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fastq_compare.py
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fastq_compare.py
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# changing author of this commit
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__author__= 'Allison MacLeay'
import sys
import os
import os.path
import argparse
import glob
import gzip
def debug_here():
# break at line 13 or 15
return
def header_row():
hr = ['ID','key', 'data']
return '\t'.join(hr)
def get_files(dir,name):
flist=[]
fpath=os.path.join(dir,name)
fpath=glob.glob(fpath)
for file in fpath:
flist.append(file)
for f in next(os.walk(dir))[1]:
folder=os.path.join(dir,f)
fpath=os.path.join(folder,name)
fpath=glob.glob(fpath)
for file in fpath:
flist.append(file)
return flist
def get_fid(fname):
return '1'
fid=''
id=['','']
for p in fname.split('_'):
if p[0]=='A':
id[0]=p
elif p[0]=='P':
id[1]=p
fid='_'.join(id)
return fid
def get_key(h):
info=h.split(':')
return info[5]+'_'+info[6]
def row_to_string(fid,key,data):
row='\t'.join([fid,key])
row=row+'\t'+ str(data)
return row
def totals_to_string(totals):
txt=''
for k in totals.keys():
txt=txt+str(k) + '\t' + str(totals[k]) + '\t'
return txt
def get_stats(d,flist):
ct_same=0
ct_diff=0
ct_miss_left=0
ct_miss_right=0
if 'count_files' not in d.keys():
d['count_files']=0
if 'totals' not in d.keys():
d['totals']={}
if 'pass' not in d.keys():
d['pass']=0
else:
ct_miss_right=d['totals'][d['pass']]
d['pass']=d['pass']+1
d['totals'][d['pass']]=0
if 'fq' not in d.keys():
d['fq']={}
for file in flist:
fh=''
fid=get_fid(file.split('/')[-1])
if fid not in d['fq'].keys():
d['fq'][fid]={}
d['fq'][fid]['fname'+str(d['pass'])]=file
d['count_files']=d['count_files']+1
if file.split('.')[-1]=='gz':
fh=gzip.open(file,'rb')
else:
fh=open(file,'r')
t=0
ct_line=0
entry=[]
for line in fh:
entry.append(line)
t+=1
if t==4:
# parse data
k=get_key(entry[0])
d['totals'][d['pass']]=d['totals'][d['pass']]+1
if (d['totals'][d['pass']] % 10000 ==0):
print str(d['totals'][d['pass']]) +' reads in pass '+str(d['pass'])
if d['pass']==2:
debug_here()
if d['pass']>1:
if k in d['fq'][fid].keys():
ct_miss_right-=1
# diff
cmp_res='same'
diff=[]
cmp=d['fq'][fid][k]['data']
lcmp=len(cmp)
if (lcmp +1) > len(entry):
print "ERROR: length of comparison array longer than entry array"
print str(entry)
else:
for l in range(len(cmp)):
if cmp[l] != entry[l+1]:
cmp_res='diff'
diff.append(str(cmp[l]) + '<>' + str(entry[l+1]))
d['fq'][fid][k]['diff']=cmp_res
d['fq'][fid][k]['diffa']=diff
del d['fq'][fid][k]['data']
if cmp_res=='diff':
ct_diff+=1
if ct_diff % 100 == 0:
print str(ct_diff) + ' found '
print diff
else:
ct_miss_left+=1
# add
d['fq'][fid][k]={}
d['fq'][fid][k]['data']=entry[1:]
d['fq'][fid][k]['diff']='missing on left'
d['fq'][fid][k]['right']=ct_line
else:
# add
d['fq'][fid][k]={}
d['fq'][fid][k]['data']=entry[1:]
d['fq'][fid][k]['diff']='missing on right'
d['fq'][fid][k]['left']=ct_line
t=0
entry=[]
d['totals']['miss_l']=ct_miss_left
d['totals']['miss_r']=ct_miss_right
#return d
return
def write_stats(d,out,quiet):
if out != 'stdout':
sys.stdout=open(out,'w')
file=['f1','f2']
print header_row()
for fid in d['fq'].keys():
if type(d['fq'][fid]) is not dict:
continue #break
for kval in d['fq'][fid].keys():
if type(d['fq'][fid][kval]) is not dict:
continue
if 'diff' in d['fq'][fid][kval].keys():
if d['fq'][fid][kval]['diff'] != 'same':
if quiet & (d['fq'][fid][kval]['diff'].find('miss') > -1):
pass
# don't print
else:
#print diff_row_to_string(fid,kval,d['bc'][fid][kval])
print row_to_string(fid,kval,d['fq'][fid][kval])
print totals_to_string(d['totals'])
sys.stdout.close()
return
#-----------------------------------------
# MAIN
#-----------------------------------------
if __name__ == '__main__':
parser=argparse.ArgumentParser(description="Compare unordered fastq files")
parser.add_argument('--dir1', required=True, help='First directory containing fusion caller output. Could be substituted for a filename.')
parser.add_argument('--dir2', required=True, help='Second directory containing fusion caller output. Could be substituted for a filename.')
parser.add_argument('--out', default="stdout", help='name of output.')
parser.add_argument('--miss_off', action='store_true', help='skip missing file output.')
args=parser.parse_args()
stats={}
stats['f1']={}
stats['f2']={}
stats['f1']['filename']=args.dir1
stats['f2']['filename']=args.dir2
if (os.path.isdir(args.dir1)) and (os.path.isdir(args.dir2)):
files1=get_files(args.dir1,'*.fastq.gz')
files2=get_files(args.dir2,'*.fastq.gz')
elif (os.path.isfile(args.dir1)) and (os.path.isfile(args.dir1)):
files1=[args.dir1]
files2=[args.dir2]
else:
exit("Error with dir1 or dir2. Both must be valid files or both must be directories")
get_stats(stats,files1)
get_stats(stats,files2)
write_stats(stats,args.out,args.miss_off)