test_Ace
Test to check that ACEParser can parse the whole file into one record. ... 
Input file: Ace/contig1.ace

Contigs: 2 ; Reads: 16
all WA:
phrap_params phrap 040203:114710 ['phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates', 'phrap version 0.990329']

--------------------
Contig no. 0 has 2 reads.
CO: Contig1 856 2 31 U
aatacgGGAT ... ACATCATCTG ... cATCTAGtac
[0, 0, 0, 0, 0, 0, 22, 23, 25, 28] ... [90, 90, 90, 90, 90, 90, 90, 90, 90, 90] ... [15, 22, 30, 24, 28, 22, 21, 15, 19, 0]
# AF: 2 ; # BS: 31
AF(1) BL060c3-LR0R.b.ab1 U 1 ; AF(-1) BL060c3-LR0R.b.ab1 U 1 ;
BS(15) BL060c3-LR5.g.ab1 434 438 ; BS(-1) BL060c3-LR0R.b.ab1 823 856 ;
CT:
Contig1 repeat phrap 52 53 555456:555432 ['This is the forst line of comment for c1', 'and this the second for c1']
WA: none
RD: BL060c3-LR5.g.ab1 868 0 0 tagcgaggaa ... CCGAGGCCAA ... gaaccatcag
QA: 80 853 22 856
DS: none
RT:
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 590 607 040217:110357
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR:
BL060c3-LR5.g.ab1 unaligned phrap 040217:110357
RD: BL060c3-LR0R.b.ab1 856 0 0 aatacgGGAT ... ACATCATCTG ... cATCTAGtac
QA: 7 778 1 856
DS: none
RT: none
WR: none

