BAM files with : in header

[pascalg]

Hi,

My BAM file has additional ":" in the header, so the script crashes, as exacltly 5 fields are expected.

File "breakmer.py", line 104, in r.run(tic) File "/home/pgellert/bin/BreaKmer-master/sv_processor.py", line 195, in run if not trgt.get_sv_reads() : File "/home/pgellert/bin/BreaKmer-master/sv_processor.py", line 471, in get_sv_reads self.clean_reads('norm') File "/home/pgellert/bin/BreaKmer-master/sv_processor.py", line 684, in clean_reads self.files['%s_cleaned_fq'%type], self.cleaned_read_recs[type], self.read_len = get_fastq_reads(self.files['%s_cleaned_fq'%type], self.sv_reads[type]) File "/home/pgellert/bin/BreaKmer-master/utils.py", line 372, in get_fastq_reads for header,seq,qual in FastqFile(fn) : File "/home/pgellert/bin/BreaKmer-master/utils.py", line 926, in next inst,lane,tile,x,y_end = header.split(':') ValueError: too many values to unpack

[ryanabo]

Thanks for sending me this! I will work on this fix. Can you send me a couple of lines in your BAM?

Ryan

On Thu, Jan 22, 2015 at 10:07 AM, Pascal notifications@github.com wrote:

Hi,

My BAM file has additional ":" in the header, so the script crashes, as exacltly 5 fields are expected.

File "breakmer.py", line 104, in r.run(tic) File "/home/pgellert/bin/BreaKmer-master/sv_processor.py", line 195, in run if not trgt.get_sv_reads() : File "/home/pgellert/bin/BreaKmer-master/sv_processor.py", line 471, in get_sv_reads self.clean_reads('norm') File "/home/pgellert/bin/BreaKmer-master/sv_processor.py", line 684, in clean_reads self.files['%s_cleaned_fq'%type], self.cleaned_read_recs[type], self.read_len = get_fastq_reads(self.files['%s_cleaned_fq'%type], self.sv_reads[type]) File "/home/pgellert/bin/BreaKmer-master/utils.py", line 372, in get_fastq_reads for header,seq,qual in FastqFile(fn) : File "/home/pgellert/bin/BreaKmer-master/utils.py", line 926, in next inst,lane,tile,x,y_end = header.split(':') ValueError: too many values to unpack

— Reply to this email directly or view it on GitHub https://github.com/a-bioinformatician/BreaKmer/issues/1.

[pascalg]

Thanks, Ryan. Here are some lines:

