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Fix obsolete unicode functions from py2 (thanks @aipolly, #266) (#303)
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* Fix obsolete unicode functions from py2 (thanks @aipolly, #266)

* don't use a class
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@tanghaibao
tanghaibao authored Jun 29, 2024
1 parent d0ba53e commit 60479ca
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267 changes: 135 additions & 132 deletions goatools/gosubdag/plot/go_name_shorten.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,146 +4,149 @@
__author__ = "DV Klopfenstein"


class ShortenText(object):
"""Shorten text for concise display."""

greek2hex = {'alpha':0x03b1, 'beta':0x03b2, 'gamma':0x03b3, 'delta':0x03b4}
greek2tex = {'alpha':r'$\alpha$', 'beta':r'$\beta$', 'gamma':r'$\gamma$', 'delta':r'$\delta$'}

def __init__(self):
self.greek2uni = {g:unichr(h).encode('utf-8') for g, h in self.greek2hex.items()}
self.keep = [
"defense response to protozoan",
"defense response to bacterium",
"cellular response to interferon-beta",
"defense response to virus",
"response to interferon-gamma",
"innate immune response",
"inflammatory response",
"response to virus",
"immune response"]

def get_short_plot_name(self, goobj):
"""Shorten some GO names so plots are smaller."""
name = goobj.name
if self._keep_this(name):
return self.replace_greek(name)
name = name.replace("cellular response to chemical stimulus",
"cellular rsp. to chemical stim.")
depth = goobj.depth
if depth > 1:
name = name.replace("regulation of ", "reg. of ")
name = name.replace("positive reg", "+reg")
name = name.replace("negative reg", "-reg")
name = name.replace("involved in", "in")
if depth > 2:
name = name.replace("antigen processing and presentation", "a.p.p")
name = name.replace("MHC class I", "MHC-I")
if depth == 4:
if goobj.id == "GO:0002460":
before = " ".join([
greek2uni = {
"alpha": "α",
"beta": "β",
"gamma": "γ",
"delta": "δ",
}
greek2tex = {
"alpha": r"$\alpha$",
"beta": r"$\beta$",
"gamma": r"$\gamma$",
"delta": r"$\delta$",
}
keep = [
"defense response to protozoan",
"defense response to bacterium",
"cellular response to interferon-beta",
"defense response to virus",
"response to interferon-gamma",
"innate immune response",
"inflammatory response",
"response to virus",
"immune response",
]


def get_short_plot_name(goobj):
"""Shorten some GO names so plots are smaller."""
name = goobj.name
if _keep_this(name):
return replace_greek(name)
name = name.replace(
"cellular response to chemical stimulus", "cellular rsp. to chemical stim."
)
depth = goobj.depth
if depth > 1:
name = name.replace("regulation of", "reg. of")
name = name.replace("positive reg", "+reg")
name = name.replace("negative reg", "-reg")
name = name.replace("involved in", "in")
if depth > 2:
name = name.replace("antigen processing and presentation", "a.p.p")
name = name.replace("MHC class I", "MHC-I")
if depth == 4:
if goobj.id == "GO:0002460":
before = " ".join(
[
"adaptive immune response based on somatic recombination of",
"immune receptors built from immunoglobulin superfamily domains"])
name = name.replace(
before,
"rsp. based on somatic recombination of Ig immune receptors")
if depth > 3:
name = name.replace("signaling pathway", "sig. pw.")
name = name.replace("response", "rsp.")
name = name.replace("immunoglobulin superfamily domains", "Ig domains")
name = name.replace("immunoglobulin", "Ig")
if depth > 4:
name = name.replace("production", "prod.")
if depth == 6 or depth == 5:
name = name.replace("tumor necrosis factor", "TNF")
name = self.replace_greek(name)
return name
"immune receptors built from immunoglobulin superfamily domains",
]
)
name = name.replace(
before,
"rsp. based on somatic recombination of Ig immune receptors",
)
if depth > 3:
name = name.replace("signaling pathway", "sig. pw.")
name = name.replace("response", "rsp.")
name = name.replace("immunoglobulin superfamily domains", "Ig domains")
name = name.replace("immunoglobulin", "Ig")
if depth > 4:
name = name.replace("production", "prod.")
if depth == 6 or depth == 5:
name = name.replace("tumor necrosis factor", "TNF")
name = replace_greek(name)
return name

def shorten_go_name_ptbl1(self, name):
"""Shorten GO name for tables in paper."""
if self._keep_this(name):
return name
name = name.replace("negative", "neg.")
name = name.replace("positive", "pos.")
name = name.replace("response", "rsp.")
name = name.replace("regulation", "reg.")
name = name.replace("antigen processing and presentation", "app.")
return name

