Module `cstag.to_html`

Expand source code

from __future__ import annotations

import re

from cstag.split import split
from cstag.utils.validator import validate_cs_tag, validate_long_format

HTML_HEADER = """<!DOCTYPE html>
    <html>
    <head>
    <style>
    h1 {
    font-family: Consolas, 'Courier New', monospace;
    color: #333;
    padding: 0.1em 0;
    border-top: solid 3px #333;
    border-bottom: solid 3px #333;
    }
    .p_seq {
    font-family: Consolas, 'Courier New', monospace;
    color: #585858;
    word-wrap: break-word;
    letter-spacing: 0.15em;
    }
    .p_legend {
    font-family: Consolas, 'Courier New', monospace;
    color: #585858;
    word-wrap: break-word;
    }

    .Ins {
    color: #333;
    border: 0.1em solid;
    background-color: #ee827c;
    font-weight: bold;
    }
    .Del {
    color: #333;
    border: 0.1em solid;
    background-color: #a0d8ef;
    font-weight: bold;
    }
    .Sub {
    color: #333;
    border: 0.1em solid;
    background-color: #98d98e;
    font-weight: bold;
    }
    .Splice {
    color: #333;
    border: 0.1em solid;
    background-color: #f8e58c;
    font-weight: bold;
    }
    .Unknown {
    color: #333;
    border: 0.1em solid;
    background-color: #c0c6c9;
    font-weight: bold;
    }

    </style>
    </head>
    <body>
"""

HTML_LEGEND = """
<p class = "p_legend">
Labels:
<span class="Ins">Insertion</span>
<span class="Del">Deletion</span>
<span class="Sub">Substitution</span>
<span class="Splice">Splice</span>
<span class="Unknown">Unknown</span>
</p>
<hr>
"""

HTML_FOOTER = """
</body>
</html>
"""


def append_mark_to_n(cs_tag: str) -> str:
    """Process each cs tag by adding specific markers `@` to `N`."""

    def append_mark(cs: str) -> str:
        if cs.startswith("N"):
            return "@" + cs
        elif re.match(r"^[ACGT]", cs):
            return "=" + cs
        return cs

    cs_tag = cs_tag.replace("=N", "N")
    cs_tag_processed = [append_mark(cs) for cs in re.split(r"(N+)", cs_tag) if cs and cs != "="]

    return "".join(cs_tag_processed)


def build_html_parts(cs: str, css_class: str) -> str:
    return f"<span class='{css_class}'>{cs.upper()}</span>"


def process_cs_tag(cs_tag: str) -> str:
    # Format cs_tag
    cs_tag = cs_tag.replace("cs:Z:", "")
    cs_tag_marked = append_mark_to_n(cs_tag)
    cs_tag_split = split(cs_tag_marked)
    # Build html
    html_parts = []
    idx = 0
    while idx < len(cs_tag_split):
        cs = cs_tag_split[idx]
        if cs.startswith("="):
            html_parts.append(cs[1:])
        elif cs.startswith("@"):
            html_parts.append(build_html_parts(cs[1:], "Unknown"))
        elif cs.startswith("*"):
            substitutions = [cs[2]]
            while idx < len(cs_tag_split) - 1 and cs_tag_split[idx + 1].startswith("*"):
                substitutions.append(cs_tag_split[idx + 1][2])
                idx += 1
            html_parts.append(build_html_parts("".join(substitutions), "Sub"))
        elif cs.startswith("+"):
            html_parts.append(build_html_parts(cs[1:], "Ins"))
        elif cs.startswith("-"):
            html_parts.append(build_html_parts(cs[1:], "Del"))
        elif cs.startswith("~"):
            left, right = cs[1:3], cs[-2:]
            splice = "-" * (int(cs[3:-2]) - 4)
            html_parts.append(build_html_parts(f"{left}{splice}{right}", "Splice"))
        idx += 1

    return f"<p class='p_seq'>{''.join(html_parts)}</p>"


def to_html(cs_tag: str, description: str = "") -> str:
    """Output HTML string showing a sequence with mutations colored
    Args:
        cs_tag (str): cs tag in the **long** format
        description (str): (optional) header information in the output string
    Return:
        HTML string
    Example:
        >>> import cstag
        >>> cs_tag = "=AC+ggg=T-acgt*at~gt10cg=GNNN"
        >>> description = "Example"
        >>> html_string = cstag.to_html(cs_tag, description)
    """
    validate_cs_tag(cs_tag)
    validate_long_format(cs_tag)
    description_str = f"<h1>{description}</h1>" if description else ""
    html_parts = process_cs_tag(cs_tag)
    report = "\n".join(
        [
            HTML_HEADER,
            description_str,
            HTML_LEGEND,
            html_parts,
            HTML_FOOTER,
        ]
    )
    return report

