   $Id: README,v 1.2 1996/01/24 14:30:18 mieg Exp $


EXAMPLE FOR D1044
   pgassemble d1044.fasta > d1044.assemble
	 mv contigs.seq d1044.contigs.seq
   seqpress <  d1044.con > d1044.xbap.pg
   echo " " >> d1044.xbap.pg
   cat d1044.contigs.seq >> d1044.xbap.pg
   pgassemble d1044.xbap.pg > d1044.xbap.pg.assemble
   #mv contigs.seq d1044.xbap.pg.contigs.seq
	now, names the output file d1044.xbap.pg.contigs for me
  

EXPLANATION OF THE VARIOUS FILES:
d1044.seq - the "answer"...the big contig from the final xbap database
D1044.final.showrel - final show relationships file from xbap
d1044.assemble - output of Phil's assemble on d1044.fasta , version 940603
d1044.assemble.new - output of Phil's assemble on d1044.fasta, version 940605
d1044.con - fasta formatted file of file xbap contigs...this
		is the final con file for the final xbap database
		since this is a finished cosmid
d1044.contigs.seq - contigs.seq file Phil outputs as contigs.seq
d1044.fasta - fasta formatted file containing all original data (no vector)
		including r1, s2, etc.
d1044.s1.fasta - fasta formatted file containing all original s1 data
		without vector
d1044.s1.fasta.assemble.new  - output of Phil's assembly, version 940605
		when run on d1044.s1.fasta
d1044.xbap.pg - contains xbap final contigs and "assemble" contigs.seq
			used as input to assemble to compare the final
			contigs for xbap and assemble
d1044.xbap.pg.assemble  - output from running "assemble d1044.xbap.pg"
d1044.xbap.pg.contigs.seq - contigs.seq file from running "assemble d1044.xbap.pg"
d1044.xbap.orig.showrel - show relationships from xbap after assembling in
			all the original data (comparable to phils d1044.assemble)
			so I can compare the number of contigs made...when I
			ran xbap, I sorted the file alphabetically so as not
			to give xbap the files in the same order as they were
			in the showrelationships file.
d1044.xbap.orig.con	- consensus from xbap after assembling in all
			original data...see d1044.xbap.orig.showrel
d1044.s1.fasta	- fasta formatted file of all of the s1's in the final xbap
			database
TIME TO ASSEMBLE:
C05D11
81.0u 0.0s 1:23 97% 0+0k 0+0io 0pf+0w
T20B12
79.0u 0.0s 1:21 96% 0+0k 0+0io 0pf+0w

NUMBER OF READS IN EACH DATABASE
b0280.fasta
    1272    
c05d11.fasta
     934   
c05d2.fasta (went into two contigs)
    1413  
d1044.fasta
    1151 
t20b12.fasta (went into two big contigs)
     896


USING XBAP TO ASSEMBLE ALL THE ORIGINAL DATA:
C05D2:
	xbap
	5 major contigs:
	28 kb
	6.4 kb
	10.5 kb
	2.28 kb
	1.53 kb

	"assemble"
	2 major contigs 40kb and 7 kb

T20B12:
	xbap
	4 major contigs:
	9.5 kb
	13 kb
	13.8 kb
	1.3 kb

	assemble"
	2 major contigs 15 kb and 21 kb


-------

foreach file (b0280 c05d11
 c05d2 d1044 t20b12)
? \cp $file.fasta.contigs fff
? echo " " >> fff
? cat $file.con >> fff
? mv fff $file.xbapfinal.pg.new
? pgassemble $file.xbapfinal.pg.new > $file.xbapfinal.pg.assemble.new
? \rm -f $file.xbapfinal.pg.new
? \cp $file.s1.fasta.contigs fff
? echo " " >> fff
? cat $file.con >> fff
? mv fff $file.xbapfinal.pg.s1.new
? pgassemble $file.xbapfinal.pg.s1.new > $file.xbapfinal.pg.s1.assemble.new
? \rm -f $file.xbapfinal.pg.s1.new


MORE EXPLANATIONS OF FILENAMES
d1044.fasta.assemble.new - assemble output from running d1044.fasta (which is
		a fasta formatted file containing all the original data 
		from d1044 (minus vector of course))`
d1044.s1.fasta.assemble.new - assembly output from running d1044.s1.fasta
		(which is all of the original s1 data from d1044, minus
		vector)
d1044.xbapfinal.pg.assemble.new - this is the ouptut from comparing "assemble"
		run on d1044.fasta (all the original data)
		with the FINAL contigs in xbap (the contigs when the database
		was turned in as being finished)
d1044.xbapfinal.pg.s1.assemble.new - this is the output from comparing
		assemble run on d1044.s1.fasta (just s1 original data)
		with the FINAL contigs in xbap (contigs when the database
		was turned in as being finished)
d1044.s1.xbap.con - contigs from xbap being run on only the s1 data
d1044.s1.showrel - show relatoinships from xbap after being run on s1 data alone

foreach file ( b0280 c05d11 c05d2 d1044 t20b12 )
? cp $file.xbap.s1.con $file.xbap_s1.pg_s1
? echo " " >> $file.xbap_s1.pg_s1
? cat $file.s1.fasta.contigs >> $file.xbap_s1.pg_s1
? pgassemble $file.xbap_s1.pg_s1 > $file.xbap_s1.pg_s1.assemble
? cp $file.xbap.orig.con $file.xbap_orig.pg_orig
? echo " " >> $file.xbap_orig.pg_orig
? cat $file.fasta.contigs >> $file.xbap_orig.pg_orig
? pgassemble $file.xbap_orig.pg_orig > $file.xbap_orig.pg_orig.assemble
? end

MORE FILENAME EXPLANATIONS
d1044.xbap_orig.pg_orig - file containing contigs from xbap
		after it assembled all the original reads, but no editing
		and phil's assembly of all the original reads
d1044.xbap_orig.pg_orig.assemble - output of "assemble" for
	d1044.xbap_orig.pg_orig
d1044.xbap_orig.pg_orig.contigs - contigs created during assemble run on
	d1044.xbap_orig.pg_orig
d1044.xbap_s1.pg_s1 - file containing contigs from xbap after just
	assembling the s1 data and contigs from phil assembling just the
	original s1 data
d1044.xbap_s1.pg_s1.assemble - output from d1044.xbap_s1.pg_s1
d1044.xbap_s1.pg_s1.contigs - contigs generated during run of assemble
		on d1044.xbap_s1.pg_s1