--------------------
Contig no. 1 has 14 reads.
CO: Contig2 3296 14 214 U
cacggatgat ... TTTGAATATT ... Atccttgtag
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ... [90, 90, 90, 90, 90, 90, 90, 90, 90, 90] ... [24, 0, 0, 0, 0, 0, 0, 0, 0, 0]
# AF: 14 ; # BS: 214
AF(7) BL060-LR3R.b.ab1 C 1601 ; AF(-1) BL060c2-LR0R.b.ab1 C 2445 ;
BS(107) BL060-c1-LR3R.b.ab1 2286 2292 ; BS(-1) BL060c2-LR0R.b.ab1 3236 3296 ;
CT:
Contig2 repeat phrap 42 43 123456:765432 ['This is the forst line of comment for c2', 'and this the second for c2']
WA:
phrap_params phrap 040203:114710 ['phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates', 'phrap version 0.990329']
RD: BL060-c1-LR12.g.ab1 862 0 0 cacggatgat ... GTTCTCGTTG ... CGTTTACCcg
QA: 81 842 1 862
DS: CHROMAT_FILE: BL060-c1-LR12.g.ab1 PHD_FILE: BL060-c1-LR12.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR11.g.ab1 880 0 0 ctttctgacC ... CTGTGGTTTC ... cggagttacg
QA: 11 807 8 880
DS: CHROMAT_FILE: BL060-c1-LR11.g.ab1 PHD_FILE: BL060-c1-LR11.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR9.g.ab1 864 0 0 cacccaCTTT ... ACCAAACATT ... GGTAGCACgc
QA: 7 840 4 864
DS: CHROMAT_FILE: BL060-c1-LR9.g.ab1 PHD_FILE: BL060-c1-LR9.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR17R.b.ab1 863 0 0 ctaattggcc ... GGAACCTTTC ... CAACCTgact
QA: 63 857 1 861
DS: CHROMAT_FILE: BL060-c1-LR17R.b.ab1 PHD_FILE: BL060-c1-LR17R.b.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR8.5.g.ab1 877 0 0 tgCTGCGGTT ... GGCAGTTTCA ... tactcataaa
QA: 13 729 1 877
DS: CHROMAT_FILE: BL060-LR8.5.g.ab1 PHD_FILE: BL060-LR8.5.g.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR3R.b.ab1 874 0 0 ctCTTAGGAT ... AACTCACATT ... *CACCCAAac
QA: 65 874 1 874
DS: CHROMAT_FILE: BL060-LR3R.b.ab1 PHD_FILE: BL060-LR3R.b.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR3R.b.ab1 864 0 0 CCaTGTCCAA ... AAGGGTT*CA ... ACACTCGCga
QA: 73 862 1 863
DS: CHROMAT_FILE: BL060-c1-LR3R.b.ab1 PHD_FILE: BL060-c1-LR3R.b.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR3R.b.ab1 857 0 0 agaaagagga ... nnnannnnnn ... gtctttgctc
QA: 548 847 442 854
DS: CHROMAT_FILE: BL060-LR3R.b.ab1 PHD_FILE: BL060-LR3R.b.ab1.phd.1 TIME: Fri Jan 16 09:01:10 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR7.g.ab1 878 0 0 agTttc*ctc ... TCATAAAACT ... xxxxxxxxxx
QA: 20 798 1 798
DS: CHROMAT_FILE: BL060-c1-LR7.g.ab1 PHD_FILE: BL060-c1-LR7.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR7.g.ab1 880 0 0 ggctaCGCCc ... ATTGAGTTTC ... tggcgttgcg
QA: 14 765 4 765
DS: CHROMAT_FILE: BL060-LR7.g.ab1 PHD_FILE: BL060-LR7.g.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060c5-LR5.g.ab1 871 0 0 ggtTCGATTA ... ACCAATTGAC ... ACCACCCatt
QA: 12 767 1 871
DS: CHROMAT_FILE: BL060c5-LR5.g.ab1 PHD_FILE: BL060c5-LR5.g.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060c2-LR5.g.ab1 839 0 0 ggttcatatg ... TAAAATCAGT ... TCTTGCaata
QA: 11 757 10 835
DS: none
RT:
BL060c2-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR: none
RD: BL060c5-LR0R.b.ab1 855 0 0 cACTCGCGTA ... CTCGTAAAAT ... aacccctgca
QA: 94 835 1 847
DS: CHROMAT_FILE: BL060c5-LR0R.b.ab1 PHD_FILE: BL060c5-LR0R.b.ab1.phd.1 TIME: Wed Nov 12 08:16:30 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT:
BL060c5-LR0R.b.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR: none
RD: BL060c2-LR0R.b.ab1 852 0 0 cgCGTa*tTG ... GTAAAATATT ... Atccttgtag
QA: 33 831 1 852
DS: CHROMAT_FILE: BL060c2-LR0R.b.ab1 PHD_FILE: BL060c2-LR0R.b.ab1.phd.1 TIME: Wed Nov 12 08:16:29 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR:
BL060c2-LR0R.b.ab1 unaligned phrap 040217:110357
ok
Test to check that record parser parses each contig into a record. ... 
Input file: Ace/contig1.ace

--------------------
Contig no. 0 has 2 reads.
CO: Contig1 856 2 31 U
aatacgGGAT ... ACATCATCTG ... cATCTAGtac
[0, 0, 0, 0, 0, 0, 22, 23, 25, 28] ... [90, 90, 90, 90, 90, 90, 90, 90, 90, 90] ... [15, 22, 30, 24, 28, 22, 21, 15, 19, 0]
# AF: 2 ; # BS: 31
AF(1) BL060c3-LR0R.b.ab1 U 1 ; AF(-1) BL060c3-LR0R.b.ab1 U 1 ;
BS(15) BL060c3-LR5.g.ab1 434 438 ; BS(-1) BL060c3-LR0R.b.ab1 823 856 ;
CT: none
WA: none
RD: BL060c3-LR5.g.ab1 868 0 0 tagcgaggaa ... CCGAGGCCAA ... gaaccatcag
QA: 80 853 22 856
DS: none
RT:
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 590 607 040217:110357
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR:
BL060c3-LR5.g.ab1 unaligned phrap 040217:110357
RD: BL060c3-LR0R.b.ab1 856 0 0 aatacgGGAT ... ACATCATCTG ... cATCTAGtac
QA: 7 778 1 856
DS: none
RT: none
WR: none

