def __main__():
try:
input_seqs_ul = sys.argv[1]
target_seq = sys.argv[2]
output_dir = sys.argv[3]
except:
sys.exit(1)
outfile_name = os.path.basename(input_seqs_ul).split('.')[0] + '_greped.fq'
output_fq = output_dir + '/' + outfile_name
outf = open(output_fq, 'w')
greped_num = 0
for seq_id, seq, qual in MinimalFastqParser(input_seqs_ul, strict=False):
if target_seq in seq:
outf.write('@%s\n%s\n+\n%s\n' % (seq_id, seq, qual))
greped_num += 1
elif reverse_com_seq(target_seq) in seq:
outf.write('@%s\n%s\n+\n%s\n' %
(seq_id + '|reverse', reverse_com_seq(seq), qual))
greped_num += 1
else:
pass
print 'greped_num is %s' % greped_num
outf.close()
def __main__():
try:
input_seqs_ul = sys.argv[1]
mapping_ul = sys.argv[2]
output_dir = sys.argv[3]
except:
usage()
sys.exit(1)
barcodes = get_barcodes(mapping_ul)
output_fq = output_dir + '/greped.fq'
outf = open(output_fq, 'w')
grep_seqs_log = output_dir + '/grep_seqs_num_log.txt'
grep_log = open(grep_seqs_log, 'w')
#initiate an empty dic to record the greped seqs numbers.
grep_seqs_dic = {}
for barcode in barcodes:
grep_seqs_dic[barcode] = 0
#no_matched_seqs = 0
matched_seqs = 0
total_seqs_num = 0
for seq_id, seq, qual in MinimalFastqParser(input_seqs_ul, strict=False):
total_seqs_num = total_seqs_num + 1
for barcode in barcodes:
if seq.startswith(barcode):
outf.write('@%s\n%s\n+\n%s\n' % (seq_id, seq, qual))
grep_seqs_dic[barcode] = grep_seqs_dic[barcode] + 1
matched_seqs = matched_seqs + 1
break
elif seq.endswith(reverse_com_seq(barcode)):
new_seq = reverse_com_seq(seq)
new_qual = reverse_seq(qual)
outf.write('@%s\n%s\n+\n%s\n' %
(seq_id + '|reverse', new_seq, new_qual))
grep_seqs_dic[barcode] = grep_seqs_dic[barcode] + 1
matched_seqs = matched_seqs + 1
break
grep_log.write("There are %s seqs totally!\n" % total_seqs_num)
grep_log.write("Matched seqs: %s !\n" % matched_seqs)
lib_name = os.path.basename(input_seqs_ul).split('.')[0]
for key in grep_seqs_dic:
grep_log.write('%s\t%s\t%s\n' % (key, grep_seqs_dic[key], lib_name))
grep_log.close()
outf.close()
def __main__():
try:
input_seqs_ul = sys.argv[1]
primer_ul = sys.argv[2]
output_dir = sys.argv[3]
except:
usage()
sys.exit(1)
primers = primer_list( primer_ul )
output_fq = output_dir + '/greped.fq'
outf = open( output_fq , 'w')
grep_seqs_log = output_dir + '/grep_seqs_num_log.txt'
grep_log = open( grep_seqs_log, 'w' )
#initiate an empty dic to record the greped seqs numbers.
