Converting Cufflinks predictions (.GTF) into .BED annotations

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,cdsstart,cdsend,field,nline):
  try:
    estp=estart[0]-1;
    eedp=eend[-1];
    # If no CDS was found, set cdsstart = cdsend = eedp
    if cdsstart==float('-inf'):
      cdsstart=eedp
      cdsend=eedp
    # 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(cdsstart)+'\t'+str(cdsend)+'\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);


cdsstart=cdsstart=float('-inf');
cdsend=cdsend=float('inf');
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' and field[2] != 'CDS':
    #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,cdsstart,cdsend,prevfield,nline);
    cdsstart=float('-inf');
    cdsend=float('inf');  
    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);
  if field[2]=='CDS':
    try:
      cdsst=int(field[3]);
      cdsed=int(field[4]);
    except ValueError:
      print('Error: non-number fields at line '+str(nline),file=sys.stderr);
    if cdsstart==float('-inf') or cdsst < cdsstart:
      cdsstart = cdsst
    if cdsend==float('inf') or cdsed > cdsend:
      cdsend = cdsed
 
# the last record
if len(estart)!=0:
  printbedline(estart,eend,cdsstart,cdsend,field,nline);

Added additional handling for annotating CDS start & end (as thickStart & thickEnd .Bed attributes) based on the format they're given in in the GENCODE .GTF files.