Functions

def append_mark_to_n(cs_tag: str) ‑> str

Process each cs tag by adding specific markers @ to N.

Expand source code

def append_mark_to_n(cs_tag: str) -> str:
    """Process each cs tag by adding specific markers `@` to `N`."""

    def append_mark(cs: str) -> str:
        if cs.startswith("N"):
            return "@" + cs
        elif re.match(r"^[ACGT]", cs):
            return "=" + cs
        return cs

    cs_tag = cs_tag.replace("=N", "N")
    cs_tag_processed = [append_mark(cs) for cs in re.split(r"(N+)", cs_tag) if cs and cs != "="]

    return "".join(cs_tag_processed)

def build_html_parts(cs: str, css_class: str) ‑> str

Expand source code

def build_html_parts(cs: str, css_class: str) -> str:
    return f"<span class='{css_class}'>{cs.upper()}</span>"

def process_cs_tag(cs_tag: str) ‑> str

Expand source code

def process_cs_tag(cs_tag: str) -> str:
    # Format cs_tag
    cs_tag = cs_tag.replace("cs:Z:", "")
    cs_tag_marked = append_mark_to_n(cs_tag)
    cs_tag_split = split(cs_tag_marked)
    # Build html
    html_parts = []
    idx = 0
    while idx < len(cs_tag_split):
        cs = cs_tag_split[idx]
        if cs.startswith("="):
            html_parts.append(cs[1:])
        elif cs.startswith("@"):
            html_parts.append(build_html_parts(cs[1:], "Unknown"))
        elif cs.startswith("*"):
            substitutions = [cs[2]]
            while idx < len(cs_tag_split) - 1 and cs_tag_split[idx + 1].startswith("*"):
                substitutions.append(cs_tag_split[idx + 1][2])
                idx += 1
            html_parts.append(build_html_parts("".join(substitutions), "Sub"))
        elif cs.startswith("+"):
            html_parts.append(build_html_parts(cs[1:], "Ins"))
        elif cs.startswith("-"):
            html_parts.append(build_html_parts(cs[1:], "Del"))
        elif cs.startswith("~"):
            left, right = cs[1:3], cs[-2:]
            splice = "-" * (int(cs[3:-2]) - 4)
            html_parts.append(build_html_parts(f"{left}{splice}{right}", "Splice"))
        idx += 1

    return f"<p class='p_seq'>{''.join(html_parts)}</p>"

def to_html(cs_tag: str, description: str = '') ‑> str

Output HTML string showing a sequence with mutations colored

Args

cs_tag : str: cs tag in the long format
description : str: (optional) header information in the output string

Return

HTML string

Example

>>> import cstag
>>> cs_tag = "=AC+ggg=T-acgt*at~gt10cg=GNNN"
>>> description = "Example"
>>> html_string = cstag.to_html(cs_tag, description)

Expand source code

def to_html(cs_tag: str, description: str = "") -> str:
    """Output HTML string showing a sequence with mutations colored
    Args:
        cs_tag (str): cs tag in the **long** format
        description (str): (optional) header information in the output string
    Return:
        HTML string
    Example:
        >>> import cstag
        >>> cs_tag = "=AC+ggg=T-acgt*at~gt10cg=GNNN"
        >>> description = "Example"
        >>> html_string = cstag.to_html(cs_tag, description)
    """
    validate_cs_tag(cs_tag)
    validate_long_format(cs_tag)
    description_str = f"<h1>{description}</h1>" if description else ""
    html_parts = process_cs_tag(cs_tag)
    report = "\n".join(
        [
            HTML_HEADER,
            description_str,
            HTML_LEGEND,
            html_parts,
            HTML_FOOTER,
        ]
    )
    return report