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Full Discussion: awk code to reconstruct sequence from alignment
Top Forums UNIX for Dummies Questions & Answers awk code to reconstruct sequence from alignment Post 302835553 by Fahmida on Monday 22nd of July 2013 03:27:58 PM
Old 07-22-2013
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:
Code:
(Sbjct:26325115-26325094)NNNN(Sbjct:33716368-33716347)NNNN(Sbjct:33769033-33769073)NNNN(Sbjct:34869860-34869889)

The output expected is shown in 'Example Output'.
Code:
--------- 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

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

Thanks for your help.
 

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LEARN ABOUT DEBIAN

pynast

VERSION:(1)							   User Commands						       VERSION:(1)

NAME

       PyNAST - alignment of short DNA sequences

SYNOPSIS

       pynast [options] {-i input_fp -t template_fp}

DESCRIPTION

       [] indicates optional input (order unimportant) {} indicates required input (order unimportant)

   Example usage:
	      pynast -i my_input.fasta -t my_template.fasta

OPTIONS

       --version
	      show program's version number and exit

       -h, --help
	      show this help message and exit

       -t TEMPLATE_FP, --template_fp=TEMPLATE_FP
	      path to template alignment file [REQUIRED]

       -i INPUT_FP, --input_fp=INPUT_FP
	      path to input fasta file [REQUIRED]

       -v, --verbose
	      Print status and other information during execution [default: False]

       -p MIN_PCT_ID, --min_pct_id=MIN_PCT_ID
	      minimum percent sequence	identity to consider a sequence a match [default: 75.0]

       -l MIN_LEN, --min_len=MIN_LEN
	      minimum sequence length to include in NAST alignment [default: 1000]

       -m PAIRWISE_ALIGNMENT_METHOD, --pairwise_alignment_method=PAIRWISE_ALIGNMENT_METHOD
	      method for performing pairwise alignment [default: uclust]

       -a FASTA_OUT_FP, --fasta_out_fp=FASTA_OUT_FP
	      path to store resulting alignment file [default: derived from input filepath]

       -g LOG_FP, --log_fp=LOG_FP
	      path to store log file [default: derived from input filepath]

       -f FAILURE_FP, --failure_fp=FAILURE_FP
	      path to store file of seqs which fail to align [default: derived from input filepath]

       -e MAX_E_VALUE, --max_e_value=MAX_E_VALUE
	      Depreciated. Will be removed in PyNAST 1.2

       -d BLAST_DB, --blast_db=BLAST_DB
	      Depreciated. Will be removed in PyNAST 1.2

SEE ALSO

       http://pynast.sourceforge.net

Version: pynast 1.1						    August 2011 						       VERSION:(1)
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