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 CENTOS
digest
Digest(3) OCaml library Digest(3)
NAME
Digest - MD5 message digest.
Module
Module Digest
Documentation
Module Digest
: sig end
MD5 message digest.
This module provides functions to compute 128-bit ``digests'' of arbitrary-length strings or files. The digests are of cryptographic qual-
ity: it is very hard, given a digest, to forge a string having that digest. The algorithm used is MD5. This module should not be used for
secure and sensitive cryptographic applications. For these kind of applications more recent and stronger cryptographic primitives should be
used instead.
type t = string
The type of digests: 16-character strings.
val compare : t -> t -> int
The comparison function for 16-character digest, with the same specification as Pervasives.compare and the implementation shared with
String.compare . Along with the type t , this function compare allows the module Digest to be passed as argument to the functors Set.Make
and Map.Make .
Since 4.00.0
val string : string -> t
Return the digest of the given string.
val substring : string -> int -> int -> t
Digest.substring s ofs len returns the digest of the substring of s starting at character number ofs and containing len characters.
val channel : Pervasives.in_channel -> int -> t
If len is nonnegative, Digest.channel ic len reads len characters from channel ic and returns their digest, or raises End_of_file if
end-of-file is reached before len characters are read. If len is negative, Digest.channel ic len reads all characters from ic until
end-of-file is reached and return their digest.
val file : string -> t
Return the digest of the file whose name is given.
val output : Pervasives.out_channel -> t -> unit
Write a digest on the given output channel.
val input : Pervasives.in_channel -> t
Read a digest from the given input channel.
val to_hex : t -> string
Return the printable hexadecimal representation of the given digest.
val from_hex : string -> t
Convert a hexadecimal representation back into the corresponding digest. Raise Invalid_argument if the argument is not exactly 32 hexadec-
imal characters.
Since 4.00.0
OCamldoc 2014-06-09 Digest(3)