manage 'NAME' column in BED, BEDPE and PAF, 'M' CIGAR operation, GitHub workflow, strandness #4
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AndreaGuarracino
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Now we can properly manage also minimap2's CIGAR strings: minimap2 scerevisiae7.fa.gz scerevisiae7.fa.gz -X -c -t 48 > mm2.paf
impg -p mm2.paf -r UWOPS034614#1#chrI:1000-2000 | head -n 5 | column -t
UWOPS034614#1#chrI 1000 2000
S288C#1#chrVIII 570385 569601
DBVPG6765#1#chrVI 5195 5981
DBVPG6765#1#chrI 210581 209798
UWOPS034614#1#chrI 213064 212060
impg -p mm2.paf -r UWOPS034614#1#chrI:1000-2000 -P | head -n 5 | column -t
UWOPS034614#1#chrI 214332 1000 2000 + UWOPS034614#1#chrI 214332 1000 2000 1000 1000 255 cg:Z:1000=
S288C#1#chrVIII 581049 570385 569601 - UWOPS034614#1#chrI 214332 1000 2000 775 1009 255 cg:Z:10M1I29M2I8M1D11M1D78M18D6M1D5M2D1M3D23M1D6M1D19M1D26M1D27M1D39M5D1M2D19M1D94M1I72M1I21M1I10M1D21M3I22M151D205M1D22M33D
DBVPG6765#1#chrVI 257436 5195 5981 + UWOPS034614#1#chrI 214332 1000 2000 777 1009 255 cg:Z:10M1I29M2I8M1D11M1D78M18D6M1D5M2D1M1D25M1D6M1D19M1D26M1D27M1D39M5D1M2D19M1D94M1I72M1I21M1I10M1D21M3I22M151D205M1D22M33D
DBVPG6765#1#chrI 215496 210581 209798 - UWOPS034614#1#chrI 214332 1000 2000 774 1009 255 cg:Z:10M1I29M2I8M1D11M1D78M18D6M1D5M6D23M1D6M1D19M1D26M1D27M1D39M5D1M2D19M1D94M1I72M1I21M1I10M1D21M3I22M151D205M1D22M33D
UWOPS034614#1#chrI 214332 213064 212060 - UWOPS034614#1#chrI 214332 1000 2000 1000 1004 255 cg:Z:171M4I829M
# --eqx to write =/X CIGAR operators
minimap2 scerevisiae7.fa.gz scerevisiae7.fa.gz -X -c -t 48 --eqx > mm2.eqx.paf
impg -p mm2.eqx.paf -r UWOPS034614#1#chrI:1000-2000 | head -n 5 | column -t
UWOPS034614#1#chrI 1000 2000
S288C#1#chrVIII 570385 569601
DBVPG6765#1#chrVI 5195 5981
DBVPG6765#1#chrI 210581 209798
UWOPS034614#1#chrI 213064 212060
impg -p mm2.eqx.paf -r UWOPS034614#1#chrI:1000-2000 -P | head -n 5 | column -t
UWOPS034614#1#chrI 214332 1000 2000 + UWOPS034614#1#chrI 214332 1000 2000 1000 1000 255 cg:Z:1000=
S288C#1#chrVIII 581049 570385 569601 - UWOPS034614#1#chrI 214332 1000 2000 665 1009 255 cg:Z:10=1I24=1X4=2I2=1X5=1D3=1X1=1X5=1D3=2X10=1X29=1X4=1X1=2X9=2X13=18D6=1D5=2D1=3D19=2X2=1D6=1D1X16=1X1=1D10=1X12=2X1=1D1=1X2=2X3=1X17=1D15=1X18=1X1=1X2=5D1=2D4=1X1=1X3=1X1=1X1=1X4=1D1X5=1X1=1X7=1X5=1X2=1X6=1X4=1X15=1X4=3X7=1X1=1X1=2X10=1X1=1X1=1X1=1X3=1I13=1X5=1X2=3X3=1X1=1X1=1X2=1X4=1X1=1X2=1X12=1X7=1X5=1I1X1=1X3=1X4=2X2=1X3=1X1=1I10=1D4=1X4=1X2=1X8=3I16=1X5=151D17=2X7=1X23=1X5=1X14=1X20=1X2=1X2=2X4=1X5=1X12=1X4=1X5=2X4=1X3=1X1=1X1=2X2=1X1=1X3=1X2=1X11=1X2=1X8=1X3=1X4=1X4=2X4=1D17=1X4=33D
