assignment2

Assignment 2: Modifying headers of an interleaved paired-read FASTQ file using python

1. Use any GZIPPED interleaved FASTQ file in standard fastq format. I (Nikki) can provide a FASTQ file if necessary.

Your file must start out in .fastq.gz format

2. Make a python-based script to do the following:
	Modify the the headers of each pair from standard:
	
		@D00602:32:H3LN7BCXX:1:1101:1205:2112 1:N:0:1
		AAATATATATTATTCAATCACTTTGGATGAATCACCTGCTACTACTGACGGCACAAGTTTTATACTTCATTAAGGTCATAACAGAAGATTTTC
		+
		@@@FFFFDHDHFFIIIGGIJJJJJJJIEIJHIIIJJJJIHHIJIJJJIHIFHGIGIHFGHIEHGHJBHDHIJJHHEEEHFFFED@@CCEECDD
		@D00602:32:H3LN7BCXX:1:1101:1182:2112 1:N:0:1
		TTGCTGATGCAAGATACAATGAAAAGAAACAAGTGCATATG
		+
		-;CGGF:CHHD>BED?CCCCCCCACCB==CCAC>CCCD>C>
		@D00602:32:H3LN7BCXX:1:1101:1231:2198 1:N:0:1
		CTTCCAAATTAGGGCAGAGACCCAGAGATGATA
		+
		-.=?????????@@@??????=???<??>>???
		@D00602:32:H3LN7BCXX:1:1101:1401:2198 1:N:0:1
		CAGGCTGGTCTCCAACTCCTGGGCTCAAGCAGTCCTCCTGCCTCAGCCTTCCGAGTAGCTGAAACTGCAGGCATG
		+
		CC@FFFFFFHHHHGIJJJJIJJJGIJIJIIJIGIJJJJJJIJIJHIIIHIJJJBHCAHFHEGGHCHHFHFFFF?;

	to custom headers, with:
	a. A read ID that is always a set number of digits (example is 12 digits), 
	b."OP:i:x", where x indicates if it is the forward or reverse read of a pair (forward = 1, reverse = 2)
	
		@000000000001	OP:i:1
		AAATATATATTATTCAATCACTTTGGATGAATCACCTGCTACTACTGACGGCACAAGTTTTATACTTCATTAAGGTCATAACAGAAGATTTTC
		+
		@@@FFFFDHDHFFIIIGGIJJJJJJJIEIJHIIIJJJJIHHIJIJJJIHIFHGIGIHFGHIEHGHJBHDHIJJHHEEEHFFFED@@CCEECDD
		@000000000001	OP:i:2
		TTGCTGATGCAAGATACAATGAAAAGAAACAAGTGCATATG
		+
		-;CGGF:CHHD>BED?CCCCCCCACCB==CCAC>CCCD>C>
		@000000000002	OP:i:1
		CTTCCAAATTAGGGCAGAGACCCAGAGATGATA
		+
		-.=?????????@@@??????=???<??>>???
		@000000000002	OP:i:2
		CAGGCTGGTCTCCAACTCCTGGGCTCAAGCAGTCCTCCTGCCTCAGCCTTCCGAGTAGCTGAAACTGCAGGCATG
		+
		CC@FFFFFFHHHHGIJJJJIJJJGIJIJIIJIGIJJJJJJIJIJHIIIHIJJJBHCAHFHEGGHCHHFHFFFF?;

For quick info what is standard in an Illumina FASTQ:
http://support.illumina.com/content/dam/illumina-support/help/BaseSpaceHelp_v2/Content/Vault/Informatics/Sequencing_Analysis/BS/swSEQ_mBS_FASTQFiles.htm

3. Required output to present in two weeks:
a. a fully formed, submittable script... python <name of script> -<input, output, options>
b. must take input and output arguments, as well as an argument for the number of digits in the read ID
c. output in .fastq format