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test_Ace
Test to check that ACEParser can parse the whole file into one record. ...
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. ...
--------------------
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
----------------------------------------------------------------------
Ran 2 tests in 0.241s
OK
|