grep_seqs_dic = {}
for primer in primers:
grep_seqs_dic[ primer[0] ] = 0
#no_matched_seqs = 0
matched_seqs = 0
total_seqs_num = 0
for seq_id, seq, qual in MinimalFastqParser(input_seqs_ul, strict=False):
total_seqs_num = total_seqs_num + 1
for primer in primers:
barcode = primer[1]
if seq.startswith(barcode):
outf.write('>%s\n%s\n' % (primer[0]+'_'+str(matched_seqs)+' '+seq_id, seq))
grep_seqs_dic[ primer[0] ] = grep_seqs_dic[ primer[0] ] + 1
matched_seqs = matched_seqs + 1
break
grep_log.write( "There are %s seqs totally!\n" % total_seqs_num )
grep_log.write( "Matched seqs: %s !\n" % matched_seqs )
grep_log.write( "No matched seqs: %s !\n" % (total_seqs_num-matched_seqs) )
lib_name = os.path.basename(input_seqs_ul).split('.')[0]
for key in grep_seqs_dic:
grep_log.write( '%s\t%s\t%s\n' % (key, grep_seqs_dic[key], lib_name) )
grep_log.close()
outf.close()
def __main__():
try:
input_seqs_ul = sys.argv[1]
except:
sys.exit(1)
infile_name = os.path.basename(input_seqs_ul)
outfile_name = infile_name + '.tmp'
output_fq = os.path.dirname(input_seqs_ul) + '/' + outfile_name
outf = open(output_fq, 'w')
for seq_id, seq, qual in MinimalFastqParser(input_seqs_ul, strict=False):
# @/share/bioCloud/cloud/rawdata/download/PRJDA50447/DRX000300/DRR000534.sra.12 HWI-EAS370_34:2:1:0:82 length=76
seq_id_spot_info = re.split('\s+', seq_id)[1]
if '_1.fastq' in infile_name:
new_seq_id = seq_id_spot_info + '/1'
elif '_2.fastq' in infile_name:
new_seq_id = seq_id_spot_info + '/2'
else:
new_seq_id = seq_id_spot_info
outf.write('@%s\n%s\n+\n%s\n' % (new_seq_id, seq, qual))
outf.close()
os.system('mv %s %s' % (input_seqs_ul, input_seqs_ul + '.bak'))
os.system('mv %s %s' % (output_fq, input_seqs_ul))
def __main__():
try:
input_seqs_ul = sys.argv[1]
primer_ul = sys.argv[2]
output_dir = sys.argv[3]
except:
usage()
sys.exit(1)
primers = primer_list(primer_ul)
output_fq = output_dir + '/greped.fq'
outf = open(output_fq, 'w')
grep_seqs_log = output_dir + '/grep_seqs_num_log.txt'
grep_log = open(grep_seqs_log, 'w')
#initiate an empty dic to record the greped seqs numbers.
grep_seqs_dic = {}
for primer in primers:
grep_seqs_dic[primer[0]] = 0
#no_matched_seqs = 0
matched_seqs = 0
total_seqs_num = 0
#pattern = re.compile( 'ATTAGATACCC[CTG]GGTAGTCC' )#reverse primer is GGACTACCVGGGTATCTAAT containing JianBing bases,rc is ATTAGATACCC[CTG]GGTAGTCC.
rprimer = primers[0][2]
rprimer_len = len(rprimer)
rc_rprimer = change_primer_seqs(rprimer)
pattern = re.compile(rc_rprimer)
for seq_id, seq, qual in MinimalFastqParser(input_seqs_ul, strict=False):
total_seqs_num = total_seqs_num + 1
for primer in primers:
if seq.startswith(primer[1]):
try:
new_seq = pattern.split(seq)[0] #remove reverse primer
outf.write('@%s\n%s\n+\n%s\n' % (seq_id, new_seq, qual))
grep_seqs_dic[primer[0]] = grep_seqs_dic[primer[0]] + 1
matched_seqs = matched_seqs + 1
break
except:
outf.write('@%s\n%s\n+\n%s\n' % (seq_id, seq, qual))
grep_seqs_dic[primer[0]] = grep_seqs_dic[primer[0]] + 1
matched_seqs = matched_seqs + 1
break
elif reverse_com_seq(primer[1]) in seq[-20:]:
fpart_seq = seq[rprimer_len:-20]
rpart_seq = seq[-20:]
new_rpart = rpart_seq[:rpart_seq.
index(reverse_com_seq(primer[1]))]
new_seq = primer[1] + reverse_com_seq(fpart_seq + new_rpart)
#new_qual = qual[ :seq.index( reverse_com_seq(primer[1]) ) + len(primer[1]) ]
new_qual = qual[:len(new_seq)]
outf.write('@%s\n%s\n+\n%s\n' %
(seq_id + '|reverse', new_seq, new_qual))
grep_seqs_dic[primer[0]] = grep_seqs_dic[primer[0]] + 1
matched_seqs = matched_seqs + 1
break
#else:
#no_matched_seqs = no_matched_seqs + 1
#break
grep_log.write("There are %s seqs totally!\n" % total_seqs_num)
grep_log.write("Matched seqs: %s !\n" % matched_seqs)
grep_log.write("No matched seqs: %s !\n" % (total_seqs_num - matched_seqs))
grep_log.write("Reverse primer is: %s !\n" % rprimer)
grep_log.write("RC. reverse primer is: %s !\n" % rc_rprimer)
lib_name = os.path.basename(input_seqs_ul).split('.')[0]
for key in grep_seqs_dic:
grep_log.write('%s\t%s\t%s\n' % (key, grep_seqs_dic[key], lib_name))
grep_log.close()
outf.close()