def cutadapt(fq):
readDict = {}
for fqreads in fq:
if int(cu_ver) >= 3:
info = ModificationInfo(None)
info.matches = []
else:
matches = []
if qiagenumi:
currentSeq = fqreads.sequence
umi_seq = ""
for modifier in ingredients:
if int(cu_ver) >= 3:
fqreads = modifier(fqreads, info)
else:
fqreads = modifier(fqreads, matches)
try:
umi_seq = currentSeq.split(str(fqreads.sequence))[1]
umi_cut = umi.split(",")
max_ad = len(qiaAdapter) + int(umi_cut[1])
umi_seq = umi_seq[:max_ad][-int(umi_cut[1]):]
except ValueError:
umi_seq = ""
final_seq = fqreads.sequence + umi_seq
if int(len(final_seq)) >= int(min_len):
if str(final_seq) in readDict:
readDict[str(final_seq)] += 1
else:
readDict[str(final_seq)] = 1
else:
for modifier in ingredients:
if int(cu_ver) >= 3:
fqreads = modifier(fqreads, info)
else:
fqreads = modifier(fqreads, matches)
if int(len(fqreads.sequence)) >= int(min_len):
if str(fqreads.sequence) in readDict:
readDict[str(fqreads.sequence)] += 1
else:
readDict[str(fqreads.sequence)] = 1
trimmed_pairs = list(readDict.items())
return trimmed_pairs
def cutadapt(fq):
#ourDir_n = str("miRge3_temp")
#tempDir = Path.cwd()/ourDir_n
#Path(tempDir).mkdir(exist_ok=True, parents=True)
#tempFile = Path(tempDir)/"input_EC.fastq"
in_fqfile = open("input.fq", "a+")
in_fqfileCor = open("correct_read.fastq", "a+")
id_read = open("id_read.txt", "a+")
id_read_qc = open("ID_read_quality_cor.txt", "a+")
id_read_qcin = open("ID_read_quality_input.txt", "a+")
readDict = {}
for fqreads in fq:
if int(cu_ver) >= 3:
info = ModificationInfo(None)
info.matches = []
else:
matches = []
if qiagenumi:
currentSeq = fqreads.sequence
umi_seq = ""
for modifier in ingredients:
if int(cu_ver) >= 3:
fqreads = modifier(fqreads, info)
else:
fqreads = modifier(fqreads, matches)
try:
umi_seq = currentSeq.split(str(fqreads.sequence))[1]
umi_cut = umi.split(",")
max_ad = len(qiaAdapter) + int(umi_cut[1])
umi_seq = umi_seq[:max_ad][-int(umi_cut[1]):]
except ValueError:
umi_seq = ""
final_seq = fqreads.sequence + umi_seq
if int(len(final_seq)) >= int(min_len):
if str(final_seq) in readDict:
readDict[str(final_seq)] += 1
else:
readDict[str(final_seq)] = 1
else:
for modifier in ingredients:
if int(cu_ver) >= 3:
fqreads = modifier(fqreads, info)
else:
fqreads = modifier(fqreads, matches)
if int(len(fqreads.sequence)) >= int(min_len):
in_fqfile.write("@" + str((fqreads.name).split(" ")[0]) +
"\n" + str(fqreads.sequence) + "\n" +
str("+") + "\n" + str((fqreads.qualities)) +
"\n")
in_fqfileCor.write("@" + str((fqreads.name).split(" ")[0]) +
"\n" + str(fqreads.sequence) + "\n" +
str("+") + "\n" + str((fqreads.qualities)) +
"\n")
id_read.write("@" + str((fqreads.name).split(" ")[0]) + " " +
str(fqreads.sequence) + " " +
str((fqreads.qualities)) + "\n")
id_read_qc.write("@" + str((fqreads.name).split(" ")[0]) +
" " + str(fqreads.sequence) + " " +
str((fqreads.qualities)) + "\n")
id_read_qcin.write("@" + str((fqreads.name).split(" ")[0]) +
" " + str(fqreads.sequence) + " " +
str((fqreads.qualities)) + "\n")
if str(fqreads.sequence) in readDict:
readDict[str(fqreads.sequence)] += 1
#<Sequence(name='SRR772403.13 SN603_WA038_2_1102_1455.00_139.00_0 length=50', sequence='TACCCTGTAGAAACGAATTTGT', qualities='@@@DDDDDFFFF<+AFFGFEIF')>
#<Sequence(name='SRR772403.133926 SN603_WA038_2_1205_884.60_9723.70_0 length=50', sequence='TGAGATGAAGCACTGTAGCT', qualities='CCCFFFFFHHHHHJJIIJJJ')>
else:
readDict[str(fqreads.sequence)] = 1
trimmed_pairs = list(readDict.items())
return trimmed_pairs