10-08-2012
jim, thanks for taking a look.
Using the code you provide, I get the following in terminal:
Quote:
awk: illegal primary in regular expression >m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+) at ) comp1001102_c0_seq1:3-416(+)
input record number 3, file source.txt
source line number 3
cat newfile returns:
Quote:
> comp100001_c0_seq1
comp1002314_c0_seq1
>m.49518 g.49518 ORF g.49518 m.49518 type:internal len:169 (-) comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPNKVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLT TNDAYMYVWNESMASRGPQEIGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+)
Just to verify, here are the input files:
Quote:
$ cat source.txt
>m.49518 g.49518 ORF g.49518 m.49518 type:internal len:169 (-) comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPNKVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLT TNDAYMYVWNESMASRGPQEIGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+)
YGDLDDSALDAEGPAGPVYRFSRRKSDTKSDDNSQSNGEGVMMMINGELVKVEQLKREEIINCTCGYTEEDGLMIQCDLCLCWQHGHCNGIEREKDVPEK YICYICSHPYRQRPSRKYIHDQDWIKEGKLVSLTKRK
>m.54557 g.54557 ORF g.54557 m.54557 type:internal len:113 (+) comp1002314_c0_seq1:2-343(+)
SIKARQIYDSRGNPTVEVDLVTENGLFRAAVPSGASTGVHEALELRDNDKSMYHGKSVFKAVDNINSIIAPELLKANIEVTEQAEIDNFLLKLDGTPNKS KLGANAILGVSLA
$ cat ID.txt
comp100001_c0_seq1
comp1002314_c0_seq1
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LEARN ABOUT DEBIAN
io_waitread
io_waitread(3) Library Functions Manual io_waitread(3)
NAME
io_waitread - read from a descriptor
SYNTAX
#include <io.h>
int io_waitread(int64 fd,char* buf,int64 len);
DESCRIPTION
io_waitread tries to read len bytes of data from descriptor fd into buf[0], buf[1], ..., buf[len-1]. (The effects are undefined if len is 0
or smaller.) There are several possible results:
o o_waitread returns an integer between 1 and len: This number of bytes was available for immediate reading; the bytes were read into the
beginning of buf. Note that this number can be, and often is, smaller than len; you must not assume that io_waitread always succeeds in
reading exactly len bytes.
o io_waitread returns 0: No bytes were read, because the descriptor is at end of file. For example, this descriptor has reached the end of
a disk file, or is reading an empty pipe that has been closed by all writers.
o io_waitread returns -3, setting errno to something other than EAGAIN: No bytes were read, because the read attempt encountered a persis-
tent error, such as a serious disk failure (EIO), an unreachable network (ENETUNREACH), or an invalid descriptor number (EBADF).
SEE ALSO
io_nonblock(3), io_waitread(3), io_waitreadtimeout(3)
io_waitread(3)