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get fasta from gff with fasta block
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| # create fasta file from gff with fasta blocks using bedtools | |
| # see rationale at the end | |
| gffFile=$1; | |
| tmpid=tmp_${$} | |
| # make tmp dir | |
| mkdir $tmpid | |
| echo entering to tempdir: >&2 | |
| cd $tmpid | |
| echo $(pwd) >&2 | |
| # get fasta lines (The fasta directive is the last one in gff if present) | |
| perl -lane 'print if $fasta_line; if(/^##FASTA/){$fasta_line=1}' ../$gffFile > fasta_from_gff.fa; | |
| # get only gff files | |
| perl -lane 'if(/^##FASTA/){last};print' ../$gffFile > test.nofasta.gff; | |
| # generate de fasata from gff features | |
| bedtools getfasta -fi fasta_from_gff.fa -bed test.nofasta.gff -fullHeader -fo fasta_out.fa | |
| # put the final fasta in the initial dir and rename ass the gff file | |
| cp fasta_out.fa ../$gffFile.fa | |
| # return to initial dir | |
| cd .. | |
| # tmp dir is not deleted on pourpose, just in case I need it for debuging. It is easy to remove by hand wit 'rm -rf tmp_*' | |
| ############ | |
| # rationale: | |
| # bedtools does not work with gff with fasta blocks, you need to split in plain gff and fasta | |
| ############ | |
| # | |
| ############ | |
| # USAGE | |
| ############ | |
| # #script to print out fasta: | |
| # $ perl -lane 'print if $fasta_line; if(/^##FASTA/){$fasta_line=1}' test.gff > fasta_from_gff.fa; | |
| # | |
| # #scritp to print plain gff | |
| # $ perl -lane 'if(/^##FASTA/){last};print' test.gff > test.nofasta.gff; | |
| # | |
| # # get fasta | |
| # $ sh get_fasta_for_gff.sh test.gff | |
| # mving to tempdir | |
| # /Users/pmg/workspace/genomics/bedtools_tests/tmp_19560 | |
| # index file fasta_from_gff.fa.fai not found, generating... | |
| # |
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| ########### | |
| ## output | |
| ########### | |
| ## $ head test.gff.fa | |
| ## >ctg123:99-900 | |
| ## atctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaaaagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttataatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaatcttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattcgtatttgatttgggtttactatcgaataatgag | |
| ## aattttcaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttagaatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattccttctgggcgtacccgattctcggagaacttgccgcaccattccgccttgtgttcattgctgcctgcatg | |
| ## ttcattgtctacctcggctacgtgtggctatctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaaaagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttataatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaatcttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattcgtatttg | |
| ## atttgggtttactatcgaataatgagaattttcaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt | |
| ## >ctg123:99-101 | |
| ## at | |
| ## >ctg123:104-900 | |
| ## tcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaaaagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttataatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaatcttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattcgtatttgatttgggtttactatcgaataatgagaattt | |
| ## tcaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttagaatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattccttctgggcgtacccgattctcggagaacttgccgcaccattccgccttgtgttcattgctgcctgcatgttcat | |
| ## tgtctacctcggctacgtgtggctatctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaaaagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttataatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaatcttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattcgtatttgatttg | |
| ## ggtttactatcgaataatgagaattttcaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt | |
| ## >ctg123:104-120 | |
| ## tcctcggtgccctcgt | |
| ## >ctg123:119-150 | |
| ## .... |
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| ##gff-version 3.2.1 | |
| ##sequence-region ctg123 1 1500 | |
| ctg123 . gene 100 900 . + . ID=gene00001;Name=EDEN | |
| ctg123 . TF_binding_site 100 101 . + . ID=tfbs00001;Parent=gene00001 | |
| ctg123 . mRNA 105 900 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 | |
| ctg123 . five_prime_UTR 105 120 . + . Parent=mRNA00001 | |
| ctg123 . CDS 120 150 . + 0 ID=cds00001;Parent=mRNA00001 | |
| ctg123 . CDS 300 390 . + 0 ID=cds00001;Parent=mRNA00001 | |
| ctg123 . CDS 500 550 . + 0 ID=cds00001;Parent=mRNA00001 | |
| ctg123 . CDS 700 760 . + 0 ID=cds00001;Parent=mRNA00001 | |
| ctg123 . three_prime_UTR 761 900 . + . Parent=mRNA00001 | |
| ctg123 . cDNA_match 105 150 5.8e-42 + . ID=match00001;Target=cdna0123+12+57 | |
| ctg123 . cDNA_match 500 550 8.1e-43 + . ID=match00001;Target=cdna0123+463+963 | |
| ctg123 . cDNA_match 700 900 1.4e-40 + . ID=match00001;Target=cdna0123+964+2964 | |
| ##FASTA | |
| >ctg123 | |
| cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg | |
| tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta | |
| tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa | |
| aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat | |
| aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat | |
| cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc | |
| gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc | |
| ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt | |
| aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag | |
| aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc | |
| cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg | |
| tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta | |
| tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa | |
| aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat | |
| aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat | |
| cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc | |
| gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc | |
| ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt | |
| aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag | |
| aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc | |
| cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg | |
| tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta | |
| tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa | |
| aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat | |
| aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat | |
| cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc | |
| gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc | |
| ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt | |
| aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag | |
| aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc | |
| >cnda0123 | |
| ttcaagtgctcagtcaatgtgattcacagtatgtcaccaaatattttggc | |
| agctttctcaagggatcaaaattatggatcattatggaatacctcggtgg | |
| aggctcagcgctcgatttaactaaaagtggaaagctggacgaaagtcata | |
| tcgctgtgattcttcgcgaaattttgaaaggtctcgagtatctgcatagt | |
| gaaagaaaaatccacagagatattaaaggagccaacgttttgttggaccg | |
| tcaaacagcggctgtaaaaatttgtgattatggttaaagg |
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