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Top Forums Shell Programming and Scripting parse fasta file to tabular file Post 302584712 by yifangt on Saturday 24th of December 2011 06:22:17 PM
Old 12-24-2011
Thanks Kato!
Your second version is much better. Is it possible to remove the tabs within the sequence fields? i.e. merge the sequence to a single field instead of being separated with the tab. gsub the first "\n" with "\t", but gsub the second "\n" and after with nothing. One step from what I want.
Merry Christmas!!!

Last edited by yifangt; 12-24-2011 at 07:39 PM.. Reason: improve the algorithm
 

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SFDDIFF(1)						      General Commands Manual							SFDDIFF(1)

NAME
sfddiff - compare two font files SYNOPSIS
sfddiff [--help] [--ignorehints] [--ignorenames] [--ignoregpos] [--ignoregsub] [--ignorebitmaps] [--exact] [--warn] [--merge outfile] [--usage] [--version] fontfile1 fontfile2 DESCRIPTION
The program sfddiff compares two font files, which may be in any format fontforge(1) can read. It will notice the following differences: 1) Characters are present in one font but not in the other. 2) Characters are present in both fonts but have different sets of outlines or references. The outlines may be compared so that only exact matches are accepted, or so that a fuzzier match is used. Similarly references may need to match exactly, or may be matched after an unlink. This fuzzy comparison is useful when comparing truetype and postscript fonts, or when comparing a font with references to one with- out. 3) The postscript hints or truetype instructions are different. 4) The font names (the truetype `name' table) differ. 5) The kerning (and other `gpos' information) differs. 6) The ligatures (and other `gsub' information) differ. 7) Any bitmap strikes present in one font but not in the other. 8) Any bitmap characters present in one strike of one font but in the equivalent strike of the other. 9) Any bitmap characters which differ. OPTIONS
--help Provide a description with a list of the available options. --ignorehints Suppress the reporting of hint/instruction differences. --ignoregpos Suppress the reporting of kerning (and other `gpos') differences. --ignoregsub Suppress the reporting of ligature (and other `gsub') differences. --ignorenames Suppress the reporting of name string differences. --ignorebitmaps Suppress the reporting of bitmap differences. --exact Require outlines to match exactly. --warn Warn if the outlines/references are slightly different. --merge outfile Store a merged version of the two fonts into the specified output file. The merged data will be based on sfdfile1, as well as any characters present in sfdfile2 but not in sfdfile1 will be added, and the outlines of sfdfile2 will be placed in the background. Finally, for any characters with different outlines or references the background of the the character will contain the outlines from sfdfile2 (references will be unlinked into outlines and those outlines also will be added). --usage Display the usage description. --version Display the current version. SEE ALSO
fontforge(1) The HTML version of the fontforge manual at: http://fontforge.sourceforge.net/ AUTHOR
Copyright (C) 2000-2006 by George Williams (gww@silcom.com). Manual page heavily rewritten and modified to use standard -man(5) macros by R.P.C. Rodgers (rodgers@nlm.nih.gov), 23 October 2002. 8 April 2006 SFDDIFF(1)
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