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Full Discussion: Filter (by max length) only lines not matching regex
Top Forums Shell Programming and Scripting Filter (by max length) only lines not matching regex Post 302785161 by pathunkathunk on Monday 25th of March 2013 03:27:32 AM
Old 03-25-2013
Both of these work, thank you.

The problem with my original code was obscured by my choice of an example file with unrealistically short sequences. In reality my sequences are longer, and the problem with my code is that it captures headers along with short sequences.
 

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LEARN ABOUT DEBIAN

alifmt

ALIFMT(5)							   User Manuals 							 ALIFMT(5)

NAME

       alifmt - Aligned sequences formats

DESCRIPTION

       This document illustrates some common formats used for aligned sequences representation.

       CLUSTAL
	    CLUSTAL W (1.82) multiple sequence alignment

	    MALK_ECOLI	    MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
	    MALK_SALTY	    MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
	    MALK_ENTAE	    MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
	    MALK_PHOLU	    MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
			    *:** *:**:**:*:.::**:***:*::***

	    MALK_ECOLI	    LRMIAGLETITSGDLACRRLHKEPGV
	    MALK_SALTY	    LRMIAGLETITSGDLACRRLHQEPGV
	    MALK_ENTAE	    LRMIAGLETVTSGDL-----------
	    MALK_PHOLU	    LRM-----------------------
			    ***

	   Warning: Names must not contain spaces or exceed 30 characters.

       FASTA
	    >MALK_ECOLI
	    MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
	    GLETITSGDLACRRLHKEPGV
	    >MALK_SALTY
	    MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
	    GLETITSGDLACRRLHQEPGV
	    >MALK_ENTAE
	    MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
	    GLETVTSGDL-----------
	    >MALK_PHOLU
	    MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM--
	    ---------------------

       MEGA
	    #mega
	    !Title Multiple Sequence Alignment;

	    #MALK_ECOLI
	    MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
	    GLETITSGDLACRRLHKEPGV
	    #MALK_SALTY
	    MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
	    GLETITSGDLACRRLHQEPGV
	    #MALK_ENTAE
	    MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
	    GLETVTSGDL-----------
	    #MALK_PHOLU
	    MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
	    ---------------------

       MSF
	    !!AA_MULTIPLE_ALIGNMENT 1.0
	    PileUp of: @pep.list

	     msf.seq	   MSF: 55  Type: P  Nov 22, 2001 11:02  Check: 2529 ..

	     Name: m73237	    Len:   655	Check: 7493  Weight:  1.00
	     Name: l28824	    Len:   655	Check: 5456  Weight:  1.00
	     Name: u04379	    Len:   655	Check: 9580  Weight:  1.00

	    //

		    1							50
	    m73237  ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
	    l28824  MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
	    u04379  ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG

		    51
	    m73237  ~~~~~
	    l28824  ~~~~~
	    u04379  AACG*

	   Warning: This format cannot handle more than 500 sequences in a single alignment.

       NEXUS
	    #NEXUS

	    begin data;
	      dimensions ntax=2 nchar=89;
	      format datatype=Protein interleave gap=- missing='.';
	      matrix
	    [		1						50]
	    btdDm	-------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ
	    TSp1	--------------------AEH-----------PSLR--------GTPL

	    [		51			    80]
	    btdDm	YACPICSKKFSRSDHLSKHKKTHF------
	    TSp1	FACPICNKRFMRSDHLAKHVKTHN------

		;
	    endblock;

	   Warning: Text enclosed in brackets is considered as comment, and thus ignored.

       PHYLIP
	   Sequential (PHYLIPS):

		 2   109
	    ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
		      ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
		      YGHTKGGN---
	    POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
		      ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
		      YGHTKGGN---

	   Interleaved (PHYLIPI):

		 2   109
	    ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
	    POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD

		      GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
		      GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG

		      DEYGHTKGGN---
		      DEYGHTKGGN---

	   Warning: Species names may not contain characters `( ) : ; , [ ]' and exceed 10 characters.

       STOCKHOLM
	    # STOCKHOLM 1.0

	    MALK_ECOLI	MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
	    MALK_SALTY	MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
	    MALK_ENTAE	MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
	    MALK_PHOLU	MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------

	    MALK_ECOLI	RCHLFREDGTACRRLHKEPGV
	    MALK_SALTY	RCHLFREDGSACRRLHQEPGV
	    MALK_ENTAE	---------------------
	    MALK_PHOLU	---------------------
	    //

SEE ALSO

       squizz(1), seqfmt(5)

AUTHOR

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

Unix								    2009-05-19								 ALIFMT(5)
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