HWI-ST720:137778324:D22C0ACXX:6:1306:8503:19725 163 1 10008 0 100M = 10339 430 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC CCCFFFFFHHHHHJJJJJIIJJJJJJJJJJJJJJJJHIIJJJJJBHIIIIFHIIAEGGIFEHHHFFDCDEDCACDDDDAC<ABDC?A?<A3<?<ABC388 X0:i:331 MD:Z:100 PG:Z:MarkDuplicates.3 RG:Z:2892445281 XG:i:0 AM:i:0 NM:i:0 SM:i:0 XM:i:0 XO:i:0 XT:A:R HWI-ST720:137778324:D22C0ACXX:6:1215:7300:35023 65 1 10023 20 100M 18 78016187 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAA CCCFFFFFHHGHHJJJJJJJJJJJJJIJJJJJFIJJJJCHHIJJIJJJJIGIJJJJJIJJHHH@DDBDEEEEEDD5=AB@A5<BDDD(8AB39<ABD<A# X0:i:1 X1:i:2 XA:Z:12,-95581,100M,2;1,+10017,100M,2; MD:Z:86A13 PG:Z:MarkDuplicates.3 RG:Z:2892445281 XG:i:0 AM:i:20 NM:i:1 SM:i:20 XM:i:1 XO:i:0 XT:A:U HWI-ST720:137778324:D22C0ACXX:5:1204:3142:48450 69 1 10055 0 * = 10055 0 TTAGGGTTAGGGTGAGGGTTAGGGTGAGGGTGAGGGTTAGGGTGAGGGTGAGGGTTAGGGTGAGGGTGAGGGTTAGGGTGAGGGTGAGGGTTAGGGTTAG CCCFFFDDHHHHDFHHIJAFHHAHEBHGHG?F=FD=0?F@FG*<B@B7;F@EHEEEEEFF75;ABA;?AAA?55?595,8A?AB288?BB?A<?ABCBB< PG:Z:MarkDuplicates RG:Z:2892445465 HWI-ST720:137778324:D22C0ACXX:5:1204:3142:48450 137 1 10055 15 60M40S = 10055 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAAACCTAACCCTCACCCTACCCCTAAACCTAACCCTCACC @CCFFFEFHHDHFBHGGBFGEECFHHAGGG@CHDGGCEHIIGI>FD;CH)8@G(-=1AB######################################### X0:i:1 X1:i:6 XC:i:60 MD:Z:60 PG:Z:MarkDuplicates RG:Z:2892445465 XG:i:0 AM:i:0 NM:i:0 SM:i:15 XM:i:0 XO:i:0 XT:A:U HWI-ST720:137778324:D22C0ACXX:5:2207:11909:40241 73 1 10066 16 69M31S = 10066 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTCTAACCCTACCCCCCTAACCC @CCDFDDDHGHHGJJJJJJJIJJJIJIJJGIGGFHGIEGCAAG7?DH68BCEHCEG@EF/(.;@A62@################################ X0:i:1 X1:i:5 XC:i:69 MD:Z:54T14 PG:Z:MarkDuplicates RG:Z:2892445465 XG:i:0 AM:i:0 NM:i:1 SM:i:16 XM:i:1 XO:i:0 XT:A:U HWI-ST720:137778324:D22C0ACXX:5:2207:11909:40241 133 1 10066 0 74M26S = 10066 0 GTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGAGGGTTAGGGTTAGAGGGTTAGGGTTAGGGGGGTAGGGTTAGAGGGTTAGG @@@DDFFDHFHFHIGFHIGHGFEAGIJ?FFHHI9CAGHFD>BFHHB@=B48BF-=663@).623?DF5;=B@?########################### XC:i:74 PG:Z:MarkDuplicates RG:Z:2892445465 HWI-ST720:137778324:D22C0ACXX:6:2212:3000:37796 99 1 10188 9 47M53S = 10376 256 ACCCTAACCCGAACCCTAACCCTAACCCGAACCCTAACCCGAACCCCAAACCCCACCCCCCACCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCFFFFFHHHHHJJJJJJJJJIIIJJJHIJJJJJJIJJJ@EE8=D###################################################### X0:i:20 X1:i:0 XC:i:47 MD:Z:10T17T11T6 PG:Z:MarkDuplicates.3 RG:Z:2892445281 XG:i:0 AM:i:0 NM:i:3 SM:i:0 XM:i:3 XO:i:0 XT:A:R HWI-ST720:137778324:D22C0ACXX:5:1103:13566:13795 73 1 10267 0 18M1D55M27S = 10267 0 TAACCCTAACCCTAACCCAACCCCAACCCCAACCCCCACCCCAACCCCAACCCCAACCCTAACCCCTAACCCCAACCCCAACCCTAACCCTAACCCCAAA CCCFFFFFHHHHDGIIIIGHEHII1??DGH;)0?FH0;;@FF;@5;BH;?;?AC;5(9@(5?5<BB72<8?B############################ X0:i:2 X1:i:0 XA:Z:1,-249240340,55M1D18M,3; XC:i:73 MD:Z:18^T18A35T0 PG:Z:MarkDuplicates RG:Z:2892445465 XG:i:1 AM:i:0 NM:i:3 SM:i:0 XM:i:2 XO:i:1 XT:A:R HWI-ST720:137778324:D22C0ACXX:5:1103:13566:13795 133 1 10267 0 68M32S = 10267 0 GTTTAGGGTTTAGGGTTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTTAGGGGTTAGGGGTTAGGGTTGGGGTTGGGGTTAGGGTTGGGGGTTGGGGTG @@BFFFFFHHHHHIIAGHHGIJEHGHII?EDHII?D@@FGBGCHIFI;068@EG@8(=AED,'(;@?################################# XC:i:68 PG:Z:MarkDuplicates RG:Z:2892445465 HWI-ST720:137778324:D22C0ACXX:5:2308:17431:53297 117 1 10329 0 67M33S = 10329 0 GGGTTAGGGTTAGGGTTAGAGGGTTAGGGTTAGAGGGTTATGGTTAGAGGGTTAGGGTTAGAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGGTTA ##################################?:E??7)EHC@AC;@=88)B=>FDD?DEGBF@EGG@FA?88IHEADGIHIEIFHHHHGFFFFFCCC XC:i:67 PG:Z:MarkDuplicates RG:Z:2892445465

[ryanabo]

This issue has been resolved in the latest release v0.0.2.