# Usage: python refine_tissue.py > ../Data/information/experiment.and.tissue.2.txt
# Set cmd =
#
# Purpose: for each RNA-seq in experiment.and.tissue.1.txt, add a column suggested.tissue as its tissue annotation.
#
# 2 June 2017, slcu, hui
# Last modified 19 June 2017, slcu, hui
import os, sys, operator
import string
def get_singular_form(w):
d = {'seedlings':'seedling', 'roots':'root', 'leaves':'leaf', 'flowers':'flower', 'floral':'flower', 'shoots':'shoot', 'apices':'apex', 'stems':'stem', 'seeds':'seed', 'petals':'petals', 'sepals':'sepal', 'embryos':'embryo', 'embryonic':'embryo', 'cotyledons':'cotyledon', 'hairs':'hair', 'meristems':'meristem', 'epidermal':'epidermis', 'apical':'apex', 'buds':'bud', 'vacuoles':'vacuole', 'vacuolar':'vacuole', 'tips':'tip', 'pollens':'pollen', 'hypocotyls':'hypocotyl', 'tubes':'tube', 'stomatal':'stomata', 'ovule':'ovules', 'pistils':'pistil', 'anthers':'anther', 'carpels':'carpel', 'pedicle':'pedicel', 'vascular':'vasculum', 'whole plant':'seedling', 'inflorescence':'flower.inflorescence', 'inflorescences':'flower.inflorescence', 'whole seedling':'seedling', 'whole rosette':'leaf.rosette', 'whole aerial seedling':'seedling.aerial', 'vegatative shoot apical meristem':'shoot.apical.meristem', 'inflorescence containing stage 8 and younger flowers':'flower.inflorescence', 'plant roots':'root', 'entire vegetative rosette':'leaf.rosette', 'fungal-colonized plant roots':'root.fungal.colonized', 'rosettes - 5 leaves stage':'leaf.rosette', '2-week old seedlings without roots':'seedling.no.roots', 'immature inflorescence':'inflorescence.immature', 'rosette leaves':'leaf.rosette', 'plant seedling':'seedling', 'entire aerial part':'aerial.tissue', '14-d-old entire seedlings':'seedling', 'rosette leaf':'leaf.rosette', 'whole seedlings':'seedling', 'etiolated 5d-old seedlings':'seedling.etiolated', 'root structure':'root', 'mature leaves':'leaf.mature', 'root tip':'root.tip', '10d-old seedling':'seedling','primary root tip':'root.tip',
'epidermis including guard cells':'epidermis',
'root tip tissue':'root.tip',
'anther stage 4-7':'flower.anther',
'anther':'flower.anther',
'embryo':'seed.embryo',
'etiolated seedlings':'seedling.etiolated',
'21 days-old seedlings':'seedling',
'aerial tissue':'aerial.tissue',
'endosperm':'seed.endosperm',
'whole seed':'seed',
'pistils pollinated for 8 hours':'flower.pistil.pollinated',
'primary root':'root',
'whole floral bud':'flower.bud',
'whole seedling root':'seedling.root',
'whole root':'seedling.root',
'whole plants':'seedling',
'aerial shoots':'shoot',
'flower bud':'flower.bud',
'aerial seedling':'seedling.aerial',
'anthers at stage 4-7':'flower.anther',
'carpels (collected manually from 15 developing inflorescences)':'flower.carpel',
'ath_shoot_meristem_1':'shoot.meristem',
'ath_whole_plant_1':'seedling',
'ath_whole_plant_2':'seedling',
'whole seeds':'seed',
'3-day-old root':'root',
'unopened flower buds':'flower.bud',
'first true leaf':'leaf',
'3-day-old root':'root',
'7 dag seedlings':'seedling',
'facs-sorted protoplasts from aerial tissue of 10-day old seedlings':'seedling.protoplasts',
'root tip':'root.tip',
'inflorescences and siliques':'inflorescences.and.siliques',
'Epidermis including guard cells epidermis including guard cells':'leaf.stomata.epidermis',
