DANPOS3 does not work with paired end bam file or bed file

[Bn Li]

Hi 

DANPOS is really a great tool, but it does not work with paired-end bam file on my computer, it would be great if someone could help me to figure out the reason and make it work on the computer

1 seems it does not even parse the bam file

danpos 3.0.0  version

command:

python /Users/git/DANPOS3/danpos.py dpos -m 1 Input_WT_t2_rep1_S7.bam

 Namespace(bg=None, clonalcut=0, command='dpos', count=None, distance=100, edge=0, exclude_high_percent=0, exclude_low_percent=0, extend=80, fdr=1, fs=None, gapfill=0, height=5, lmd=300, mafrsz=300, mifrsz=50, name='result', nonzero=0, nor='F', nor_region_file=None, paired=1, path='Input_WT_t2_rep1_S7.bam', pheight='0', position_reference=None, ratio=0.9, save=0, separator1=None, smooth_width=20, span=10, testcut='0', width=40)

rd 100 , step 10  fcut, 55.843532999999994

parsing from bam file Input_WT_t2_rep1_S7.bam ...

parsing finished, 0 reads parsed

Traceback (most recent call last):

  File "/Users/git/DANPOS3/danpos.py", line 1365, in <module>

    if sys.argv[1]=='dpos':runDANPOS(command='dpos')

  File "/Users/git/DANPOS3/danpos.py", line 424, in runDANPOS

    pcfer=0)#args.pcfer)#0)

  File "/Users/git/DANPOS3/functions.py", line 88, in danpos

    step=step,extend=extend,mifrsz=mifrsz,mafrsz=mafrsz,paired=paired,starttime=starttime)

  File "/Users/git/DANPOS3/functions.py", line 945, in loadinput

    rd=reads(path,step=step,paired=paired,cut=cut,format='bam')

  File "/Users/git/DANPOS3/reads.py", line 34, in __init__

    elif file!="" and format=='bam' and paired:self.loadBamPaired(file=file,step=self.step,cut=cut)

  File "/Users/git/DANPOS3/reads.py", line 701, in loadBamPaired

    maxv,lths=max(fragsizes.values()),list(fragsizes.keys())

ValueError: max() arg is an empty sequence

For input samtools view Input_WT_t2_rep1_S7.bam | head

NB501365:432:HF2GMBGXC:4:13603:21629:4490 163 I 66 255 38M = 158 131 TAACACTACCCTAACACAGCCCTAATCTAACCCTGGCC AAAAAEEEEEEEA/EAEEEEEEEEEEEEEAE/EEEEEE AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:-9 YT:Z:CP

NB501365:447:HWFNWAFXY:2:21203:15993:6632 163 I 66 255 70M = 154 163 TAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCT AAAAAAEE/EEEEEEEEAEEE<EEEEEE/EEAEEEEEEEEEEE<EEEEEEEEEA/EE/EEE<EEEEA/<A AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YS:i:0 YT:Z:CP

NB501365:432:HF2GMBGXC:4:22409:7409:10060 163 I 67 255 38M = 191 162 AACACTACCCTAACACAGCCCTAATCTAACCCTGGCCA AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP

NB501365:447:HWFNWAFXY:1:21205:7605:12019 163 I 67 255 58M = 145 153 AACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACAC AAA/AEEEEE/EEEEEAEAEAEEEEEEEEEAEEEEEEEEEEE/EE/EEEEEE/EE6/E AS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:56C1 YS:i:0 YT:Z:CP

NB501365:447:HWFNWAFXY:2:11106:9713:16322 99 I 68 38 76M = 145 152 ACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCAC AAAAAEEEEEEEEEEAAEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEE<EAEEAEEEEEE/< AS:i:0 XS:i:-43 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:0 YT:Z:CP

NB501365:447:HWFNWAFXY:4:21611:24177:4282 99 I 72 255 42M = 164 157 TACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTC AAAAAEEEEAEEEAE/<EE/E/EAE<E</EEEA<EEEAEE/< AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP

NB501365:432:HF2GMBGXC:1:11208:22653:6789 163 I 73 255 27M1D12M = 173 138 ACCCTAACACAGCCCTAATCTAACCCTTCCAACCTGTCT AAAAAEEEEEEEEEEEEEEEEE/EEAEEEEEEEEEAEEE AS:i:-13 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:27^G0G11 YS:i:-15 YT:Z:CP