--------------------
Contig no. 1 has 14 reads.
CO: Contig2 3296 14 214 U
cacggatgat ... TTTGAATATT ... Atccttgtag
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ... [90, 90, 90, 90, 90, 90, 90, 90, 90, 90] ... [24, 0, 0, 0, 0, 0, 0, 0, 0, 0]
# AF: 14 ; # BS: 214
AF(7) BL060-LR3R.b.ab1 C 1601 ; AF(-1) BL060c2-LR0R.b.ab1 C 2445 ;
BS(107) BL060-c1-LR3R.b.ab1 2286 2292 ; BS(-1) BL060c2-LR0R.b.ab1 3236 3296 ;
CT:
Contig2 repeat phrap 42 43 123456:765432 ['This is the forst line of comment for c2', 'and this the second for c2']
unrelated_Contig repeat phrap 1142 143 122226:722232 ['This is the forst line of comment for the unrelated ct tag', 'and this the second']
Contig1 repeat phrap 52 53 555456:555432 ['This is the forst line of comment for c1', 'and this the second for c1']
WA:
phrap_params phrap 040203:114710 ['phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates', 'phrap version 0.990329']
RD: BL060-c1-LR12.g.ab1 862 0 0 cacggatgat ... GTTCTCGTTG ... CGTTTACCcg
QA: 81 842 1 862
DS: CHROMAT_FILE: BL060-c1-LR12.g.ab1 PHD_FILE: BL060-c1-LR12.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR11.g.ab1 880 0 0 ctttctgacC ... CTGTGGTTTC ... cggagttacg
QA: 11 807 8 880
DS: CHROMAT_FILE: BL060-c1-LR11.g.ab1 PHD_FILE: BL060-c1-LR11.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT:
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR: none
RD: BL060-c1-LR9.g.ab1 864 0 0 cacccaCTTT ... ACCAAACATT ... GGTAGCACgc
QA: 7 840 4 864
DS: CHROMAT_FILE: BL060-c1-LR9.g.ab1 PHD_FILE: BL060-c1-LR9.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR17R.b.ab1 863 0 0 ctaattggcc ... GGAACCTTTC ... CAACCTgact
QA: 63 857 1 861
DS: CHROMAT_FILE: BL060-c1-LR17R.b.ab1 PHD_FILE: BL060-c1-LR17R.b.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT:
BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR: none
RD: BL060-LR8.5.g.ab1 877 0 0 tgCTGCGGTT ... GGCAGTTTCA ... tactcataaa
QA: 13 729 1 877
DS: CHROMAT_FILE: BL060-LR8.5.g.ab1 PHD_FILE: BL060-LR8.5.g.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR3R.b.ab1 874 0 0 ctCTTAGGAT ... AACTCACATT ... *CACCCAAac
QA: 65 874 1 874
DS: CHROMAT_FILE: BL060-LR3R.b.ab1 PHD_FILE: BL060-LR3R.b.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR3R.b.ab1 864 0 0 CCaTGTCCAA ... AAGGGTT*CA ... ACACTCGCga
QA: 73 862 1 863
DS: CHROMAT_FILE: BL060-c1-LR3R.b.ab1 PHD_FILE: BL060-c1-LR3R.b.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR3R.b.ab1 857 0 0 agaaagagga ... nnnannnnnn ... gtctttgctc
QA: 548 847 442 854
DS: CHROMAT_FILE: BL060-LR3R.b.ab1 PHD_FILE: BL060-LR3R.b.ab1.phd.1 TIME: Fri Jan 16 09:01:10 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-c1-LR7.g.ab1 878 0 0 agTttc*ctc ... TCATAAAACT ... xxxxxxxxxx
QA: 20 798 1 798
DS: CHROMAT_FILE: BL060-c1-LR7.g.ab1 PHD_FILE: BL060-c1-LR7.g.ab1.phd.1 TIME: Tue Feb  3 11:01:16 2004 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060-LR7.g.ab1 880 0 0 ggctaCGCCc ... ATTGAGTTTC ... tggcgttgcg
QA: 14 765 4 765
DS: CHROMAT_FILE: BL060-LR7.g.ab1 PHD_FILE: BL060-LR7.g.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060c5-LR5.g.ab1 871 0 0 ggtTCGATTA ... ACCAATTGAC ... ACCACCCatt
QA: 12 767 1 871
DS: CHROMAT_FILE: BL060c5-LR5.g.ab1 PHD_FILE: BL060c5-LR5.g.ab1.phd.1 TIME: Fri Nov 14 09:46:03 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060c2-LR5.g.ab1 839 0 0 ggttcatatg ... TAAAATCAGT ... TCTTGCaata
QA: 11 757 10 835
DS: none
RT:
BL060c2-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR: none
RD: BL060c5-LR0R.b.ab1 855 0 0 cACTCGCGTA ... CTCGTAAAAT ... aacccctgca
QA: 94 835 1 847
DS: CHROMAT_FILE: BL060c5-LR0R.b.ab1 PHD_FILE: BL060c5-LR0R.b.ab1.phd.1 TIME: Wed Nov 12 08:16:30 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: BL060c2-LR0R.b.ab1 852 0 0 cgCGTa*tTG ... GTAAAATATT ... Atccttgtag
QA: 33 831 1 852
DS: CHROMAT_FILE: BL060c2-LR0R.b.ab1 PHD_FILE: BL060c2-LR0R.b.ab1.phd.1 TIME: Wed Nov 12 08:16:29 2003 CHEM: term DYE: big TEMPLATE:  DIRECTION: 
RT:
BL060c5-LR0R.b.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
WR:
BL060c2-LR0R.b.ab1 unaligned phrap 040217:110357
ok
Test to check that ACEParser can parse the whole file into one record. ... 
Input file: Ace/seq.cap.ace

