def mainfunc(data, name, numrows):
'''
This function searches for primer and anchor in reads and pulls out STRseq between them.
@param data: The tibble/data frame.
@param name: The output file name.
@param numrows: Number of rows of the input data to be used to generate random UMIs
@return: Writes a output file with STRseq and other metadata.
'''
mypydata = data.set_index('ID').T.to_dict('list')
UmiSTRLociList = []
counter_P_A = 0
counter_P = 0
umilistIdx = 0
umilist = umidict(numrows)
for mydatakey, mydataitems in mypydata.items():
ID = mydatakey
ReadCount = mydataitems[0]
readR1 = mydataitems[1]
for key, items in dict_primer.items():
Pos = key
anchor = items[4]
anchorIndex = strfuzzy.fuzzyFind(readR1, anchor, fuzz=1)
primer = items[3]
if readR1.startswith(primer, 0, len(primer)):
counter_P += 1
if ((readR1.startswith(primer, 0, len(primer))) and (anchorIndex >= 0)):
Loci = items[0]
STRseq = readR1[len(primer):anchorIndex]
counter_P_A += 1
umi = umilist[umilistIdx]
umilistIdx +=1
#print("umilist index: %s" % umilistIdx)
#UMI = ''.join(random.choice('AGTC') for _ in range(12))
UmiSTRLociList.append((Loci, STRseq, umi, primer, anchor, ReadCount))
#print(len(umilist))
UmiSTRLociCount = collections.defaultdict(int)
for k in UmiSTRLociList:
UmiSTRLociCount[k] += 1
outfilename = name + "_noN.tsv"
with open(outfilename, 'w') as fh:
fh.writelines("Number of Primer match = %d, Number of Primer and Anchor = %d\n" % (counter_P, counter_P_A))
fh.writelines('{}\t{}\n'.format('\t'.join(k),v) for k,v in UmiSTRLociCount.items() )
else:
pass
dict_primer_empty[keyPos] = [
val1Locus, val2Chr, val3Strand, val4Primer, val5Anchor
]
#sprint (testcount)
return dict_primer_empty
dict_primer = {}
file_primer = "PrimedAnchors.txt"
dict_for_primer(file_primer, dict_primer)
#print(dict_primer)
s = "CCCACACGGCCTGGCAACTTATATGTATTTTTGTATTTCATGTGTACATTCGTATCTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATTCCCCACAGTGAAAATAATCTACAGGATAGGTAAATAAATTAAGGCATATTCACGCAATGGGATACGATACAGTGATGAAAATGAACTAATTATAGCTACGTGAAACTATACTCATGAACACAATTTTGTAAAAGAAACAGGACTCCAATTTTCGCTCTTCC"
for items in dict_primer.items():
#print(items[1][3])
#myregex = re.escape(items[1][3]) + (r".*") + re.escape(items[1][4])
anchor = items[1][4]
anchorIndex = strfuzzy.fuzzyFind(s, anchor, fuzz=1)
primer = items[1][3]
if (s.startswith(primer, 0, len(primer)) and (anchorIndex >= 0)):
#print(re.match(r'%s(.*)%s' % (primer, anchor), s).group(1))
print(s[len(primer):anchorIndex])
#m = re.match(r'%s.*' % items[1][3], s)
#print(r'%s(.*)
else:
print('no match')
dict_fastq_R1 = dict_for_fastq(file_fastq_R1)
dict_fastq_R2 = dict_for_fastq(file_fastq_R2)
UmiSTRLociList = []
counterCS_P_A = 0
counterCS_P = 0
counterCS = 0
counter_noCS_match = 0
for key in set(dict_fastq_R1) & set(dict_fastq_R2):
readR1 = dict_fastq_R1[key]
readR2 = dict_fastq_R2[key]
if re.match(r'(.{12})(ATTGGAGTCCT)', readR2) is not None:
counterCS += 1
for items in dict_primer.items():
# do fuzzy matching of anchor
anchor = items[1][4]
anchorIndex = strfuzzy.fuzzyFind(readR1, anchor, fuzz=1)
primer = items[1][3]
if readR1.startswith(primer, 0, len(primer)):
counterCS_P += 1
if ((readR1.startswith(primer, 0, len(primer))) \
and (anchorIndex >= 0)):
Loci = items[1][0]
STRseq = readR1[len(primer):anchorIndex]
searchCS = re.match(r'(.{12})(ATTGGAGTCCT)', readR2)
UMI = searchCS.group(1)
counterCS_P_A += 1
print (counterCS_P_A)
UmiSTRLociList.append((Loci, STRseq, UMI, primer, anchor))
else:
counter_noCS_match += 1
s = "CAAAAGCCTATTTAGTCAGGGTTTTCCAAGAGATAGACCAATTAGATAGATAGATAGATAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAAGATAGATATGAGTAGGGATTTATGAGAGGAATTGGCTCACATGATGATGGAGGCTGAGAATTCTAGGACTCCAATACCTTTTAGC" s_1 = "GAAAAGCCTATTTAGTCAGGGTTTTCCAAGAGATAGACCAATTAGATAGATAGATAGATAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAAGATAGATATGAGTAGGGATTTATGAGAGGAATTGGCTCACATGATGATGGAGGCTGAGAATTCTAGGACTCCAATACCTTTTAGC" s_2 = "GGAAAGCCTATTTAGTCAGGGTTTTCCAAGAGATAGACCAATTAGATAGATAGATAGATAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAAGATAGATATGAGTAGGGATTTATGAGAGGAATTGGCTCACATGATGATGGAGGCTGAGAATTCTAGGACTCCAATACCTTTTAGC" primer = "CAAAAGCCTATTTAGTCAGGGTTTTCCAAGAGATAG" anchor = "TTGGCTCACAT" import strfuzzy primer_fuzz_tup = strfuzzy.fuzzyFind(s, primer, fuzz=2, end=len(primer)) print(primer_fuzz_tup[0], primer_fuzz_tup[1], primer_fuzz_tup[2])