DBVPG6765#1#chrVI 257436 5195 5981 + UWOPS034614#1#chrI 214332 1000 2000 667 1009 255 cg:Z:10=1I24=1X4=2I2=1X5=1D3=1X1=1X5=1D3=2X10=1X29=1X4=1X1=2X9=2X13=18D6=1D5=2D1=1D21=2X2=1D6=1D1X16=1X1=1D10=1X12=2X1=1D1=1X2=2X3=1X17=1D15=1X18=1X1=1X2=5D1=2D4=1X1=1X3=1X1=1X1=1X4=1D1X5=1X1=1X7=1X5=1X2=1X6=1X4=1X15=1X4=3X7=1X1=1X1=2X10=1X1=1X1=1X1=1X3=1I13=1X5=1X2=3X3=1X1=1X1=1X2=1X4=1X1=1X2=1X12=1X7=1X5=1I1X1=1X3=1X4=2X2=1X3=1X1=1I10=1D4=1X4=1X2=1X8=3I16=1X5=151D17=2X7=1X23=1X5=1X14=1X20=1X2=1X2=2X4=1X5=1X12=1X4=1X5=2X4=1X3=1X1=1X1=2X2=1X1=1X3=1X2=1X11=1X2=1X8=1X3=1X4=1X4=2X4=1D17=1X4=33D
DBVPG6765#1#chrI 215496 210581 209798 - UWOPS034614#1#chrI 214332 1000 2000 664 1009 255 cg:Z:10=1I24=1X4=2I2=1X5=1D3=1X1=1X5=1D3=2X10=1X29=1X4=1X1=2X9=2X13=18D6=1D5=6D19=2X2=1D6=1D1X16=1X1=1D10=1X12=2X1=1D1=1X2=2X3=1X17=1D15=1X18=1X1=1X2=5D1=2D4=1X1=1X3=1X1=1X1=1X4=1D1X5=1X1=1X7=1X5=1X2=1X6=1X4=1X15=1X4=3X7=1X1=1X1=2X10=1X1=1X1=1X1=1X3=1I13=1X5=1X2=3X3=1X1=1X1=1X2=1X4=1X1=1X2=1X12=1X7=1X5=1I1X1=1X3=1X4=2X2=1X3=1X1=1I10=1D4=1X4=1X2=1X8=3I16=1X5=151D17=2X7=1X23=1X5=1X14=1X20=1X2=1X2=2X4=1X5=1X12=1X4=1X5=2X4=1X3=1X1=1X1=2X2=1X1=1X3=1X2=1X11=1X2=1X8=1X3=1X4=1X4=2X4=1D17=1X4=33D
UWOPS034614#1#chrI 214332 213064 212060 - UWOPS034614#1#chrI 214332 1000 2000 1000 1004 255 cg:Z:171=4I829= |
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Now we properly manage the strandness too for all output formats: impg -p input.paf -r UWOPS034614#1#chrI:1000-2000 | head -n 5 | column -t
UWOPS034614#1#chrI 1000 2000 . +
S288C#1#chrVIII 569601 570385 . -
DBVPG6765#1#chrVI 5195 5981 . +
DBVPG6765#1#chrI 209798 210581 . -
UWOPS034614#1#chrI 212060 213064 . -
impg -p input.paf -b x.bed | head -n 5 | column -t
S288C#1#chrXII 1000 100000 S288C#1#chrXII 1000 100000 annotation1 0 + +
S288C#1#chrIII 3 878 S288C#1#chrXII 1000 100000 annotation1 0 + +
S288C#1#chrV 19 6566 S288C#1#chrXII 1000 100000 annotation1 0 + +
DBVPG6044#1#chrX 725146 726056 S288C#1#chrXII 1000 100000 annotation1 0 - +
DBVPG6765#1#chrXVI 948 5546 S288C#1#chrXII 1000 100000 annotation1 0 + +
impg -p input.paf -b x.bed -P | head -n 5 | column -t
S288C#1#chrXII 1075542 1000 100000 + S288C#1#chrXII 1075542 1000 100000 99000 99000 255 cg:Z:99000= an:Z:annotation1
S288C#1#chrIII 341580 3 878 + S288C#1#chrXII 1075542 1000 100000 809 882 255 cg:Z:7=2D11=1X2=1I27=4I7=2X3=1X4=2X5=1X1=1D5=1X2=1X8=1I1=2X5=1X4=1X3=1X3=1X78=3I6=1X2=1I30=1X5=1X35=1X130=1X5=2X1=1X4=1X26=1D18=1X3=1X78=1X19=1X5=1X1=1X43=1X46=1X36=1X8=1X15=1X21=1D4=1I2=1I2=1D6=2X2=2X1=1X7=1X1=1X1=1X1=1X3=1D1X4=4X2=1X5=1X30=1X1=1X1=1X23= an:Z:annotation1
S288C#1#chrV 583092 19 6566 + S288C#1#chrXII 1075542 1000 100000 5158 6656 255 cg:Z:10=2D15=1I20=1D9=1I3=1X3=1X2=1X2=1I7=1X18=1X26=3I19=1X3=1X15=1X5=1X12=3I2=7I390=1X6=1X42=1X45=1X50=1X49=1X24=1X168=1X10=1X217=1X16=1X10=1X106=1X37=1X46=1X272=1X35=1I1=35I3=1X5=1X34=1X7=1X28=36I7=1X9=1X12=1X26=1X4=1X3=1X4=1X3=2X6=1X2=3X28=1X16=1X35=1X102=96I66=1X29=1X199=1X201=1X7=1X39=1X110=1X60=1X126=1X59=1X249=1X231=1X63=1X56=1X8=1X1=1X109=484I46=31I12=1X16=24I4=1X19=1X4=32I17=14I8=1X47=522I1=1X8=1X138=15D1=1D18=16D2=1X19=1X43=1X47=1X145=1X2=1X1=2D3=11D1=4D61=1X26=1X5=1X349=5D12=1X22=11D6=2D4=1X3=2D2=9D31=10I33=1I140=1X14=1X11=27D28=1X53=1X39=1X11=1X3=1D14=1X13=1X14=1X20= an:Z:annotation1
