awk code to reconstruct sequence from alignment Post: 302835321

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Top Forums UNIX for Dummies Questions & Answers awk code to reconstruct sequence from alignment Post 302835321 by Fahmida on Monday 22nd of July 2013 08:29:44 AM

07-22-2013

Registered User

awk code to reconstruct sequence from alignment

Hi Everyone,

I need some help to construct a long 'Sbjct' string from the following input using incremental order of 'Sbjct' starting number (e.g. 26325115,33716368,33769033,34869860 etc.)
Different 'Sbject' string will be separated by 'NNNN's as:

(Sbjct:26325115-26325094)NNNN(Sbjct:33716368-33716347)NNNN(Sbjct:33769033-33769073)NNNN(Sbjct:34869860-34869889)

The output expected is shown in 'Example Output'.

--------- Example Input (just a small segment of the whole file)-----------

Score = 44.1 bits (22), Expect = 0.30
Identities = 28/30 (93%)
Strand = Plus / Plus

Query: 1684 atcaaaatgaccaaaatatttcattaaaaa 1713
|||||||||| |||||| ||||||||||||
Sbjct: 34869860 atcaaaatgaacaaaatgtttcattaaaaa 34869889

Score = 44.1 bits (22), Expect = 0.30
Identities = 22/22 (100%)
Strand = Plus / Minus

Query: 1758 ttagggtttagagttaaggggt 1779
||||||||||||||||||||||
Sbjct: 26325115 ttagggtttagagttaaggggt 26325094

Score = 44.1 bits (22), Expect = 0.30
Identities = 22/22 (100%)
Strand = Plus / Minus

Query: 1687 aaaatgaccaaaatatttcatt 1708
||||||||||||||||||||||
Sbjct: 33716368 aaaatgaccaaaatatttcatt 33716347

Score = 44.1 bits (22), Expect = 0.30
Identities = 38/42 (90%), Gaps = 1/42 (2%)
Strand = Plus / Plus

Query: 1734 ccctagggttaactaattcaaaccttagggtttagagttaag 1775
||||||| ||||||||| |||| ||||||||||||||||||
Sbjct: 33769033 ccctaggattaactaatctaaac-ttagggtttagagttaag 33769073

----------------------

---------------------- Example Output -----------
Whole Sbjct string
ttagggtttagagttaaggggtNNNNaaaatgaccaaaatatttcattNNNNccctaggattaactaatctaaac-ttagggtttagagttaagNNNNatcaaaatgaacaaaatgtttcattaaaaa

Thanks for your help.

Fahmida

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LEARN ABOUT DEBIAN

squizz

SQUIZZ(1)							   User Manuals 							 SQUIZZ(1)

NAME

       squizz - Sequence format checker

SYNOPSIS

       squizz [-AShlns] [-c format] [-f format] file

OPTIONS

       Following command line options are allowed:

       -A  Restrict detection/verification to alignment formats (conflict with -S option).

       -S  Restrict detection/verification to sequence formats (conflict with -A option).

       -c format
	   Convert detected sequence/alignment into format. This option implies strict alignment checking.

       -f format
	   Assume input format is format. Do not try to detect the format, just verify that the given one is correct.

       -h  Usage display.

       -l  List all supported formats.

       -n  Count and report detected entries. This option is only available when the detection is restricted to a single type (with -A or -S
	   options) and strict checks (without -s option) are enabled.

       -s  Disable strict format checks (enabled by default).

DESCRIPTION

       squizz is a sequence format file checker, but it has some conversion capabilities too.

       squizz can detect the most common sequence and alignment formats :

       * EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT.

       * CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM.

       squizz can do some conversions too, if the format the input format is supported. Only 3 types are available : sequence to sequence, align-
       ment to alignment, and alignment to sequence (the last one, sequence to alignment, require multiple alignments algorithms and cannot be
       handled with formatting tools).

       Strict format checks validate the previously detected objects, by making some sanity checks:

       - sequence strings must exists.
       - alignment is made of more than one sequence.
       - alignment sequence strings must have the same length.
       - alignment sequence names must exists, and be unique.

SEE ALSO

       seqfmt(5), alifmt(5)

AUTHOR

       Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

Unix								    2009-05-19								 SQUIZZ(1)

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