extracts sequences and quality scores from FASTQSOLEXA data fastqsolexa_to_fasta_qual.py $input1 $output1 $output2 $input1.extension

.. class:: warningmark IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64. ----- **What it does** This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset. ----- **Example1** - Converting the following Solexa fastq data:: @seq1 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT +seq1 hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh @seq2 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG +seq2 hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO - will extract the following sequences:: >seq1 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT >seq2 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG - and quality scores:: >seq1 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40 >seq2 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15 **Example2** - Converting the following Solexa fastq data:: @HANNIBAL_1_FC302VTAAXX:2:1:228:167 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT +HANNIBAL_1_FC302VTAAXX:2:1:228:167 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4 @HANNIBAL_1_FC302VTAAXX:2:1:156:340 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG +HANNIBAL_1_FC302VTAAXX:2:1:156:340 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9 - will extract the following sequences:: >HANNIBAL_1_FC302VTAAXX:2:1:228:167 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT >HANNIBAL_1_FC302VTAAXX:2:1:156:340 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG - and quality scores:: >HANNIBAL_1_FC302VTAAXX:2:1:228:167 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4 >HANNIBAL_1_FC302VTAAXX:2:1:156:340 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9