fbfbfb;}\n" + classes += "]]></style>\n" + body = "" + groups = "" + # Pre-calculate, so we can use for testing 'in' + + match_list = aa + prevIndex = -1 + boxLen = 0 + page = "" + title = "" + + yInd = 60 + yInc = 15 + seqIndent = 35 + idIndent = 20 + letterLen = 8.4375 + recNum = -1 + + title += ( + '<text x="' + + str(idIndent * 0.5) + + '" y="' + + str(yInd) + + '" style="font-weight:bold; font-size:40px">Charges</text>\n' + ) + yInd += 2 * yInc + title += ( + '<text x="' + + str(idIndent) + + '" y="' + + str(yInd) + + '" style="font-size:18px">Legend:</text>\n' + ) + yInd += 2 * yInc + + for i in range(len(classList)): + title += ( + '<rect x="' + + str(seqIndent) + + '" y="' + + str(yInd - yInc + 2) + + '" width="' + + str(len(classList[i]) * letterLen) + + '" height="' + + str(yInc) + + '" class="rect_%s"/>\n' % classList[i] + ) + title += ( + '<text x="' + + str(seqIndent) + + '" y="' + + str(yInd) + + '" class="text_%s" font-family="monospace" font-size="14">%s</text>\n' + % (classList[i], classList[i]) + ) + yInd += yInc + 3 + yInd += yInc * 1.5 + + # Parse sequences from fasta file + for record in SeqIO.parse(fasta, "fasta"): + + recNum += 1 + seqHeader = ( + '<g><text x="' + + str(idIndent) + + '" y="' + + str(yInd) + + '" style="font-weight:bold">>%s %s</text>\n' + % (record.id, record.description) + ) + body += seqHeader + seq = list(str(record.seq).upper()) + yTop = yInd - yInc - 3 + yInd += yInc + idx = 0 + for i in range(0, len(seq), width): + line_charges = [] + line_residues = seq[i : i + width] + line_numbers = [] + + boxList = [] + groupList = [] + seqList = [] + prevIndex = -1 + boxLen = 0 + for char in range(len(line_residues)): + + thisInd = 0 + for x in match_list: + + if line_residues[char] in x: + break + thisInd += 1 + + if thisInd == len(match_list): + thisInd = -1 + + if char != 0 and thisInd != prevIndex: + boxList.append(boxLen) + seqList.append((line_residues[char - boxLen : char])) + groupList.append(prevIndex) + boxLen = 0 + prevIndex = thisInd + boxLen += 1 + + if line_residues[char] in "KRkr": + line_charges.append("+") + elif line_residues[char] in "DEde": + line_charges.append("-") + else: + line_charges.append(" ") + + # Could be swapped out for math with i+char... + idx += 1 + if idx % 10 == 0: + line_numbers.append("%10s" % idx) + + # Replace with <span> + # for m in match_list: + # if line_residues[char].upper() in m: + # line_residues[char] = '<span class="%s">%s</span>' % (m, line_residues[char]) + + seqList.append((line_residues[-boxLen:])) + boxList.append(boxLen) + groupList.append(prevIndex) + # Write line charges + line = "".join(line_charges) + body += ( + '<text x="' + + str(seqIndent) + + '" y="' + + str(yInd) + + '" class="info_text" font-family="monospace" font-size="14">%s</text>\n' + % line + ) + yInd += yInc + # Write sequence + sumSeq = 0 + for i in range(len(seqList)): + res = "" + for sub in seqList[i]: + res += sub + body += ( + '<rect x="' + + str(0.5 + seqIndent + (letterLen * sumSeq)) + + '" y="' + + str(yInd - yInc + 2) + + '" width="' + + str(boxList[i] * letterLen) + + '" height="' + + str(yInc) + + '" class="rect_%s"/>\n' % classList[groupList[i]] + ) + body += ( + '<text x="' + + str(seqIndent + (letterLen * sumSeq)) + + '" y="' + + str(yInd) + + '" class="text_%s" font-family="monospace" font-size="14">%s</text>\n' + % (classList[groupList[i]], res) + ) + sumSeq += len(seqList[i]) + yInd += yInc + # Write numbers + line = "".join(line_numbers) + "\n" + body += ( + '<text x="' + + str(seqIndent) + + '" y="' + + str(yInd) + + '" class="info_text" font-size="14" font-family="monospace">%s</text>\n' + % line + ) + yInd += yInc + + body += "</g>\n" + yInd += yInc + if recNum % 2 == 0: + groups += ( + '<rect x="0" y="' + + str(yTop) + + '" width="' + + str(svgWidth + 1) + + '" height="' + + str(yInd - yTop) + + '" class="rEven"/>\n' + ) + else: + groups += ( + '<rect x="0" y="' + + str(yTop) + + '" width="' + + str(svgWidth + 1) + + '" height="' + + str(yInd - yTop) + + '" class="rOdd"/>\n' + ) + svgHeight = yInd + + return ( + (SVG_HEADER % (svgWidth, svgHeight)) + + title + + classes + + groups + + body + + SVG_FOOTER + ) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Top related genomes") + parser.add_argument("--svg", action="store_true") + parser.add_argument("fasta", type=argparse.FileType("r"), help="Fasta protein file") + parser.add_argument("--width", type=int, help="Plot width", default=120) + parser.add_argument("--aa", nargs="+") + parser.add_argument("--fgColor", nargs="+") + parser.add_argument("--bgColor", nargs="+") + + args = parser.parse_args() + if args.svg: + print(charges_svg(**vars(args))) + else: + print(charges_html(**vars(args)))