bioSyntax: Syntax Highlighting For
Computational Biology
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Aliations:
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Correspondence
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(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
Abstract:
/)96(()6=(H#
8:-=6>@0/",85(>,=
=6=(6)-=6(#bioSyntax
6)GII>-#=%=-666)&=vim,
geditSublime(less,B66())(B&B6
6(J#
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
Background:
C)=)6%%6((
)6=(H:=(>,14>,K14
==",14%=0/1!4)(=85
1'+4(9)>@1D461L4#*6
))6(6H=
6M()-(6(
(()=9(=(B)#
>-666(()%6)=-HB6B:
(H(666))==(=
(N)=&B((#A
(%)(=6((OD1O4(.PPOLE1E4-
666B96)#>-666(
&)==))()-6
)%)614#
)6=6(:(B:(-6)%M
()(1QO4#B%6))9-:
())(((9&)-
()#
,6C%= bioSyntax)%66(=H(:
=66(-666(
B&B6B:%(H#bioSyntax)(=6-
(Vim(GVimgedit(6-(6GTKSourceView
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
(Sublime-Text-3 B6(:))less#
((bioSyntax =)B66-666
(HH()(6=((HH=#
Results:
Syntax Highlighting for Computational Biology File Formats
bioSyntaxM>,>,K/.?>,.5",85>@(0/
=6-((less#?)bioSyntax
MH:-(-666
6(H#
,6H=-666())66(
>))()6(=
%6):-/7"3#6H:=
&B(&H(#$(((
666(B6(B=(9()
)6#5H(68359
))((#
,6%=666(()%
H=>)),#(&:%(=
(5",>@(0/%==B66
>@=)%-)(&:5",B=6
=6=6H(B6)(>@H>))#
?bioSyntax6)))6((
%)666666)-666#*66(
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
(6%()6)B(%B()
(=6())%(
)1E4#,6)-H6>@B668/3:
()(=&)((())-(6
(=(#
bioSyntax nucleotide representation
bioSyntax)%(6=6)7?8/
14&6:B66((==H%
#,6=)666((%
-))#6(
()((6$B6#,6:
%(66"/(B&,B(
)%B=%))-=9"/:
/#((66::6%(%
)(:(>))#
The bioSyntax repository
,6=(HH:=B66B(H=
-666#,==(%)=-(HH
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6=H-666(:(
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6:=H:=9&(%)(6B-(H
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
Conclusions:
bioSyntaxB6%((%H6
-==(-(#,6:==
6=((6)(()=(
%B6)&B((6H:=#6>-
)%6=((6)6&
6(#
Methods:
Availability and Use
bioSyntax=%6)GII>-#=vim .-@A>
*(Bless.-@A>gedit.-@A>*(B(sublime-text-3
.-@A>*(B("$?"8.%#E#>(
%6)GIIBBB#6#I>-I>-#
bioSyntax =less()(6source-highlight )&#gedit -
666bioSyntaxB(%)(=69GTKSourceView3#
66=>,>,K/.?>,.5",850/(>@H
((H-(B6-:
(=HB6:((H:-#7gedit, sublime (vim, a(
>,H(/.?>,.14,1!4F))14
()61!46#
.()(())((less6(GRsam-
lessRRvcf-lessRS#-)Rsamtools view -h NA12878.bam |
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
sam-less - RRgzip -dc gencode.v26.gtf.gz | grep ‘MYC’ - | gtf-less -x
10 - R#
File Speci)cations
>-=-:666(HHB66
6%)(=-)#
*6%-:H((=NJH
)H>@%#'6)GII#6#I6:)I>@%#)(= ),0/%!#
6)GII#6#I6:)I0/%!##)(= )85%#E=)GII=)#BB)(#I
)I)(I(I =T() IT%T.#)(= ),5+
6)GII##(IKIK=#6 ), ",%#6)GII#B#(I
",#6 ),-)H=($/7$(I81'4>9
3(6%1+4(>$81D43=>91L43/>1'4(?/>/"B1D4N
)%(EEE)C1O4$/A51E4N(
(()=(=Bsamtools[7]GATK[31]bowtie2[32]
cu/inks[33](Clustalx[23]#
List of Abbreviations:
",G",=
7?8/G7?=8())(/6
85G85
>@G>9@)
0/G0/
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
Figure Legends
Figure 1:
>-666=9)#H=#A) ,
6=6`less HG00128_hgr1.sam`(##B6
>-#3(=66((()(
(N)=)###)%#
6(:B(%(9(##/7"3
)666(666(#B)
(%B=6((835:=E(#=(#=
-666#?(==6(%
%68/3:()&B()9((
B(#835#
Figure 2:
bioSyntax(6#A) ,6=)(B
)=#7?8/6(
6=6))--(#,(!:(
:(@/( ",(&#B)
)=(:66#C) >-
B=))-=9"/:6BB66"/
66,))#
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
Supplementary Figure and Table Legends
Supplementary Figure 1:
>6=bioSyntax NA) gedit=6(9>,(
>,B6/.?>,.6(>,KH(NB) sublime-text-3 =85
H#
Supplementary Figure 2:
>6=bioSyntaxN A) vim=66(>$86L(:'E0/H
(NB) less=6"(%+",(C) -)>@H#76
",=6B&(=UT(VU)T(VU/5>V(
U?,3V)6(6):()=:()#
Supplementary Figure 3:
,6(((66:>-=7?8/((6
(==(:(#(6%6
((6B=B6:(#,6%66:
66%(B%66%#
Supplementary Table 1:
(H((H=6(=>-6
6-(gedit, sublime, gvimvim(L:$>7)6less
#
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
References:
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(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
Author Contributions:
%(((6(I(%)=bioSyntax#6(
(()#6B(())%(6H)#
Acknowledgements:
bioSyntaxB(6hackseq176)GIIBBB#6&9#
6&61!4#*B(&6&6M=6((&6
%6))())((%)#*<(&6&/68
/6=B&(%)-)=6>@=(
)6A<=66(%)66:)=
(#
Funding:
))(63@#&B6)@(36#"$
))(6?/75B6)B(#8B
=(()hackseq#$=((B`(6(%)=6
=BB=6)#
Ethics Approval:
$))#
Con&ict of Interests:
$((#
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adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
adapt this material for any purpose without crediting the original authors.
(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
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(which was not certified by peer review) in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or
The copyright holder has placed this preprintthis version posted December 20, 2017. ; https://doi.org/10.1101/235820doi: bioRxiv preprint
