Created
March 20, 2011 15:47
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Use filo's "groupBy" to create cDNA of transcripts.
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| ################################################################### | |
| # Assume we have a file of BED exons for every gene and transcript. | |
| # The exons are listed in genomic order for each gene/transcipt | |
| ################################################################### | |
| $ head -n 5 exons.bed | |
| chr1 1337462 1337636 MRPL20 exon1 - | |
| chr1 1340996 1341266 MRPL20 exon2 - | |
| chr1 1341188 1341266 MRPL20 exon3 - | |
| chr1 1342288 1342399 MRPL20 exon4 - | |
| chr1 1342510 1342597 MRPL20 exon5 - | |
| ####################################################################### | |
| # We can use BEDTools' fastaFromBed to grab the relevant sequence | |
| # for each exon and place the sequence on a single, tab separated line. | |
| # | |
| # I've truncated the sequences for email clarity... | |
| ####################################################################### | |
| $ fastaFromBed -tab -name -fi hg19.fa -bed exons.bed -fo exons.tab.fa -s | |
| MRPL20 TGCCAGGTGGAGCTCAACAGGAAAGTCCTAGCGGATCTGGCCATCTACGAGCC... | |
| MRPL20 CTCTGGATTAATCGAATTACAGCTGCTAGCCAGGAACATGGACTGAAGTATCCA... | |
| MRPL20 CTCTGGATTAATCGAATTACAGCTGCTAGCCAGGAACATGGACTGAAGTATCCA... | |
| MRPL20 CACTTCCGGGGAAGGAAAAATCGCTGCTACAGGTTGGCGGTCAGAACCGTGAT... | |
| MRPL20 ATGGTCTTCCTCACCGCGCAGCTCTGGCTGCGGAATCGCGTCACCGACCGCTA... | |
| ####################################################################### | |
| # Now we use filo's groupBy to concatenate the exon sequences into a | |
| # single transcript. | |
| ####################################################################### | |
| # In this case, | |
| $ groupBy -i exons.tab.fa -g 1 -o concat -c 2 | |
| MRPL20 TGCCAGGTGGAGCTCAACAGGAAAGTCCTAGCGGATCTGGCCATCTACGAGCCTCTGGATTAATCGAATTACAGCTGCTAGCCAGGAACATGGACTGAAGTATCCACTCTGGATTAATCGAATTA... | |
| ####################################################################### | |
| # We can do all of this in a single command. | |
| ####################################################################### | |
| $ fastaFromBed -tab -name -s -fi hg19.fa -bed exons.bed -fo stdout \ | |
| groupBy -i exons.tab.fa -g 1 -o concat -c 2 | |
| MRPL20 TGCCAGGTGGAGCTCAACAGGAAAGTCCTAGCGGATCTGGCCATCTACGAGCCTCTGGATTAATCGAATTACAGCTGCTAGCCAGGAACATGGACTGAAGTATCCACTCTGGATTAATCGAATTA... |
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