7 Nov 2008 21:59
SeqIO & multi-line fastq
Tristan Lefebure <tristan.lefebure <at> gmail.com>
2008-11-07 20:59:07 GMT
2008-11-07 20:59:07 GMT
Hi there, I'm parsing with SeqIO a FastQ file made by MAQ. SeqIO complains because this is a multiline fastq file. By looking at the Bio::SeqIO::fastq, it's pretty obvious that it can't handle multilines. Who is wrong? MAQ, SeqIO, or am I missing something? Some more details below: ### [tristan <at> trudy maq_easyrun] seq2seq.pl cns.fq fastq cns.fna fasta ------------- EXCEPTION ------------- MSG: AACTATTTATCAAATTTAAAATTCAACGAAAAACAAAGCAAAGCAGATCTTTTAGTTTTT doesn't match fastq descriptor line type STACK Bio::SeqIO::fastq::next_seq /usr/local/share/perl/5.10.0/Bio/SeqIO/fastq.pm:113 STACK toplevel /home/tristan/bin/seq2seq.pl:25 ------------------------------------- ### The fastq file looks like that: ----------- <at> nctc11168 atgAATCCAAGCCAAATACTTGAAAATTTAAAAAAAGAATTAAGTGAAAACGAATACGAA AACTATTTATCAAATTTAAAATTCAACGAAAAACAAAGCAAAGCAGATCTTTTAGTTTTT AATGCTCCAAATGAACTCATGGCTAAATTCATACAAACAAAATACGGCAAAAAAATCGCG CATTTTTATGAAGTGCAAAGCGGAAATAAAGCCATCATAAATATACAAGCACAAAGTGCT AAACAAAGCAACAAAAGCACAAAAATCGACATAGCTCATATAAAAGCACAAAGCACGATT TTAAATC[...] [some 20000 lines later] AACCTTTTTTTATAAAATTTAAGATAAAATTTATACATTATGCAAAATTTAAAGAGAgat n + EQWWZ`cffilmu~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~[...] --------- Thanks! -Tristan
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