NB501365:447:HWFNWAFXY:1:11301:3635:5652 99 I 77 255 76M = 145 144 TAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCC AAAAAEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEE<A AS:i:0 XS:i:-43 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:0 YT:Z:CP

NB501365:447:HWFNWAFXY:3:21503:20478:19324 163 I 77 255 76M = 154 152 TAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE<EAEEEEEAEEEAEEAEE/A AS:i:0 XS:i:-43 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:0 YT:Z:CP

NB501365:432:HF2GMBGXC:1:11107:3941:11025 163 I 78 255 38M = 191 151 AACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTC AAAAA/EEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEE AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP

2 does not work with paired-end bed files

danpos 3.0.0  version

command:

python /Users/bingnanli/git/DANPOS3/danpos.py dpos -m 1 Input_WT.sortname.bed

 Namespace(bg=None, clonalcut=0, command='dpos', count=None, distance=100, edge=0, exclude_high_percent=0, exclude_low_percent=0, extend=80, fdr=1, fs=None, gapfill=0, height=5, lmd=300, mafrsz=300, mifrsz=50, name='result', nonzero=0, nor='F', nor_region_file=None, paired=1, path='Input_WT.sortname.bed', pheight='0', position_reference=None, ratio=0.9, save=0, separator1=None, smooth_width=20, span=10, testcut='0', width=40)

rd 100 , step 10  fcut, 55.843532999999994

parsing from bed file Input_WT.sortname.bed ...

Traceback (most recent call last):

  File "/Users/git/DANPOS3/danpos.py", line 1365, in <module>

    if sys.argv[1]=='dpos':runDANPOS(command='dpos')

  File "/Users/git/DANPOS3/danpos.py", line 424, in runDANPOS

    pcfer=0)#args.pcfer)#0)

  File "/Users/git/DANPOS3/functions.py", line 88, in danpos

    step=step,extend=extend,mifrsz=mifrsz,mafrsz=mafrsz,paired=paired,starttime=starttime)

  File "/Users/git/DANPOS3/functions.py", line 925, in loadinput

    rd=reads(path,step=step,paired=paired,cut=cut,format='bed')

  File "/Users/git/DANPOS3/reads.py", line 32, in __init__

    if file!="" and format=='bed' and paired:self.loadBedPaired(file=file,step=self.step,cut=cut)

  File "/Users/git/DANPOS3/reads.py", line 425, in loadBedPaired

    chm,mid,fragsize=end1[0],int(functions.div((end1[1]+end2[2])),(2*step)),end2[2]-end1[1]

TypeError: div() missing 1 required positional argument: 'b'

For my input bed file : 

$ head Input_WT.sortname.bed

X 640808 640847 NB501365:432:HF2GMBGXC:1:11101:1058:10866/1 255 +

X 640894 640933 NB501365:432:HF2GMBGXC:1:11101:1058:10866/2 255 -

III 116211 116250 NB501365:432:HF2GMBGXC:1:11101:1071:9746/1 255 -

III 116125 116164 NB501365:432:HF2GMBGXC:1:11101:1071:9746/2 255 +

IX 391507 391545 NB501365:432:HF2GMBGXC:1:11101:1084:6386/1 1 -

IX 391428 391467 NB501365:432:HF2GMBGXC:1:11101:1084:6386/2 1 +

II 410453 410492 NB501365:432:HF2GMBGXC:1:11101:1101:11144/1 255 -

II 410320 410358 NB501365:432:HF2GMBGXC:1:11101:1101:11144/2 255 +

IV 439035 439074 NB501365:432:HF2GMBGXC:1:11101:1143:12567/1 255 -

IV 438928 438967 NB501365:432:HF2GMBGXC:1:11101:1143:12567/2 255 +

3 Session Info: 

Python version 3.7.6

numpy.version. '1.18.5'

samtools version 1.9

htslib version 1.9

R version 3.5.1

rpy2 version 3.3.3

[Sammy Klasfeld]

Thank you so much for reporting this error. Try pulling the repository again. I think I fixed the bug. Let me know if anything else comes up.

Sammy