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m6a_mysql_table_prepare.py
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m6a_mysql_table_prepare.py
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#!/usr/bin/env python
# coding: utf-8
import os
import sys
import glob
import pandas as pd
try:
infile = sys.argv[1]
infile2 = sys.argv[2]
except:
sys.exit('<m6a_table, m6adb e.g Homo_sapiens.GRCh38.95.utr_table.m6a.tmp2, RMVar_Human_basic_info_m6Am.txt>')
outfile = '.'.join(infile.split('.')[:-3]) + '.m6a' #strip('.tmp2') + '.phastConsElements'
def rel_canvas_pos(elem_genomic_start, elem_genomic_end, utr_length):
elem_genomic_start, elem_genomic_end, utr_length = int(elem_genomic_start), int(elem_genomic_end), int(utr_length)
segment = round((1/float(utr_length) * 200),5)
if elem_genomic_start == 1:
#pos_start = round(((int(elem_genomic_start) * 200)/float(utr_length)),5)
pos_start = 1
if elem_genomic_end == utr_length:
pos_end = 200.0
else:
pos_end = round((elem_genomic_end * segment),5)
span = pos_end - pos_start
elif elem_genomic_start == utr_length:
pos_start = 200.0
pos_end = 0.0
span = pos_end
elif elem_genomic_start == elem_genomic_end:
pos_start = round(((int(elem_genomic_start) * 200)/float(utr_length)),5)
pos_end = 0.0
span = pos_end
else:
pos_start = round(((int(elem_genomic_start) * 200)/float(utr_length)),5)
if elem_genomic_end == utr_length:
pos_end = 200 - pos_start
span = pos_end
else:
pos_end = round((elem_genomic_end * segment),5)
span = pos_end - pos_start
#if str(pos_start).startswith('0.'):
# pos_start = pos_start + 1
return (pos_start, span)
def genomic_pos(line):
if line != []:
chrom = line[0]
utr_start = int(line[1])
utr_end = int(line[2])
editing_start = int(line[8])
editing_end = int(line[9])
overlap = int(line[-1])
if overlap == -1:
overlap = 0
strand = line[5]
utr_length = (utr_end - utr_start) + 1
if line[5] == '+':
if utr_start < editing_start and utr_end > editing_end: #phast interna
genomic_editing_start = str((editing_start - utr_start)+1)
genomic_editing_end = str(((editing_start - utr_start)+1) + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start < editing_start and utr_end < editing_end: #phast cavallo 3 primo
genomic_editing_start = str((editing_start - utr_start)+1)
genomic_editing_end = str(((editing_start - utr_start)+1) + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start > editing_start and utr_end > editing_end: #phast cavallo 5 primo
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start > editing_start and utr_end < editing_end: #phast esterna > utr_length
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start == editing_start and utr_end == editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start < editing_start and utr_end == editing_end:
genomic_editing_start = str((editing_start - utr_start)+1)
genomic_editing_end = str(((editing_start - utr_start)+1) + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start > editing_start and utr_end == editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start == editing_start and utr_end > editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start == editing_start and utr_end < editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
else:
if utr_start < editing_start and utr_end > editing_end: #phast interna
genomic_editing_start = str((utr_end - editing_end)+1)
genomic_editing_end = str(((utr_end - editing_end)+1) + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start > editing_start and utr_end > editing_end: #phast cavallo 3 primo
genomic_editing_start = str((utr_end - editing_end)+1)
genomic_editing_end = str(((utr_end - editing_end)+1) + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start < editing_start and utr_end < editing_end: #phast cavallo 5 primo
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start > editing_start and utr_end < editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start == editing_start and utr_end == editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start == editing_start and utr_end < editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start == editing_start and utr_end > editing_end:
genomic_editing_start = str((utr_end - editing_end)+1)
genomic_editing_end = str(((utr_end - editing_end)+1) + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(utr_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start > editing_start and utr_end == editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(utr_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
elif utr_start < editing_start and utr_end == editing_end:
genomic_editing_start = str(1)
genomic_editing_end = str(1 + overlap)
return(genomic_editing_start, genomic_editing_end, chrom, str(editing_start), str(editing_end), strand, rel_canvas_pos(genomic_editing_start, genomic_editing_end, utr_length))
df = pd.read_csv(infile2, sep='\t')
d = {}
for i in range(0, len(df)):
row = df.iloc[i,]
d.setdefault(row.rm_id, [row.modification_sample, row.modification_sample_information, row.pubmed_id, row.confidence_level, row.rbp_id])
dic_line = {} #1 ENSG00000142609 ENST00000642590 - [5_utr] [5_utr_phastcons] [3_utr] [3_utr_phastcons]
with open(infile,'r') as f:
for line in f:
line = line.strip('\n').split('\t')
genomic_editing = genomic_pos(line)
dic_line.setdefault((line[0],line[3], line[4], line[5]), ([], [], [], []))
if line[6] == '5_utr':
dic_line.setdefault((line[0],line[3], line[4], line[5]))[0].append(line + d.get(line[10]))
dic_line.setdefault((line[0],line[3], line[4], line[5]))[1].append(genomic_editing)
else:
dic_line.setdefault((line[0],line[3], line[4], line[5]))[2].append(line + d.get(line[10]))
dic_line.setdefault((line[0],line[3], line[4], line[5]))[3].append(genomic_editing)
with open(outfile, 'w+') as g:
g.write('{}\t{}\t{}\t{}\t{}\n'.format('Chrom','Gene_ID','Transcript_id','Strand','m6a_events'))
for k,v in sorted(dic_line.items(), key= lambda x: int(x[0][0]) if x[0][0].isdigit() else x[0][0]):
g.write('{}\t{}\n'.format('\t'.join(k), v))
#cmd = 'rm -rf {}'
#file_to_remove = glob.glob('*.tmp*')
#print 'Removing temporary files..'
#for elem in file_to_remove:
# os.system(cmd.format(elem))
#print 'DONE!'
#print '----------------------------'
print('Gzipping {}'.format(outfile))
cmd2 = 'gzip {}'.format(outfile)
os.system(cmd2)
print('DONE!')