{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Getting Fasta from GFF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
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   "outputs": [
    {
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     "text": [
      "\n",
      "Tool:    bedtools getfasta (aka fastaFromBed)\n",
      "Version: v2.30.0\n",
      "Summary: Extract DNA sequences from a fasta file based on feature coordinates.\n",
      "\n",
      "Usage:   bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>\n",
      "\n",
      "Options: \n",
      "\t-fi\t\tInput FASTA file\n",
      "\t-fo\t\tOutput file (opt., default is STDOUT\n",
      "\t-bed\t\tBED/GFF/VCF file of ranges to extract from -fi\n",
      "\t-name\t\tUse the name field and coordinates for the FASTA header\n",
      "\t-name+\t\t(deprecated) Use the name field and coordinates for the FASTA header\n",
      "\t-nameOnly\tUse the name field for the FASTA header\n",
      "\t-split\t\tGiven BED12 fmt., extract and concatenate the sequences\n",
      "\t\t\tfrom the BED \"blocks\" (e.g., exons)\n",
      "\t-tab\t\tWrite output in TAB delimited format.\n",
      "\t-bedOut\t\tReport extract sequences in a tab-delimited BED format instead of in FASTA format.\n",
      "\t\t\t- Default is FASTA format.\n",
      "\t-s\t\tForce strandedness. If the feature occupies the antisense,\n",
      "\t\t\tstrand, the sequence will be reverse complemented.\n",
      "\t\t\t- By default, strand information is ignored.\n",
      "\t-fullHeader\tUse full fasta header.\n",
      "\t\t\t- By default, only the word before the first space or tab \n",
      "\t\t\tis used.\n",
      "\t-rna\tThe FASTA is RNA not DNA. Reverse complementation handled accordingly.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!/Applications/bioinfo/bedtools2/bin/fastaFromBed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">scaffold22 dna_sm:supercontig supercontig:oyster_v9:scaffold22:1:1964558:1 REF\n",
      "TATTTGCAATTAGCCAGTTGAAATATATTATACATTAATCTCCATTATTCTTATCTATAA\n",
      "ATCATATTCGTTCGTAAAATGTAAGTATCAAACGATTCATTTTTGAAATCATAAGTGATT\n",
      "TTATGACTGTTAATCTTCCTTATATTGTTAATTTACGTAGTTTCCACTGCTTTATTAttt\n",
      "ttttttATATCGTCTAGTATAACATTGTAATTTCAGTTTAACATATCATATCAGTGTACC\n",
      "GAAAATTTTATCCCTAGCAAGTCAAAGTTTGCATTGTTCCAATCCAGTTTCCATCTGGAG\n",
      "TGATGAAAAGTTTCTTTTGAGAATTTTTACTTCCTATCCACACCATCTTGGTCTCATTGT\n",
      "TACAAACCACGGATTTGAGAATCGATGTGAATCACAAGTGGGTCACCGATGATGTCTTGG\n",
      "CCTTAGAAAAGTTAATATTTAGTCCTGATATATCAGCAAAAAAATCTATTTCCCTAAGAA\n",
      "TACCGTCTTAAGTTTCTGGTGGTCCATTTCTAAATAAAGATGTGTCATCTGCATATTTGT\n"
     ]
    }
   ],
   "source": [
    "!head data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "!/Applications/bioinfo/bedtools2/bin/fastaFromBed \\\n",
    "-fi data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa \\\n",
    "-bed data/oyster-EE2-DMR.gff \\\n",
    "-fullHeader \\\n",
    "-fo analyses/ee2-old.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">scaffold1017:117843-118366\n",
