I extracted sequences with fastaFromBed and have no complains about the BEDTools which is really awesome thing.
Otherwise extracted sequences look like this:
>chr19:13985513-13985622 GGAAAATTTGCCAAGGGTTTGGGGGAACATTCAACCTGTCGGTGAGTTTGGGCAGCTCAGGCAAACCATCGACCGTTGAGTGGACCCTGAGGCCTGGAATTGCCATCCT >chr19:13985689-13985825 TCCCCTCCCCTAGGCCACAGCCGAGGTCACAATCAACATTCATTGTTGTCGGTGGGTTGTGAGGACTGAGGCCAGACCCACCGGGGGATGAATGTCACTGTGGCTGGGCCAGACACG
And my input file looks like this:
>chr19 agtcccagctactcgggaggctaaggcaggagaatcgcttgaacccagga ggtggaggttgcagggagccgagatcgcaccactgcactccagcctgggc gacagagcgagattccgtctcaaaaagtaaaataaaataaaataaaaaat aaaagtttgatatattcagaatcagggaggtctgctgggtgcagttcatt tgaaaaattcctcagcattttagtGATCTGTATGGTCCCTCtatctgtca gggtcctagcaggaaattgttgcactctcaaaggattaagcagaaagagt
I was using this:
fastaFromBed -fi input -bed seq.bed -fo output
So shouldn't those sequences be formed in FASTA format (as ncbi says "It is recommended that all lines of text be shorter than 80 characters in length") or at least the same line length as my input file?
What I am doing wrong that I am getting linearized (fasta?) output with fastaFromBed?
What is the quickest way to turn those linear sequences to nicely formatted columns using command line?