def shorten_go_name_ptbl3(self, name, dcnt):
"""Shorten GO description for Table 3 in manuscript."""
if self._keep_this(name):
return name
name = name.replace("positive regulation of immune system process",
"+ reg. of immune sys. process")
name = name.replace("positive regulation of immune response",
"+ reg. of immune response")
name = name.replace("positive regulation of cytokine production",
"+ reg. of cytokine production")
if dcnt < 40:
name = name.replace("antigen processing and presentation", "a.p.p.")
if dcnt < 10:
name = name.replace("negative", "-")
name = name.replace("positive", "+")
#name = name.replace("tumor necrosis factor production", "tumor necrosis factor prod.")
name = name.replace("tumor necrosis factor production", "TNF production")
if dcnt < 4:
name = name.replace("regulation", "reg.")
name = name.replace("exogenous ", "")
name = name.replace(" via ", " w/")
name = name.replace("T cell mediated cytotoxicity", "cytotoxicity via T cell")
name = name.replace('involved in', 'in')
name = name.replace('-positive', '+')
def shorten_go_name_ptbl1(name):
"""Shorten GO name for tables in paper."""
if _keep_this(name):
return name
name = name.replace("negative", "neg.")
name = name.replace("positive", "pos.")
name = name.replace("response", "rsp.")
name = name.replace("regulation", "reg.")
name = name.replace("antigen processing and presentation", "app.")
return name

def replace_greek(self, name):
"""Replace text representing greek letters with greek letters."""
name = name.replace('gamma-delta', 'gammadelta')
name = name.replace('interleukin-1 beta', 'interleukin-1beta')
greek_present = False
for greek_txt, uni in self.greek2uni.items():
if greek_txt in name:
greek_present = True
name = name.replace(greek_txt, "{B}".format(B=uni))
if greek_present is True:
name = unicode(name, 'utf-8') # For writing to xlsx
return name

def replace_greek_tex(self, name):
"""Replace text representing greek letters with greek letters."""
name = name.replace('gamma-delta', 'gammadelta')
name = name.replace('interleukin-1 beta', 'interleukin-1beta')
# greek_present = False
for greek_txt, tex in self.greek2tex.items():
if greek_txt in name:
# greek_present = True
name = name.replace(greek_txt, "{B}".format(B=tex))
# if greek_present is True:
# name = texcode(name, 'utf-8') # For writing to xlsx
def shorten_go_name_ptbl3(name, dcnt):
"""Shorten GO description for Table 3 in manuscript."""
if _keep_this(name):
return name
name = name.replace(
"positive regulation of immune system process",
"+ reg. of immune sys. process",
)
name = name.replace(
"positive regulation of immune response", "+ reg. of immune response"
)
name = name.replace(
"positive regulation of cytokine production",
"+ reg. of cytokine production",
)
if dcnt < 40:
name = name.replace("antigen processing and presentation", "a.p.p.")
if dcnt < 10:
name = name.replace("negative", "-")
name = name.replace("positive", "+")
name = name.replace("tumor necrosis factor production", "TNF production")
if dcnt < 4:
name = name.replace("regulation", "reg.")
name = name.replace("exogenous ", "")
name = name.replace(" via ", " w/")
name = name.replace("T cell mediated cytotoxicity", "cytotoxicity via T cell")
name = name.replace("involved in", "in")
name = name.replace("-positive", "+")
return name

def shorten_go_name_all(self, name):
"""Shorten GO name for tables in paper, supplemental materials, and plots."""
name = self.replace_greek(name)
name = name.replace("MHC class I", "MHC-I")
return name

def _keep_this(self, name):
"""Return True if there are to be no modifications to name."""
for keep_name in self.keep:
if name == keep_name:
return True
return False

#@staticmethod
#def _shorten_go_name(name):
# name = name.replace(' and ', ' & ')
# if gont.dcnt < 15:
# name = name.replace('MHC class I', 'MHC-I')
# name = name.replace('antigen processing & presentation', 'a. p. p.')
# name = name.replace('positive regulation', 'pos. reg.')
# elif gont.depth > 2:
# name = name.replace(' & presentation', ' & pres.')
# return name
def replace_greek(name):
"""Replace text representing greek letters with greek letters."""
name = name.replace("gamma-delta", "gammadelta")
name = name.replace("interleukin-1 beta", "interleukin-1beta")
for greek_txt, uni in greek2uni.items():
if greek_txt in name:
name = name.replace(greek_txt, uni)
return name


def replace_greek_tex(name):
"""Replace text representing greek letters with greek letters."""
name = name.replace("gamma-delta", "gammadelta")
name = name.replace("interleukin-1 beta", "interleukin-1beta")
for greek_txt, tex in greek2tex.items():
if greek_txt in name:
name = name.replace(greek_txt, tex)
return name


def shorten_go_name_all(name):
"""Shorten GO name for tables in paper, supplemental materials, and plots."""
name = replace_greek(name)
name = name.replace("MHC class I", "MHC-I")
return name


def _keep_this(name):
"""Return True if there are to be no modifications to name."""
for keep_name in keep:
if name == keep_name:
return True
return False


# Copyright (C) 2016-2017, DV Klopfenstein, H Tang, All rights reserved.
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