Entering edit mode
2.6 years ago
pixie@bioinfo
★
1.5k
Hello, I am new to pysam. I have a list of taxids (tid) as a python list. I want to extract sequences from the matching reads in the bam file (only primary alignments). How should I go about it ? Any other options ?
82f70c23-fedb-42fd-acf4-f252a6dfeceb 0 W1236514429|tid|34199|NC_035506.1|Aloe_vera_voucher_Aloe_vera_chloroplast_complete_genome 104188 0 3S17M1D17M2D12M1I3M2D12M2D87M1I8M3D5M1I4M3D2M1D18M4D36M30S * 0 0 CACGGATACCTGGGCACCCAAGACGAGGAAGGGCGTAATGCGCAGAAATGGCTGAGGAGTTGAAAAAGCGTAGATCAGGAGATTCCCGAATAGGTCAACCTTTCAAACTGCTGCTGGATCCATGGGCAGGCAAGAGACAACCTGGCGAACTGAAAACATCTTAGCCTTGAGAAAAAGCAAAAGCGATTCCCTTGCGGCGAGCGAAATGGGAGCAGCCTAAACCGTGAGAAAAAAAACGAAAAGGTTGTGAAGTCAAA@>?;;:9.--,**)*-./,-)',-.73)().5.2311/02+(((%%'--*''('&&($'&&&&+('&&78::3366/.,*...1>?<=:8:21112>5555CFDABD>@??@?>44566;557<;88///098*-.+%$$%'(,/1.+++)(()-+,++5541+'%$%$%&)*/-**()25:=><<=@:9'$##%')50//00::;9.)()(&&(0/06<*))))()'&)*(+/.-,(&&&%'&&&%++)('(/103 NM:i:31 ms:i:148 AS:i:148 nn:i:0 tp:Z:P cm:i:22 s1:i:129 s2:i:129 de:f:0.0905 rl:i:0RG:Z:a8763ed2dbe639724b8879ecd3fdd5920283fa0f_barcode11_2004_016_Pelargonium_Hexamers pr:Z:primary ti:Z:1437197 er:Z:sa MD:Z:8A8^G17^GC1A3A0C8^TC1G10^AT4A6C39A43^TAG5A3^GAA2^G18^GTAG1A34
