davidliwei/gtf2bed.py

## gtf2bed.py
#!/usr/bin/env python3
'''
gtf2bed.py converts GTF file to BED file.
Usage: gtf2bed.py {OPTIONS} [.GTF file]

History
    Nov.5th 2012:
        1. Allow conversion from general GTF files (instead of only Cufflinks supports).
        2. If multiple identical transcript_id exist, transcript_id will be appended a string like "_DUP#" to separate.
'''

import sys;
import re;

if len(sys.argv)<2:
  print('This script converts .GTF into .BED annotations.\n');
  print('Usage: gtf2bed {OPTIONS} [.GTF file]\n');
  print('Options:');
  print('-c color\tSpecify the color of the track. This is a RGB value represented as "r,g,b". Default 255,0,0 (red)');
  print('\nNote:');
  print('1\tOnly "exon" and "transcript" are recognized in the feature field (3rd field).');
  print('2\tIn the attribute list of .GTF file, the script tries to find "gene_id", "transcript_id" and "FPKM" attribute, and convert them as name and score field in .BED file.');
  print('Author: Wei Li (li.david.wei AT gmail.com)');
  sys.exit();

color='255,0,0'


for i in range(len(sys.argv)):
  if sys.argv[i]=='-c':
    color=sys.argv[i+1];


allids={};

def printbedline(estart,eend,field,nline):
  try:
    estp=estart[0]-1;
    eedp=eend[-1];
    # use regular expression to get transcript_id, gene_id and expression level
    geneid=re.findall(r'gene_id \"([\w\.]+)\"',field[8])
    transid=re.findall(r'transcript_id \"([\w\.]+)\"',field[8])
    fpkmval=re.findall(r'FPKM \"([\d\.]+)\"',field[8])
    if len(geneid)==0:
      print('Warning: no gene_id field ',file=sys.stderr);
    else:
      geneid=geneid[0];
    if len(transid)==0:
      print('Warning: no transcript_id field',file=sys.stderr);
      transid='Trans_'+str(nline);
    else:
      transid=transid[0];
    if transid in allids.keys():
      transid2=transid+'_DUP'+str(allids[transid]);
      allids[transid]=allids[transid]+1;
      transid=transid2;
    else:
      allids[transid]=1;
    if len(fpkmval)==0:
      #print('Warning: no FPKM field',file=sys.stderr);
      fpkmval='100';
    else:
      fpkmval=fpkmval[0];
    fpkmint=round(float(fpkmval));
    print(field[0]+'\t'+str(estp)+'\t'+str(eedp)+'\t'+transid+'\t'+str(fpkmint)+'\t'+field[6]+'\t'+str(estp)+'\t'+str(eedp)+'\t'+color+'\t'+str(len(estart))+'\t',end='');
    seglen=[eend[i]-estart[i]+1 for i in range(len(estart))];
    segstart=[estart[i]-estart[0] for i in range(len(estart))];
    strl=str(seglen[0]);
    for i in range(1,len(seglen)):
      strl+=','+str(seglen[i]);
    strs=str(segstart[0]);
    for i in range(1,len(segstart)):
      strs+=','+str(segstart[i]);
    print(strl+'\t'+strs);
  except ValueError:
    print('Error: non-number fields at line '+str(nline),file=sys.stderr);


estart=[];
eend=[];
# read lines one to one
nline=0;
prevfield=[];
prevtransid='';
for lines in open(sys.argv[-1]):
  field=lines.strip().split('\t');
  nline=nline+1;
  if len(field)<9:
    print('Error: the GTF should has at least 9 fields at line '+str(nline),file=sys.stderr);
    continue;
  if field[1]!='Cufflinks':
    pass;
    #print('Warning: the second field is expected to be \'Cufflinks\' at line '+str(nline),file=sys.stderr);
  if field[2]!='exon' and field[2] !='transcript':
    #print('Error: the third filed is expected to be \'exon\' or \'transcript\' at line '+str(nline),file=sys.stderr);
    continue;
  transid=re.findall(r'transcript_id \"([\w\.]+)\"',field[8]);
  if len(transid)>0:
    transid=transid[0];
  else:
    transid='';
  if field[2]=='transcript' or (prevtransid != '' and transid!='' and transid != prevtransid):
    #print('prev:'+prevtransid+', current:'+transid);
    # A new transcript record, write
    if len(estart)!=0:
      printbedline(estart,eend,prevfield,nline);
    estart=[];
    eend=[];
  prevfield=field;
  prevtransid=transid;
  if field[2]=='exon':
    try:
      est=int(field[3]);
      eed=int(field[4]);
      estart+=[est];
      eend+=[eed];
    except ValueError:
      print('Error: non-number fields at line '+str(nline),file=sys.stderr);
# the last record
if len(estart)!=0:
  printbedline(estart,eend,field,nline);
	#!/usr/bin/env python3
	'''
	gtf2bed.py converts GTF file to BED file.
	Usage: gtf2bed.py {OPTIONS} [.GTF file]