DBVPG6044#1#chrX 728645 725146 726056 - S288C#1#chrXII 1075542 1000 100000 624 977 255 cg:Z:36=1X3=1X11=1X15=1X48=1X9=1X1=1X5=9D1=1D1=1X2=3D1=2X1=2X3=2X2=2I1=3X4=6I1=1X3=1X1=4I3=1X5=2D1=1D1=2X1=2D1=1I3=1I1=1X2=3I2=2X2=1X2=1X1=1X3=1I1=1X2=1X1=2X1=3I3=1X1=2I1=2I1=1X1=2I2=1D2=2X4=1X2=1D3=2I2=1X1=3X3=1D1=2I1X3=2D3=2X1=1X1=1X2=1I1=1I4=1I3=3X3=1X1=1X3=2D2=1X1=5D2=1X1=1X1=1X3=1I1X2=1X3=3D2=1D1X3=4I4=1X2=6I2=7I4=1I2=3I1=1I3=4I3=7I3=1X1=1I2X2=1X1=3I1X7=2X2=3D2X2=1I2=1X1=1X1=2I1X2=1X4=7I4=1X3=2X4=1D1=2I6=6I1X3=1X2=1I1=1X1=2I1=2X1=1D4=3I2=1I2=2X3=1I3=2X2=2D1=2X3=1I2=2X2=6X2=1X1=1I3=1X2=3D1=1X3=1I1=3I1=2I2=5I3=7I1=1I2=1X5=1X1=5I4=1X1=1I1=1X7=1X1=1D1=5D5=2X1=1X4=1X2=1X2=5D2=1D3=1X2=5D2=2X3=2I1=1X3=2X1=4I2=1X1=1X2=1I3=4D3=1I2=1X1=1I2=1X2=4I3=2X1=1X1=1X1=4I2=1X104=15I8=1D1=1D1X2=1X1=1I1X2=1X5=1X26=1X21= an:Z:annotation1
DBVPG6765#1#chrXVI 920208 948 5546 + S288C#1#chrXII 1075542 1000 100000 4550 4711 255 cg:Z:529=1X109=1X102=1X35=1X3=1X5=1X9=108D4=1X15=1X5=1X6=1X9=1X35=1X12=1X5=1X8=1X6=1X254=1X261=1X629=1X283=1X232=1X75=1X324=1X36=1X146=1X128=1I182=1X40=1X355=5D12=1X31=1X13=1X11=1X35=10I11=1X21=1I202=1X127=1X16=1X28=1X201= an:Z:annotation1 |
AndreaGuarracino
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AndreaGuarracino
changed the title
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column -t x.bed S288C#1#chrXII 1000 100000 annotation1 S288C#1#chrXII 500000 900000 annotation2 S288C#1#chrXII 1000000 2000000 impg -p scerevisiae7.aln.paf -b x.bed | column -t S288C#1#chrXII 1000 100000 S288C#1#chrXII 1000 100000 annotation1 SK1#1#chrXII 15000 49816 S288C#1#chrXII 1000 100000 annotation1 UWOPS034614#1#chrXII 70000 92908 S288C#1#chrXII 1000 100000 annotation1 Y12#1#chrXII 90000 104447 S288C#1#chrXII 1000 100000 annotation1 S288C#1#chrXII 500000 900000 S288C#1#chrXII 500000 900000 annotation2 YPS128#1#chrXII 479121 500000 S288C#1#chrXII 500000 900000 annotation2 Y12#1#chrXII 483399 564848 S288C#1#chrXII 500000 900000 annotation2 UWOPS034614#1#chrXII 471803 854819 S288C#1#chrXII 500000 900000 annotation2 Y12#1#chrXII 585000 780000 S288C#1#chrXII 500000 900000 annotation2 YPS128#1#chrXII 590000 790000 S288C#1#chrXII 500000 900000 annotation2 SK1#1#chrXII 730000 865468 S288C#1#chrXII 500000 900000 annotation2 Y12#1#chrXII 860000 872245 S288C#1#chrXII 500000 900000 annotation2 S288C#1#chrXII 1000000 2000000 S288C#1#chrXII 1000000 2000000 UWOPS034614#1#chrXII 944197 1000000 S288C#1#chrXII 1000000 2000000 Y12#1#chrXII 980000 1029536 S288C#1#chrXII 1000000 2000000