'base stem':'stem',
'siliques':'silique',
'whole organism':'seedling',
'seedling shoot':'seedling.shoot',
'aerial tissue':'aerial.tissue',
'10-day-old seedlings and inflorescences from 25-day-old plants':'seedling.and.inflorescence',
'shoot apical meristem':'shoot.apical.meristem',
'expanded mature leaves from 28 day old plants':'leaf',
'aerial tissues of 15 day seedlings': 'aerial.tissue',
'whole parts':'seedling',
'aerial organs':'aerial.tissue',
'lower stem':'stem',
'upper stem':'stem',
'rosette':'leaf.rosette',
'root and shoot':'root.and.shoot',
'cell culture':'cell.culture',
'aerial part':'aerial.tissue',
'aerial':'aerial.tissue',
'whole plantlet without root':'seedling',
'sorted endodermis (facs)':'endodermis.facs-sorted',
'whole root':'root',
'siluge without seeds':'seed',
'first internode':'stem',
'rosettes':'leaf.rosette',
'hypocotyl':'seedling.hypocotyl',
'somatic embryo':'seed.embryo'
}
if w in d:
return d[w]
return w
def remove_parenthese(s):
if '(' in s:
return s[:s.find('(')]
return s
def make_singular(lst):
result = []
# map plural to singular
d = {'roots':'root', 'shoots':'shoot',
'leaves':'leaf', 'flowers':'flower',
'anthers':'anther', 'hairs':'hair',
'seedlings':'seedling', 'apices':'apex',
'buds':'bud', 'siliques':'silique',
'rosettes':'rosette', 'meristems':'meristem',
'sepals':'sepal', 'petals':'petal',
'inflorescences':'inflorescence', 'carpels':'carpel',
'seeds':'seed', 'pistils':'pistil',
'stamens':'stamen', 'ovules':'ovule',
'tissues':'tissue', 'ovaries':'ovary',
'veins':'vein', 'nodes':'node',
'internodes':'internode', 'fibres':'fibre',
'hypocotyls':'hypocotyl', 'cotyledons':'cotyledon',
'plants':'plant', 'embryos':'embryo'}
for x in lst:
if x in d:
result.append(d[x])
else:
result.append(x)
return result
def map_tissue(s):
''' given a string s, if all words in a key of d are in s, then the corresponding value is a likely tissue. '''
d = {
'hypocotyl':'seedling.hypocotyl',
'hypocotyl seedling':'seedling.hypocotyl',
'leaf':'leaf',
'leaf petiole':'leaf.petiole',
'petiole':'leaf.petiole',
'leaf blade':'leaf.blade',
'leaf first true':'leaf',
'leaf stomata':'leaf.stomata',
'stomata':'leaf.stomata',
'chlorophyll':'leaf.chlorophyll',
'vein':'leaf.vein',
'leaf vein':'leaf.vein',
'leaf lamina':'leaf.lamina',
'leaf rosette':'leaf rosette',
'rosette':'leaf.rosette',
'rosette leaf':'leaf.rosette',
'shoot':'shoot',
'aerial shoot':'aerial.shoot',
'shoot apex':'shoot.apex',
'shoot tip':'shoot.apex',
'flower':'flower',
'flower petal':'flower.petal',
'flower sepal':'flower.sepal',
'flower stamen':'flower.stamen',
'flower anther':'flower.anther',
'flower carpel':'flower.carpel',
'flower pistil':'flower.pistil',
'flower inflorescence':'flower.inflorescence',
'stigma':'flower.stigma',
'filament':'flower.filament',
'style':'flower.style',
'anther':'flower.anther',
'petal':'flower.petal',
'sepal':'flower.sepal',
'stamen':'flower.stamen',
'carpel':'flower.carpel',
'pistil':'flower.pistil',
'ovary':'flower.ovary',
'pedicel':'flower.pedicel',
'ovule':'flower.ovule',
'inflorescence':'flower.inflorescence',
'seed':'seed',
'epicotyl':'seed.epicotyl',
'radicle':'seed.radicle',
'embryo':'seed.embryo',
'endosperm':'seed.endosperm',
'endodermis':'endodermis',
'stem':'stem',
'pith':'pith',