Contigs: 1 ; Reads: 6
all WA: none

--------------------
Contig no. 0 has 6 reads.
CO: Contig1 1222 6 0 U
AGTTTTAGTT ... TGTGCGCGCA ... ATATCACATT
[61, 66, 67, 70, 71, 73, 73, 77, 77, 87] ... [97, 97, 97, 97, 97, 97, 97, 97, 97, 97] ... [56, 51, 49, 41, 38, 39, 45, 44, 49, 46]
# AF: 6 ; # BS: 0
AF(3) R5 C 320 ; AF(-1) R6 C 517 ;
BS: none
CT: none
WA: none
RD: R3 919 0 0 NNNNNNNNNN ... ATGTGCGCTC ... CAGCTCACCA
QA: 55 916 55 916
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R1 864 0 0 AGCCGGTACC ... GGGATGGCAC ... GGGCTGGGAG
QA: 12 863 12 863
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R2 1026 0 0 NNNNNNNNNN ... GGATGCCTGG ... GGTTGAGGCC
QA: 55 1000 55 1000
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R5 925 0 0 NNNNNNNNNN ... CCTCCCTACA ... GCCCCCGGNN
QA: 293 874 293 874
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R4 816 0 0 CACTCAGCTC ... TCCAAAGGGT ... AGCTGAATCG
QA: 1 799 1 799
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R6 857 0 0 CCGGCAGTGA ... AAAAAAAACC ... NNNNNNNNNN
QA: 24 706 24 706
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
ok
Test to check that record parser parses each contig into a record. ... 
Input file: Ace/seq.cap.ace

