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# Usage: python assign_tissue.py > ../Data/temp/experiment.and.tissue.1.txt
# Set TPM_FILE = , d = and d2 =
#
# Purpose: for each RNA-seq column in the TPM_FILE, get its tissue information
# Excute this command to avoid encoding error: export PYTHONIOENCODING=UTF-8
#
# 2 June 2017, slcu, hui
# Last modified 19 June 2017, slcu, hui
# Last modified 5 November 2022, hui
import os, sys, json
def make_tissue_dict(fname):
f = open(fname)
d = json.load(f)
f.close()
return d
def get_experiment_id(fname):
f = open(fname)
lines = f.readlines()
f.close()
result = []
for line in lines[1:]:
line = line.strip()
lst = line.split('\t')
if len(lst) >= 2:
result.append(lst[1])
return result
def get_sra_id(x):
if 'RR' in x:
index1 = x.find('RR')
index2 = x.find('X')
if index2 == -1:
index2 = len(x)
return x[index1-1:index2]
return x
def make_sample_dict(fname):
f = open(fname)
lines = f.readlines()
f.close()
d = {}
for line in lines[1:]: # skip the head line
line = line.strip()
lst = line.split('\t')
if len(lst) >= 2:
runid = lst[0]
sample = lst[1]
d[runid] = (sample, ';'.join(lst[2:]))
return d
def stringfy_json(d):
s = ''
if "organismPart" in d["characteristics"]:
s = d["characteristics"]["organismPart"][0]["text"]
else:
s = 'part_unknown'
if "accession" in d:
s += '\t' + d["accession"]
else:
s += '\t' + '.'
if "name" in d:
s += '\t' + d["name"]
else:
s += '\t' + '.'
if "synonym" in d["characteristics"]:
s += '\t' + d["characteristics"]["synonym"][0]["text"]
else:
s += '\t' + '.'
if "ecotype" in d["characteristics"]:
s += '\t' + d["characteristics"]["ecotype"][0]["text"]
else:
s += '\t' + '.'
if "developmentStage" in d["characteristics"]:
s += '\t' + d["characteristics"]["developmentStage"][0]["text"]
else:
s += '\t' + '.'
if "description" in d:
s += '\t' + d["description"] if d["description"] != None else '.'
else:
s += '\t' + '.'
return s
def make_information(s, info_dir):
lst = s.split('...')
sample_id = lst[0] # looks like SAMD00012930
filename = '%s/%s.json' % (info_dir, sample_id)
if not os.path.exists(filename):
#cmd = 'curl -s -H Content-Type:application/json https://www.ebi.ac.uk/biosamples/api/samples/search/findByAccession\?accession\=%s > %s' % (sample_id, filename)
cmd = 'curl -s -H Content-Type:application/json https://www.ebi.ac.uk/biosamples/samples/%s.json > %s' % (sample_id, filename)
os.system(cmd)
f = open(filename)
d = json.load(f)
f.close()
if 'tissue' in d['characteristics']:
return d['characteristics']['tissue'][0]['text'].lower() + '\t' + sample_id
else:
return '.' + '\t' + sample_id
# main
BIOSAMPLE_INFO_DIR = '../Data/information/BioSample' # put downloaded BioSample json files here
if not os.path.isdir(BIOSAMPLE_INFO_DIR):
os.makedirs(BIOSAMPLE_INFO_DIR)
# get first row in the TPM file
TPM_FILE = '../Data/history/expr/TPM.txt'
cmd = 'head -1 %s | perl -ne \'@words = split /\t/; $count = 1; for $x (@words) {print $count, "\t", $x, "\n"; $count++}\' > ../Data/temp/a.txt' % (TPM_FILE)
os.system(cmd)
lst = get_experiment_id('../Data/temp/a.txt')
d = make_tissue_dict('../Data/information/rnaseq_info_database.json') # excuting parse_xml.py > rnaseq_info_database.txt, mainly for getting tissue names (inferred by word frequency in the description)
d2 = make_sample_dict('../Data/information/rnaseq_info_database.txt.temp') # parse_xml.py > rnaseq_info_database.txt, mainly for getting the BioSample id for each run
head = ''
# run.id inferred.tissue biosample.tissue biosample.id
with open('../Data/temp/experiment.and.tissue.1.txt', 'w', encoding='utf8') as f:
for x in lst:
s = x # run id, such as R0DRR016125XXX
k = get_sra_id(x) # get rid of prefix R00... and suffix ..XX
if k in d:
s += '\t' + d[k]['tissue'] + '\t' + make_information(d2[k][0], BIOSAMPLE_INFO_DIR)
elif x.startswith('R0001') and ('146' in x or '147' in x): # inhouse data
s += '\t' + 'seedling\t' + '\t'.join(8*['.'])
elif x.startswith('R0002'): # pcubas (Spain) data
s += '\t' + 'meristem\t' + '\t'.join(8*['.'])
else:
s += '\t' + '\t'.join(9*['.']) # k is gene_id
f.write(s + '\n')
head += s.replace('\t', '_') + '\t'
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