{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TODAY'S DATE:\n",
      "Tue Nov  5 07:39:45 PST 2019\n",
      "------------\n",
      "\n",
      "Distributor ID:\tUbuntu\n",
      "Description:\tUbuntu 16.04.6 LTS\n",
      "Release:\t16.04\n",
      "Codename:\txenial\n",
      "\n",
      "------------\n",
      "HOSTNAME: \n",
      "swoose\n",
      "\n",
      "------------\n",
      "Computer Specs:\n",
      "\n",
      "Architecture:          x86_64\n",
      "CPU op-mode(s):        32-bit, 64-bit\n",
      "Byte Order:            Little Endian\n",
      "CPU(s):                24\n",
      "On-line CPU(s) list:   0-23\n",
      "Thread(s) per core:    2\n",
      "Core(s) per socket:    6\n",
      "Socket(s):             2\n",
      "NUMA node(s):          1\n",
      "Vendor ID:             GenuineIntel\n",
      "CPU family:            6\n",
      "Model:                 44\n",
      "Model name:            Intel(R) Xeon(R) CPU           X5670  @ 2.93GHz\n",
      "Stepping:              2\n",
      "CPU MHz:               2925.971\n",
      "BogoMIPS:              5851.97\n",
      "Virtualization:        VT-x\n",
      "L1d cache:             32K\n",
      "L1i cache:             32K\n",
      "L2 cache:              256K\n",
      "L3 cache:              12288K\n",
      "NUMA node0 CPU(s):     0-23\n",
      "Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d\n",
      "\n",
      "------------\n",
      "\n",
      "Memory Specs\n",
      "\n",
      "              total        used        free      shared  buff/cache   available\n",
      "Mem:            70G         29G        388M        575M         40G         39G\n",
      "Swap:          4.7G        548M        4.1G\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "No LSB modules are available.\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "echo \"TODAY'S DATE:\"\n",
    "date\n",
    "echo \"------------\"\n",
    "echo \"\"\n",
    "#Display operating system info\n",
    "lsb_release -a\n",
    "echo \"\"\n",
    "echo \"------------\"\n",
    "echo \"HOSTNAME: \"; hostname \n",
    "echo \"\"\n",
    "echo \"------------\"\n",
    "echo \"Computer Specs:\"\n",
    "echo \"\"\n",
    "lscpu\n",
    "echo \"\"\n",
    "echo \"------------\"\n",
    "echo \"\"\n",
    "echo \"Memory Specs\"\n",
    "echo \"\"\n",
    "free -mh"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set variables\n",
    "`%env` variables are good for passing to bash cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "env: wd=/home/sam/analyses/20191105_swoose_pgen_v074_renaming\n",
      "env: rsync_owl=owl:/volume1/web/halfshell/genomic-databank/\n",
      "env: files_list=Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed  Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3\n",
      "env: wget_command=--directory-prefix=$/home/sam/analyses/20191105_swoose_pgen_v074_renaming --quiety --no-directories --no-check-certificate  https://owl.fish.washington.edu/halfshell/genomic-databank/\n",
      "env: new_prefix=Panopea-generosa-v1.0\n",
      "env: fa_prefix=Pgenerosa_v074\n",
      "env: gff_prefix=Panopea-generosa-vv0.74\n"
     ]
    }
   ],
   "source": [
    "# Set workding directory\n",
    "%env wd=/home/sam/analyses/20191105_swoose_pgen_v074_renaming\n",
    "wd=\"/home/sam/analyses/20191105_swoose_pgen_v074_renaming\"\n",
    "\n",
    "%env rsync_owl=owl:/volume1/web/halfshell/genomic-databank/\n",
    "%env wget_command=--directory-prefix=${wd} --quiety --no-directories --no-check-certificate  https://owl.fish.washington.edu/halfshell/genomic-databank/\n",
    "\n",
    "%env new_prefix=Panopea-generosa-v1.0\n",
    "%env fa_prefix=Pgenerosa_v074\n",
    "%env gff_prefix=Panopea-generosa-vv0.74"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Create necessary directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "mkdir --parents ${wd}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/sam/analyses/20191105_swoose_pgen_v074_renaming\n"
     ]
    }
   ],
   "source": [
    "cd {wd}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Download Pgen_v074 files\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.CDS.gff3\n",
      "     62,862,005 100%   27.44MB/s    0:00:02 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 62,869,800 bytes  9,672,281.54 bytes/sec\n",
      "total size is 62,862,005  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.exon.gff3\n",
      "     64,663,603 100%   26.86MB/s    0:00:02 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 64,671,619 bytes  9,949,484.46 bytes/sec\n",
      "total size is 64,663,603  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "     10,997,681 100%   25.90MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 10,999,145 bytes  3,142,621.43 bytes/sec\n",
      "total size is 10,997,681  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.mRNA.gff3\n",
      "     10,666,540 100%   22.46MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 10,667,964 bytes  7,111,996.00 bytes/sec\n",
      "total size is 10,666,540  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeat_region.gff3\n",
      "    390,130,212 100%   27.11MB/s    0:00:13 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 390,177,965 bytes  21,090,702.43 bytes/sec\n",
      "total size is 390,130,212  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.rRNA.gff3\n",