'protoxylem':'protoxylem',
'xylem':'xylem',
'phloem':'phloem',
'sclerenchyma':'sclerenchyma',
'bast fibre':'bast.fibre',
'cortex':'cortex',
'parenchyma':'parenchyma',
'mesophyll':'leaf.mesophyll',
'shoot apical meristem':'meristem.shoot.apical',
'root apical meristem':'.meristem.root.apical',
'apical meristem':'meristem.apical',
'floral meristem':'meristem.floral',
'inflorescence meristem':'meristem.inflorescence',
'meristem':'meristem',
'meristem shoot':'meristem.shoot',
'cotyledon':'cotyledon',
'apical':'apical',
'basal':'basal',
'root':'root',
'root apex':'root.apex',
'root tip':'root.tip',
'root primary tip':'root.primary.tip',
'root cap':'root.cap',
'root lateral':'root.lateral',
'root primary':'root.primary',
'root hair':'root.hairs',
'bud':'bud',
'bud axillary':'bud.axillary',
'bud lateral':'bud.axillary',
'bud apical':'bud.apical',
'bud floral':'bud.flower',
'bud flower':'bud.flower',
'bud meristem':'bud.meristem',
'internode':'stem.internode',
'node':'stem.node',
'vascular':'vasculum',
'epidermis':'epidermis',
'seedling':'seedling',
'plant':'seedling',
'whole plant':'seedling',
'whole':'seedling',
'whole parts':'seedling',
'whole root':'root',
'seedling root':'seedling.root',
'seedling shoot':'seedling.shoot',
'seedling etiolated':'seedling.etiolated',
'aerial':'aerial',
'aerial tissue':'aerial.tissue',
'aerial seedling':'seedling.aerial',
'silique':'silique',
'unknown':'unknown',
'siluge':'seed',
'bundle sheath':'leaf'
}
result = [] # a list of tuples, (tissue, word count)
s = s.lower()
slst = s.split()
slst2 = make_singular(slst)
for k in d: # search each key in d
klst = k.split()
count = 0
exact_count = 0
for x in klst:
count += slst2.count(x)
if x in slst2:
exact_count += 1
if count >= len(klst) and exact_count == len(klst):
result.append((d[k], count))
if result == []:
return 'unknown'
else:
sresult = sorted(result, key=operator.itemgetter(1), reverse=True)
return sresult[0][0]
def repeat_words(s):
''' s in the form of meristem(2) '''
s = s.strip()
index = s.find('(')
if index < 0:
return s
index2 = s.find(')')
word = s[:index]
n = s[(index+1):index2]
n = int(n)
return ' '.join(n*[word])
def get_words(s):
''' s in the form meristem(2);leaf(2);bud(1) or shoot.meristem '''
lst = s.split(';')
result = []
for x in lst:
index = x.find('(')
if index >= 0:
t = repeat_words(x)
result.append(t)
else:
t = x
if '.' in t:
for y in t.split('.'):
result.append(y)
return ' '.join(result)
def remove_punctuation(s):
return s.replace('_', ' ')
# main
if os.path.exists('../Data/temp/experiment.and.tissue.1.txt'):
cmd = 'cut -f 1-4 ../Data/temp/experiment.and.tissue.1.txt > ../Data/temp/a.txt' # generated by python assign_tissue.py
os.system(cmd)
else:
print('Run python assign_tissue.py > ../Data/temp/experiment.and.tissue.1.txt first.')
sys.exit()
f = open('../Data/temp/a.txt')
print('run.id\tinferred.tissue\tbiosample.tissue\tbiosample.id\tsuggested.tissue')
for line in f:
line = line.strip()
lst = line.split('\t')
if lst[2] != 'part_unknown' and lst[2] != '.':
s = lst[2].lower()
s = map_tissue(remove_punctuation(s))
# elif lst[2] == '.':
# s = lst[1]
# s = remove_parenthese(s)
else:
s = lst[1]
if not ';' in s:
s = remove_parenthese(s)
else:
s = get_words(s)
s = map_tissue(remove_punctuation(s))
print(line + '\t' + s)
f.close()