--------------------
Contig no. 0 has 6 reads.
CO: Contig1 1222 6 0 U
AGTTTTAGTT ... TGTGCGCGCA ... ATATCACATT
[61, 66, 67, 70, 71, 73, 73, 77, 77, 87] ... [97, 97, 97, 97, 97, 97, 97, 97, 97, 97] ... [56, 51, 49, 41, 38, 39, 45, 44, 49, 46]
# AF: 6 ; # BS: 0
AF(3) R5 C 320 ; AF(-1) R6 C 517 ;
BS: none
CT: none
WA: none
RD: R3 919 0 0 NNNNNNNNNN ... ATGTGCGCTC ... CAGCTCACCA
QA: 55 916 55 916
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R1 864 0 0 AGCCGGTACC ... GGGATGGCAC ... GGGCTGGGAG
QA: 12 863 12 863
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R2 1026 0 0 NNNNNNNNNN ... GGATGCCTGG ... GGTTGAGGCC
QA: 55 1000 55 1000
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R5 925 0 0 NNNNNNNNNN ... CCTCCCTACA ... GCCCCCGGNN
QA: 293 874 293 874
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R4 816 0 0 CACTCAGCTC ... TCCAAAGGGT ... AGCTGAATCG
QA: 1 799 1 799
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: R6 857 0 0 CCGGCAGTGA ... AAAAAAAACC ... NNNNNNNNNN
QA: 24 706 24 706
DS: CHROMAT_FILE:  PHD_FILE:  TIME:  CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
ok
Test to check that ACEParser can parse the whole file into one record. ... 
Input file: Ace/consed_sample.ace

Contigs: 1 ; Reads: 8
all WA:
phrap_params phrap 990621:161947 ['/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view', 'phrap version 0.990319']

--------------------
Contig no. 0 has 8 reads.
CO: Contig1 1475 8 156 U
agccccgggc ... CTTCCCCAGG ... gttgggtttg
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ... [90, 90, 90, 90, 90, 90, 90, 90, 89, 89] ... [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
# AF: 8 ; # BS: 156
AF(4) K26-291s U 828 ; AF(-1) K26-766c C 408 ;
BS(78) K26-394c 987 987 ; BS(-1) K26-822c 1303 1475 ;
CT:
Contig1 repeat consed 976 986 971218:180623 []
Contig1 comment consed 996 1007 971218:180623 ['This is line 1 of a comment', 'There may be any number of lines']
Contig1 oligo consed 963 987 971218:180623 ['standard.1 acataagacattctaaatttttact 50 U', 'seq from clone']
WA:
phrap_params phrap 990621:161947 ['/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view', 'phrap version 0.990319']
RD: K26-217c 563 0 0 tcccCgtgag ... CTCCTGcctg ... ggcccccctc
QA: 19 349 19 424
DS: CHROMAT_FILE: K26-217c PHD_FILE: K26-217c.phd.1 TIME: Thu Sep 12 15:42:38 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-526t 687 0 0 ccgtcctgag ... cacagcccT* ... Ttttgtttta
QA: 12 353 9 572
DS: CHROMAT_FILE: K26-526t PHD_FILE: K26-526t.phd.1 TIME: Thu Sep 12 15:42:33 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-961c 517 0 0 aatattaccg ... CAGATGGGTT ... ctattcaggg
QA: 20 415 26 514
DS: CHROMAT_FILE: K26-961c PHD_FILE: K26-961c.phd.1 TIME: Thu Sep 12 15:42:37 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-394c 628 0 0 ctgcgtatcg ... AGGATTGCTT ... aaccctgggt
QA: 18 368 11 502
DS: CHROMAT_FILE: K26-394c PHD_FILE: K26-394c.phd.1 TIME: Thu Sep 12 15:42:32 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-291s 556 0 0 gaggatcgct ... GTgcgaggat ... caggcagatg
QA: 11 373 11 476
DS: CHROMAT_FILE: K26-291s PHD_FILE: K26-291s.phd.1 TIME: Thu Sep 12 15:42:31 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-822c 593 0 0 ggggatccg* ... GCaAgacCCt ... gttgggtttg
QA: 25 333 16 593
DS: CHROMAT_FILE: K26-822c PHD_FILE: K26-822c.phd.1 TIME: Thu Sep 12 15:42:36 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-572c 594 0 0 agccccgggc ... ggatcACATA ... aatagtaaca
QA: 249 584 1 586
DS: CHROMAT_FILE: K26-572c PHD_FILE: K26-572c.phd.1 TIME: Thu Sep 12 15:42:34 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-766c 603 0 0 gaataattgg ... TggCCCATCT ... gaaccacacg
QA: 240 584 126 583
DS: CHROMAT_FILE: K26-766c PHD_FILE: K26-766c.phd.1 TIME: Thu Sep 12 15:42:35 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
ok
Test to check that record parser parses each contig into a record. ... 
Input file: Ace/consed_sample.ace

