def process_fasta_length(fasta_file, folder, debug):
len_Dataframe = pd.DataFrame(columns=('len', 'ID', 'seq'))
## read file
with open(fasta_file, 'r') as fh:
lines = []
for line in fh:
lines.append(line.rstrip())
if len(lines) == 2:
record = fasta_functions.process_fasta(lines)
# re-init
lines = []
len_Seq = len(record['sequence'])
len_Dataframe.loc[len(len_Dataframe)] = (len_Seq,
record['name'],
record['sequence'])
##
grouped_df = len_Dataframe.groupby(['len'])
len_dict = {}
for len_int, cluster in grouped_df:
## write file
file_name = os.path.join(folder, 'seqs_len' + str(len_int) + '.fa')
## debugging messages
if debug:
print("** Printing reads of length (%s) in file %s" %
(len_int, file_name))
with open(file_name, 'w') as outfh:
for index, row in cluster.iterrows():
outfh.write(row['ID'] + '\n' + row['seq'] + '\n')
outfh.close()
len_dict[len_int] = file_name
return (len_dict)
col_list = list(frequencies_miRNA) ## get columns
print("# Selecting variants from file:" + args.fasta)
print("# Printing isomiRs sequences in fasta: " + args.out + '.fasta')
## new df
isomiRs_seqs = pd.DataFrame(0, index=frequencies_miRNA.index, columns=col_list)
## read file
with open(args.out + '.fasta', 'w') as outfh:
with open(args.fasta, 'r') as fh:
lines = []
for line in fh:
lines.append(line.rstrip())
if len(lines) == 2:
record = fasta_functions.process_fasta(lines)
# re-init
lines = []
## discard:
# e.g. >hsa-mir-518f-5p::>hsa-mir-520c-5p|>hsa-mir-526a-5p|>hsa-mir-518d-5p|TS-7511
# e.g. >hsa-mir-548h-3p::>hsa-mir-548z|TS-5966
if (re.search('.*::>.*', record['name'])):
continue
## parse the others
list_split = record['name'].split('::')
#print (list_split)
miRNA = list_split[0].replace('>', '')
variant_list = list_split[1].split('-')
def discard_revcomp(outfile_path, reads):
##### Remove non 5'-3' simulated reads
## use art illumina aln file generated for R1
if (reads == 'PE'):
aln_file_R1 = outfile_path + '1.aln'
else:
aln_file_R1 = outfile_path + '.aln'
## read aln file
freq_fasta = defaultdict(int)
fastq_dict = defaultdict(int)
with open(aln_file_R1, 'r') as fh:
lines = []
for line in fh:
if line.startswith('#'):
continue
if line.startswith('@'):
continue
if line.startswith('>'):
line_list = line.rstrip().split('\t')
if line_list[3] == '+':
ID = line_list[1]
lines.append(ID[:-2])
continue
else:
if len(lines) == 1:
lines.append(line.rstrip())
if len(lines) == 2:
record = fasta_functions.process_fasta(lines)
##sys.stderr.write("Record: %s\n" % (str(record)))
lines = []
## add sequences & count
freq_fasta[record['sequence']] += 1
if (reads == 'PE'):
## read R1 fastq file
fastq_file = outfile_path + '1.fq'
out_file = outfile_path + '_filter_R1.fq'
else:
fastq_file = outfile_path + '.fq'
out_file = outfile_path + '_filter.fq'
## print in file
with open(out_file, 'w') as file:
with open(fastq_file, 'r') as fh:
lines = []
for line in fh:
lines.append(line.rstrip())
if len(lines) == 4:
record = fasta_functions.process_fastq(lines)
#sys.stderr.write("Record: %s\n" % (str(record)))
lines = []
fastq_ID = record['name'].replace('/1', '/2')
if record['sequence'] in freq_fasta.keys():
file.write("%s\n%s\n%s\n%s\n" %
(record['name'], record['sequence'],
record['optional'], record['quality']))
fastq_dict[fastq_ID] += 1
file.close()
return (fastq_dict)