This python module generates, checks, and corrects quaternary Hamming barcodes. The theory for generating quaternary (DNA) Hamming barcodes comes from the publication Bystrykh, L. V. (2012). Generalized DNA Barcode Design Based on Hamming Codes. PLoS ONE. Currently, the hamstring module only works with Hamming7,4 encoding, but may be generalized to other sizes of data and parity bits.
Generate Hamming DNA barcodes
generateBarcodes.py [-h] out
arguments:
out output barcode file name
-h, --help show this help message and exit
-p PARITY, --parity PARITY
length of the parity bit e.g. 4 for Hamming8,4.
default=3
example output:
index base4 nucleotide gc
0 0000000 AAAAAAA 0.0
1 3303001 TTATAAC 0.14
2 2202002 GGAGAAG 0.57
3 1101003 CCACAAT 0.43
4 0303010 ATATACA 0.14
Checksum a list of Hamming DNA barcodes
checkBarcodes.py [-h] list
arguments:
list list of barcodes to check, one per line
-h, --help show this help message and exit
-p PARITY, --parity PARITY
length of the parity bit e.g. 4 for Hamming8,4.
default=3
example output:
in fixed checksum
CATAACT CAAAACT A > T at pos 3
AGAGAGA AGAGAGA ok
TCACAGC TCACAGC ok
GAACAGG GAAAAGG A > C at pos 4
CTATAGT CTATAGT ok
TTTAAAN NNNNNNN bad
NNNNNNN NNNNNNN bad
Tag fastq reads with a barcode (for generating a simulated dataset)
tagReads.py [-h] -e nb fastq out
arguments:
nb number of barcodes to generate
fastq fastq file to process
out name for new fastq file
-e, --erate error rate for single barcode base errors. default=0.05
-p PARITY, --parity PARITY
length of the parity bit e.g. 4 for Hamming8,4.
default=3
-h, --help show this help message and exit
example input:
@HWI-EAS179_0001:5:1:7:119#0/1
CAGGGCGCGAATGNTTTGAGAGGGANATTGGAAANNNNNGATAGANNGGNCTATNNTGNNNNNNNNNNNNNNNNNN
+
HIHHHGHHHFDHH#EHHH?HHHDH>#DGGG@7@?##########################################
example output:
@HWI-EAS179_0001:5:1:7:119#0/1
CCATGGCCAGGGCGCGAATGNTTTGAGAGGGANATTGGAAANNNNNGATAGANNGGNCTATNNTGNNNNNNNNNNNNNNNNNN
+
HHHHHHHHIHHHGHHHFDHH#EHHH?HHHDH>#DGGG@7@?##########################################
Check and fix barcodes in fastq file
fixFastq.py [-h] [-s] list fastq out
arguments:
list list of barcodes used in experiment, one per line
fastq fastq file to process
out name for new fastq file
-s, --strict change all barcodes not in list to 'N'
-h, --help show this help message and exit
example input:
@HWI-EAS179_0001:5:1:7:119#0/1
GCATGGCCAGGGCGCGAATGNTTTGAGAGGGANATTGGAAANNNNNGATAGANNGGNCTATNNTGNNNNNNNNNNNNNNNNNN
+
HHHHHHHHIHHHGHHHFDHH#EHHH?HHHDH>#DGGG@7@?##########################################
example output:
@HWI-EAS179_0001:5:1:7:119#0/1
CCATGGCCAGGGCGCGAATGNTTTGAGAGGGANATTGGAAANNNNNGATAGANNGGNCTATNNTGNNNNNNNNNNNNNNNNNN
+
HHHHHHHHIHHHGHHHFDHH#EHHH?HHHDH>#DGGG@7@?##########################################
- Python 2.7 or Python 3.2+
The core hamstring module has no external module dependencies and should run under any OS.
base4Encode(n,d) is used to convert decimal notation n to quaternary notation with d leading digits. example:
hamstring.base4Encode(22, 4)
[0, 1, 1, 2]
generateHamming(data,parity) is used to generate DNA quaternary Hamming codes from list of quaternary digits data with parity number of parity bits.
example:
>>> generateHamming([0,1,1,2], 3)
Barcode(base4='1100112', nucleotide='CCAACCG', gc=0.71)
>>> generateHamming([0,1,1,2], 4)
Barcode(base4='11001122', nucleotide='CCAACCGG', gc=0.75)decodeHamming(barcode,parity) is used to decode barcode nucleotide Hamming string with parity number of parity bits, and perform error correction if needed.
example:
>>> decodeHamming('CCAACCG', 3)
CheckedBarcode(nucleotide='CCAACCG', chksum='ok')
>>> decodeHamming('CCAACCGG', 4)
CheckedBarcode(nucleotide='CCAACCGG', chksum='ok')
>>> decodeHamming('CCATCCG', 3)
CheckedBarcode(nucleotide='CCAACCG', chksum='A > T at pos 4')
>>> decodeHamming('CCATCCGG', 4)
CheckedBarcode(nucleotide='CCAACCGG', chksum='A > T at pos 4')
>>> decodeHamming('TCATCCGG', 4)
CheckedBarcode(nucleotide='NNNNNNNN', chksum='bad')Matt Shirley - mdshw5'at'gmail'.'com - http://mattshirley.com