Re: Substitution on a sequence

Update: Credited the wrong person.

I'd suggest a slight modification to ww's method. As this is a FASTA file, I'd read the file record by record (sequence by sequence), rather than line by line. The following one-liner ought to work, but is untested.

perl -e"BEGIN{$/=qq[\n>]}" -wpe"s[[-*]|DL;][]g" theFile > theOuput
[download]

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Comment on Re: Substitution on a sequence Download Code

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Re^2: Substitution on a sequence by ww (Archbishop) on Jan 29, 2007 at 16:55 UTC
Tested (albeit, non-rigorously) BrowserUK's with a data file (very modestly varied from OP) eq: `>DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGGA +GGGAGG* ">DL;H2_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGG +AGGGAGG" line 2 >DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCDLTCGCTGCCCAGC--CCCGGG +GAGGGAGG line3 >DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGGA +GGGAGG line 4 >DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGG +AGGGAGG line 5` [download] and output is: `>H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG ">H2_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG" + line 2 >H1_ENSP00000194530_chr2_202024 CCCCGCCTTCDLTCGCTGCCCAGCCCCGGGGAGGGAGG + line3 >H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG l +ine 4 >H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG l +ine 5` [download] Nice, BrowserUK; ++ Update*: Fixed the mis-attribution. Give BrowserUK another ++ and I'll do penance in the dungeon; the more so, since it was he who answered a brain_dead question about his code.	[reply] [d/l] [select]

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Re^2: Substitution on a sequence
by ww (Archbishop) on Jan 29, 2007 at 16:55 UTC

Tested (albeit, non-rigorously) BrowserUK's with a data file (very modestly varied from OP) eq:

>DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGGA
+GGGAGG*
">DL;H2_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGG
+AGGGAGG*" line 2
>DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCDLTCGCTGCCCAGC--CCCGGG
+GAGGGAGG* line3
>DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGGA
+GGGAGG line 4
>DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGG*GG
+AGGGAGG line 5
[download]

and output is:

>H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG
">H2_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG"
+ line 2
>H1_ENSP00000194530_chr2_202024 CCCCGCCTTCDLTCGCTGCCCAGCCCCGGGGAGGGAGG
+ line3
>H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG l
+ine 4
>H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG l
+ine 5
[download]

Nice, BrowserUK; ++

Update: Fixed the mis-attribution. Give BrowserUK another ++ and I'll do penance in the dungeon; the more so, since it was he who answered a brain_dead question about his code.

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