      "CCATTGAGCTATTGTGACCGAATATATTGACCAACAGTCGCACACCTGTTAACCCATTGACAAAGTTTAAACGATAGTCTGCTTGATGAATGGTTAAGGGTTGGTGGGTGTTATATCCACCGCAATGATATTAAAATAGTCGTAGATCTTATAAAATGGCTTAGATATCCTTTCTTGTTCTGTTAAGAGTCATCAAATCATCGAGTGGTCTTCTGGACAACCACTAAGATCATTCAATCTTCAATAGCCAAACCAATCTTTACAATAATGCAAAGTGTAGAGAGAGCTGACAATGTCCTATTGAGTCATAATCTGTGACGTCTGAATTAACTTTAAAATTTGTATGAAGATAAATTTATCAACAAATCGCATTTGTTAAAAAGTCAGCAGTAACTTTGTTTAACAAGAGGCCCACAGGCCTTGACAGTCACCTGAGTTACAAGAGTCGGAGGAATCTCAGATTATTTAAGATATATTGAACTTGCCATCTTAATGGTTGAATGAAAGTTCATTCTGAATTCAT\n",
      ">scaffold1017:120082-120710\n",
      "TGTCTCAAAATGCTACTATTATACATACTGTATGTGTAAGGGAAATGTTGAATTTTTTTAAAAATTGTGTACCGGTATATGAAACACGGATGCCCCATGGAAACCTACTGCATATGACTTTAGATATAAGGCGTGTTTTCCAAAAACAAAACATACGAACCCAAGTTAACAAAATATTGATCAAGTTATTATTGCGACTTTGTTCAAATTTTAATCATCCACTGACTTTAAATGAAGTATAGACAGAATATAATTACAGATAATCAGGCAGGCAATATAAAAGTTGCAAGGTTTACGCTGAAAATTGAGTACTTAATTGCACTATACATGCAGATTATTGTGTGAAGCCTAAAAGGCAATTCAATGTGTTTACATACAAACAATAGGATAATCTTAACTAAGACCTATGCTTTCAGTTTGCAAAACTCATGTGCAAAACTCTGTGTATTCATTTGCATTTTTGCTGAAAATGCGCTTTCATCTTACTCTTAAAATAGGAATGATTCAAATTAATTTGCATTTGAATAATAATGCATTGATAACTGGTGCACTTTTAAGCTTAGCCAAAACATGATACCTCAATATAAGTTAAACTATAGGCAATATGTTTTGTGTCAAGCAGTAAAAT\n",
      ">scaffold1409:145388-145656\n",
      "AATAGAATTGTGGTGTGAGGAAATTTTGAGAAAACGTTATGCAATATTTACCATAAAAAGTAGATGAAACCCGAAATTCCCCAAAAAGCCCCTTATCTGTaaaaaaaaaTTGTCGGCCGCTGCTTAATTTTGAAAACGAGTCAGAAGCTTTACATTATTTATAACGGGTATTTCTACGGCCTGACTTTATTTACGATGAAAACCTTAAAACAGTTAATGATATATTGTTTGTTTTAATTTTTTCTGGTACGAAAATAAAAGTTTTATA\n",
      ">scaffold146:686525-687786\n",
      "ATAAATCTAGTAAGTTACTTATCAAAAGTTTCTAAATCTAATAAACAAATCATTTTCCAAATAAATCTTCCCTCCATTTATTAttttttttAATGAAATCCCATCCAGTTTACCTGGAGCAAGGACACCCTTTCTTCCTCCAGTTTTGATTTTTCCTGGAAGATGAATCTGTCCAGCAGAGTTTCCTCGATGTCCGCGCGGGAGCGCTGGAAGTAGATGACGGAGGTGTACGCCGCAAGATGTCGTGGTACAATGTGTGGCTCCACCGTGGTGTGCAGGAACAGGCGGAAACGTGGATCACACTCCACTTCATGATCTTCCACCTAAAACAGAATAAATAATGGAAAAATTCAATCATTCTCATTAATATTTTACTTTGGCCAAAAATTACTCCATAttttttttttaaatctttttttttttCGGAGTCCATTATATTTTTAAAATTAAAAACTTTGACTAAAAGGTAGGATTTGTTCATGTTAGATAAGGATAATGACAAAAAACCCAAAAATAATTAAAACGCATTTTATAGTTTAACATGGATGAGCAGATTTCCTCCATAATTATGTACATGTTGTGAATATAATACTTGTCTGATGGACTTACAGTGATCTTGAACTTGAGTTTGCCGTTGATGAACTGTTTACAGCTCTGGATGGCGTCGCGGAACCGCTTGTCCTTGGCCAGCTGTTTGGTGTCGCAGTCGGTCACCAGTAGGGGGCAGCCCTCCGCTAGACAGTTCTCAAACTGAGACCGAATCTCCTACAAACACAGAGTAACAACAGATAATGACCCCTTAAACTGAGATGGAATCTACTACATGTACAATCACAAGGCTCCTCTATGTTACATCAAGGTCTTAAGAGTTACAGATCATGAATCTAAAATTTCAACAAATATTGTGACTTTTTAATCAATAAAGCAAATCAATATTTGAATATCAGGAATATAGGCAGCTCAATAAATTCTTCCCTTTTGGCCAGAGAAACACTGATCACTTTTCATACTTACCAGTACAAACTTCTAGAACTAATTACTACATTTACATGTATAACTGTACACTTATTTCAACTTTTCTGGATCTAGATCCCCTTGTGTACTTACAGAGTACTTGACCTCCACAAGTCCGGTGTTTCCGTAGAAGTTCCGAAGCCAGTCCAGGACGCGACTGGTGGGGTCACAGATGAGGGGCCAAGCCACCATGCTGTCCCGCTGCATCAGGAAGCAGGCGTTCTCCAGCATCAGCTTAGTGATGGAC\n",
      ">scaffold1532:587964-588458\n",
      "TTAATGGCATAATTTTTTGGGACTTATGAAATTTtatatatatatataattatatatatCCAGAAAATAACATATTCATCGATCTTACTAAGGAGGGAAATTATGTTCCTGCTAGCATCAGATATAATTTCCCAGACTATCAGGGGAGACTGGTGCACTAAATATAGCAGCCCTCTCTCAATTAGAAGTCTCTCCATTTTGGGGCTATGGCGTCCAACTTCTCTTGAATCCCCAACCTCTACTTGCAAAATGGCTCGTGTGTTGGTGTCCATAAATACTCCATTTGATCGGTTGGCAGAAAACCCTTTAAAATAAAGTCATAAAATGTCCATCAATATCTTACATTATTACTTTTGCAAATATCTTTCTGTACTTGATTCAATCTACCTGAAAATAAATTTTCCTTTGTTTATTACAGTAATTTTATCAGAAGTGACTTAATTTGCATAAGTACATGTATATATACACTTATCATGCATATAAAATGTGTATTA\n"
     ]
    }
   ],
   "source": [
    "!head analyses/ee2-old.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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