--------------------
Contig no. 0 has 8 reads.
CO: Contig1 1475 8 156 U
agccccgggc ... CTTCCCCAGG ... gttgggtttg
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ... [90, 90, 90, 90, 90, 90, 90, 90, 89, 89] ... [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
# AF: 8 ; # BS: 156
AF(4) K26-291s U 828 ; AF(-1) K26-766c C 408 ;
BS(78) K26-394c 987 987 ; BS(-1) K26-822c 1303 1475 ;
CT:
Contig1 repeat consed 976 986 971218:180623 []
Contig1 comment consed 996 1007 971218:180623 ['This is line 1 of a comment', 'There may be any number of lines']
Contig1 oligo consed 963 987 971218:180623 ['standard.1 acataagacattctaaatttttact 50 U', 'seq from clone']
WA:
phrap_params phrap 990621:161947 ['/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view', 'phrap version 0.990319']
RD: K26-217c 563 0 0 tcccCgtgag ... CTCCTGcctg ... ggcccccctc
QA: 19 349 19 424
DS: CHROMAT_FILE: K26-217c PHD_FILE: K26-217c.phd.1 TIME: Thu Sep 12 15:42:38 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-526t 687 0 0 ccgtcctgag ... cacagcccT* ... Ttttgtttta
QA: 12 353 9 572
DS: CHROMAT_FILE: K26-526t PHD_FILE: K26-526t.phd.1 TIME: Thu Sep 12 15:42:33 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-961c 517 0 0 aatattaccg ... CAGATGGGTT ... ctattcaggg
QA: 20 415 26 514
DS: CHROMAT_FILE: K26-961c PHD_FILE: K26-961c.phd.1 TIME: Thu Sep 12 15:42:37 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-394c 628 0 0 ctgcgtatcg ... AGGATTGCTT ... aaccctgggt
QA: 18 368 11 502
DS: CHROMAT_FILE: K26-394c PHD_FILE: K26-394c.phd.1 TIME: Thu Sep 12 15:42:32 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-291s 556 0 0 gaggatcgct ... GTgcgaggat ... caggcagatg
QA: 11 373 11 476
DS: CHROMAT_FILE: K26-291s PHD_FILE: K26-291s.phd.1 TIME: Thu Sep 12 15:42:31 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-822c 593 0 0 ggggatccg* ... GCaAgacCCt ... gttgggtttg
QA: 25 333 16 593
DS: CHROMAT_FILE: K26-822c PHD_FILE: K26-822c.phd.1 TIME: Thu Sep 12 15:42:36 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-572c 594 0 0 agccccgggc ... ggatcACATA ... aatagtaaca
QA: 249 584 1 586
DS: CHROMAT_FILE: K26-572c PHD_FILE: K26-572c.phd.1 TIME: Thu Sep 12 15:42:34 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
RD: K26-766c 603 0 0 gaataattgg ... TggCCCATCT ... gaaccacacg
QA: 240 584 126 583
DS: CHROMAT_FILE: K26-766c PHD_FILE: K26-766c.phd.1 TIME: Thu Sep 12 15:42:35 1996 CHEM:  DYE:  TEMPLATE:  DIRECTION: 
RT: none
WR: none
ok

----------------------------------------------------------------------
Ran 6 tests in 0.206s

OK
