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Appending information from 2nd file into 1st based on intervals

 


Diya123
New User

Apr 11, 2013, 4:34 PM

Post #1 of 2 (1337 views)
Appending information from 2nd file into 1st based on intervals Can't Post
To describe it in detail file 2 each row is a gene. Most genes have one 5UTR start one 5UTR stop one 3UTR start and one 3UTR stop. It can have n number of exons each with a start and a stop and n-1 introns each with intron start and intron stop

Attached is the image

So one gene can have trailing commas for exons and introns but not for UTR’s.

If position (4th column) of file 1, falls between a 5UTRstart and 5UTRstop then add a additional column in file 1 for each row and append it with 5UTR_intron
If position (4th column) of file 1, falls between a 5UTRstart and 5UTRstop and also in an exon start and stop then for that row append with 5UTR_exon
If position falls between a exon start and stop then name the row as Exon
If position falls between a intron start and stop then name it as Intron
If position (4th column) of file 1, falls between a 3UTRstart and 3UTRstop then add a additional column in file 1 for each row and append it with 3UTR_intron
If position (4th column) of file 1, falls between a 3UTRstart and 3UTRstop and also in an exon start and stop then for that row append with 3UTR_exon
If position falls in the exons of 2 genes then name it as ambiguos
If position does not fall in any above category then name it as intergenic

Column 13: Exon starts
Column 14: Exon stops
Column 15: 5UTR start
Column 16: 5UTR stop
Column 17: 3UTR start
Column 18: 3UTR stop
Column 19: Intron start
Column 20: Intron stop

Note: Some genes do not have UTR’s and some does not have any introns

File 2( 10 million rows)



<c>HWUSI-EAS000_29:2:112:15026:1079#0/1 + chr21 9827004

HWUSI-EAS000_29:2:112:1096:1083#0/1 + chr21 46529599

HWUSI-EAS000_29:2:112:6116:1092#0/1 + chr21 9827328

HWUSI-EAS000_29:2:112:7436:1103#0/1 - chr21 38597405

HWUSI-EAS000_29:2:112:3168:1114#0/1 - chr21 44836222

HWUSI-EAS000_29:2:112:12481:1110#0/1 + chr21 45089410

HWUSI-EAS000_29:2:112:16829:1109#0/1 - chr21 11087783

HWUSI-EAS000_29:2:112:6005:1121#0/1 + chr21 11180428

HWUSI-EAS000_29:2:112:12016:1128#0/1 - chr21 38187834

HWUSI-EAS000_29:2:112:4252:1140#0/1 + chr21 46534847

HWUSI-EAS000_29:2:112:14645:1133#0/1 + chr21 46493472

HWUSI-EAS000_29:2:112:16002:1130#0/1 - chr21 47700601

HWUSI-EAS000_29:2:112:13823:1144#0/1 - chr21 46189143

HWUSI-EAS000_29:2:112:16154:1152#0/1 + chr21 9827328

HWUSI-EAS000_29:2:112:9792:1159#0/1 + chr21 9827404

HWUSI-EAS000_29:2:112:1333:1168#0/1 - chr21 46269533

HWUSI-EAS000_29:2:112:6703:1175#0/1 + chr21 46517134</c>



file 1( gene position file)

Code
hg19.knownCanonical.chrom    Condition_testing    hg19.knownCanonical.chromStart    hg19.knownCanonical.chromEnd    hg19.knownCanonical.transcript    hg19.knownGene.name    hg19.knownGene.chrom    hg19.knownGene.strand    hg19.knownGene.txStart    hg19.knownGene.txEnd    hg19.knownGene.cdsStart    hg19.knownGene.cdsEnd    hg19.knownGene.exonCount    hg19.knownGene.exonStarts    hg19.knownGene.exonEnds    5'UTR_start    5'UTR_stop    3'UTR_start    3'UTR_stop    intron_stop    intron_start  
 
chr1    1    367658    368597    uc010nxu.2    uc010nxu.2    chr1    +    367658    368597    367658    368597    1    367658,    368597,    NA    NA    NA    NA          
 
chr1    1    1266725    1269844    uc010nyk.2    uc010nyk.2    chr1    +    1266725    1269844    1266725    1269844    6    1266725,1267017,1267403,1268300,1268638,1268885,    1266916,1267318,1268186,1268504,1268759,1269844,    NA    NA    NA    NA    1267016,1267402,1268299,1268637,1268884      
 
chr1    0    229761980    229795946    uc001hts.1    uc001hts.1    chr1    +    229761980    229795946    229763380    229795044    10    229761980,229763367,229768015,229770663,229779279,229781605,229783256,229786981,229789995,229794846,    229762103,229763506,229768192,229773994,229779440,229781716,229783499,229787069,229790135,229795946,    229761981    229763379    229795045    229795945    229763366,229768014,229770662,229779278,229781604,229783255,229786980,229789994,229794845      
 
chr1    0    206940947    206945839    uc001hen.1    uc001hen.1    chr1    -    206940947    206945839    206941980    206945780    5    206940947,206943173,206944251,206944700,206945615,    206942073,206943239,206944404,206944760,206945839,    206945838    206945781    206941979    206940948    206943172,206944250,206944699,206945614      
 
chr21    0    43731776    43735706    uc002zav.3    uc002zav.3    chr21    -    43731776    43735706    43732365    43735526    3    43731776,43733594,43735402,    43732379,43733741,43735706,    43735705    43735527    43732364    43731777    43733593,43735401      
 
chr21    0    43766466    43771208    uc002zaw.3    uc002zaw.3    chr21    -    43766466    43771208    43766641    43771066    4    43766466,43767594,43769989,43770987,    43766655,43767741,43770139,43771208,    43771207    43771067    43766640    43766467    43767593,43769988,43770986



output:

Code
HWUSI-EAS000_29:2:112:1096:1083#0/1    +    chr21    46529599 Exon  
 
HWUSI-EAS000_29:2:112:6116:1092#0/1    +    chr21    9827328 3'UTR  
 
HWUSI-EAS000_29:2:112:7436:1103#0/1    -    chr21    38597405 5'UTR_Intron  
 
HWUSI-EAS000_29:2:112:3168:1114#0/1    -    chr21    44836222 intergenic



The appended value in my output is just for reference..



#Note: Also the chr numbers should match in 2 files..Example if the 1st row in file2 coresponds to chr21 then we need to look only for the positions for chr21 in file 1



Thanks,


Kenosis
User

Apr 11, 2013, 6:14 PM

Post #2 of 2 (1331 views)
Re: [Diya123] Appending information from 2nd file into 1st based on intervals [In reply to] Can't Post
Did you have a question? Do you have code to share that's giving you problems?


(This post was edited by Kenosis on Apr 16, 2013, 3:16 PM)

 
 


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