[EMBOSS] Problem writing sequence files
Kim Rutherford
kmr at sanger.ac.uk
Wed Aug 20 13:28:30 UTC 2003
Hi. I'm trying to write a sequence to a named file. I tried this:
AjPFile seqout_file = ajFileNewOut(seqout_name);
AjPSeqout named_seqout = ajSeqoutNewF(seqout_file);
AjPStr format_str = ajStrNew();
ajStrAssC(&format_str, "embl");
ajSeqOutSetFormat(named_seqout, format_str);
ajSeqWrite(named_seqout, subseq);
I get a segmentation fault and this backtrace:
#0 0x1200b27a0 in ajFmtPrintF (file=0x0,
fmt=0x1400172ce "ID %-10.10S standard; DNA; UNC; %d BP.\n")
at ajfmt.c:1118
#1 0x12008c6a4 in seqWriteEmbl (outseq=0x140057840) at ajseqwrite.c:1956
#2 0x120087ae4 in ajSeqWrite (outseq=0x140057840, seq=0x140057700)
at ajseqwrite.c:540
#3 0x120019c10 in splitter_write (default_seqout=0x140057ac0,
subseq=0x140057700, start=0, end=1139, seq=0x140048f00,
seqout_name=0x14008b4a0) at splitter.c:179
#4 0x120019dd8 in splitter_ProcessChunk (seqout=0x140057ac0, seq=0x140048f00,
start=0, end=1139, outseq_name=0x14008b4a0) at splitter.c:207
#5 0x120019844 in main (argc=4, argv=0x11fffc018) at splitter.c:87
It appears that named_seqout->File is null and ajSeqWrite() is
expecting it to be non-null. Should I be calling a function other than
ajSeqoutNewF() to create the AjPSeqout object (ie. named_seqout)?
I'd appreciate if someone could let me know what I'm doing wrong or
point me to some example code that does something similar.
Thanks in advance,
Kim.
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