	History
	Nov.5th 2012:
	1. Allow conversion from general GTF files (instead of only Cufflinks supports).
	2. If multiple identical transcript_id exist, transcript_id will be appended a string like "_DUP#" to separate.
	'''

	import sys;
	import re;

	if len(sys.argv)<2:
	print('This script converts .GTF into .BED annotations.\n');
	print('Usage: gtf2bed {OPTIONS} [.GTF file]\n');
	print('Options:');
	print('-c color\tSpecify the color of the track. This is a RGB value represented as "r,g,b". Default 255,0,0 (red)');
	print('\nNote:');
	print('1\tOnly "exon" and "transcript" are recognized in the feature field (3rd field).');
	print('2\tIn the attribute list of .GTF file, the script tries to find "gene_id", "transcript_id" and "FPKM" attribute, and convert them as name and score field in .BED file.');
	print('Author: Wei Li (li.david.wei AT gmail.com)');
	sys.exit();

	color='255,0,0'


	for i in range(len(sys.argv)):
	if sys.argv[i]=='-c':
	color=sys.argv[i+1];


	allids={};

	def printbedline(estart,eend,field,nline):
	try:
	estp=estart[0]-1;
	eedp=eend[-1];
	# use regular expression to get transcript_id, gene_id and expression level
	geneid=re.findall(r'gene_id \"([\w\.]+)\"',field[8])
	transid=re.findall(r'transcript_id \"([\w\.]+)\"',field[8])
	fpkmval=re.findall(r'FPKM \"([\d\.]+)\"',field[8])
	if len(geneid)==0:
	print('Warning: no gene_id field ',file=sys.stderr);
	else:
	geneid=geneid[0];
	if len(transid)==0:
	print('Warning: no transcript_id field',file=sys.stderr);
	transid='Trans_'+str(nline);
	else:
	transid=transid[0];
	if transid in allids.keys():
	transid2=transid+'_DUP'+str(allids[transid]);
	allids[transid]=allids[transid]+1;
	transid=transid2;
	else:
	allids[transid]=1;
	if len(fpkmval)==0:
	#print('Warning: no FPKM field',file=sys.stderr);
	fpkmval='100';
	else:
	fpkmval=fpkmval[0];
	fpkmint=round(float(fpkmval));
	print(field[0]+'\t'+str(estp)+'\t'+str(eedp)+'\t'+transid+'\t'+str(fpkmint)+'\t'+field[6]+'\t'+str(estp)+'\t'+str(eedp)+'\t'+color+'\t'+str(len(estart))+'\t',end='');
	seglen=[eend[i]-estart[i]+1 for i in range(len(estart))];
	segstart=[estart[i]-estart[0] for i in range(len(estart))];
	strl=str(seglen[0]);
	for i in range(1,len(seglen)):
	strl+=','+str(seglen[i]);
	strs=str(segstart[0]);
	for i in range(1,len(segstart)):
	strs+=','+str(segstart[i]);
	print(strl+'\t'+strs);
	except ValueError:
	print('Error: non-number fields at line '+str(nline),file=sys.stderr);






	estart=[];
	eend=[];
	# read lines one to one
	nline=0;
	prevfield=[];
	prevtransid='';
	for lines in open(sys.argv[-1]):
	field=lines.strip().split('\t');
	nline=nline+1;
	if len(field)<9:
	print('Error: the GTF should has at least 9 fields at line '+str(nline),file=sys.stderr);
	continue;
	if field[1]!='Cufflinks':
	pass;
	#print('Warning: the second field is expected to be \'Cufflinks\' at line '+str(nline),file=sys.stderr);
	if field[2]!='exon' and field[2] !='transcript':
	#print('Error: the third filed is expected to be \'exon\' or \'transcript\' at line '+str(nline),file=sys.stderr);
	continue;
	transid=re.findall(r'transcript_id \"([\w\.]+)\"',field[8]);
	if len(transid)>0:
	transid=transid[0];
	else:
	transid='';
	if field[2]=='transcript' or (prevtransid != '' and transid!='' and transid != prevtransid):
	#print('prev:'+prevtransid+', current:'+transid);
	# A new transcript record, write
	if len(estart)!=0:
	printbedline(estart,eend,prevfield,nline);
	estart=[];
	eend=[];
	prevfield=field;
	prevtransid=transid;
	if field[2]=='exon':
	try:
	est=int(field[3]);
	eed=int(field[4]);
	estart+=[est];
	eend+=[eed];
	except ValueError:
	print('Error: non-number fields at line '+str(nline),file=sys.stderr);
	# the last record
	if len(estart)!=0:
	printbedline(estart,eend,field,nline);