      "          1,447 100%    1.38MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 1,570 bytes  640.00 bytes/sec\n",
      "total size is 1,447  speedup is 0.90\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.tRNA.gff3\n",
      "      2,836,671 100%   29.41MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 2,837,138 bytes  1,134,867.20 bytes/sec\n",
      "total size is 2,836,671  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Pgenerosa_v074.fa\n",
      "    958,059,901 100%   22.77MB/s    0:00:40 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 958,176,954 bytes  23,088,602.02 bytes/sec\n",
      "total size is 958,059,901  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Pgenerosa_v074.fa.fai\n",
      "          1,230 100%    1.17MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 1,338 bytes  547.20 bytes/sec\n",
      "total size is 1,230  speedup is 0.90\n",
      "receiving incremental file list\n",
      "Pgenerosa_v074.CpG.gff\n",
      "  2,623,644,046 100%   27.02MB/s    0:01:32 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 2,623,964,425 bytes  28,063,790.96 bytes/sec\n",
      "total size is 2,623,644,046  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.intergenic.bed\n",
      "      2,113,935 100%   28.80MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 2,114,319 bytes  1,409,566.00 bytes/sec\n",
      "total size is 2,113,935  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.introns.bed\n",
      "      9,488,151 100%   30.26MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 9,489,433 bytes  6,326,308.67 bytes/sec\n",
      "total size is 9,488,151  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.DNA.gff3\n",
      "      5,560,657 100%   29.96MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 5,561,463 bytes  3,707,662.00 bytes/sec\n",
      "total size is 5,560,657  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.LTR.gff3\n",
      "        752,111 100%   32.60MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 752,329 bytes  501,572.67 bytes/sec\n",
      "total size is 752,111  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.SINE.gff3\n",
      "     10,492,279 100%   29.78MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 10,493,691 bytes  6,995,814.00 bytes/sec\n",
      "total size is 10,492,279  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3\n",
      "    350,419,849 100%   29.33MB/s    0:00:11 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 350,462,756 bytes  28,037,022.88 bytes/sec\n",
      "total size is 350,419,849  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.LINE.gff3\n",
      "     18,049,492 100%   13.58MB/s    0:00:01 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 18,051,824 bytes  3,282,155.27 bytes/sec\n",
      "total size is 18,049,492  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.RC.gff3\n",
      "        143,208 100%   45.52MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 143,353 bytes  95,588.67 bytes/sec\n",
      "total size is 143,208  speedup is 1.00\n",
      "receiving incremental file list\n",
      "Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3\n",
      "      4,716,710 100%    8.63MB/s    0:00:00 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 4,717,422 bytes  3,144,968.00 bytes/sec\n",
      "total size is 4,716,710  speedup is 1.00\n",
      "total 4.3G\n",
      "-rwxr--r-- 1 sam users  60M Oct 14 10:13 Panopea-generosa-vv0.74.a4.CDS.gff3\n",
      "-rwxr--r-- 1 sam users  62M Oct 14 10:13 Panopea-generosa-vv0.74.a4.exon.gff3\n",
      "-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "-rw-rw-r-- 1 sam users 2.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.intergenic.bed\n",
      "-rw-rw-r-- 1 sam users 9.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.introns.bed\n",
      "-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.mRNA.gff3\n",
      "-rwxr--r-- 1 sam users 373M Oct 14 10:13 Panopea-generosa-vv0.74.a4.repeat_region.gff3\n",
      "-rw-rw-r-- 1 sam users 5.4M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.DNA.gff3\n",
      "-rw-rw-r-- 1 sam users  18M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3\n",
      "-rw-rw-r-- 1 sam users 735K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3\n",
      "-rw-rw-r-- 1 sam users 140K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.RC.gff3\n",
      "-rw-rw-r-- 1 sam users 4.5M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3\n",
      "-rw-rw-r-- 1 sam users  11M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3\n",
      "-rw-rw-r-- 1 sam users 335M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3\n",
      "-rwxr--r-- 1 sam users 1.5K Oct 14 10:13 Panopea-generosa-vv0.74.a4.rRNA.gff3\n",
      "-rwxr--r-- 1 sam users 2.8M Oct 14 10:13 Panopea-generosa-vv0.74.a4.tRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 2.5G Aug 21 11:45 Pgenerosa_v074.CpG.gff\n",
      "-rw-rw-rw- 1 sam users 914M Jun 26 08:49 Pgenerosa_v074.fa\n",
      "-rw-rw-rw- 1 sam users 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "# Create array of files from list\n",
    "files_array=(Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3)\n",
    "\n",
    "\n",
    "for file in \"${files_array[@]}\"\n",
    "do\n",
    "  rsync \\\n",
    "  --archive \\\n",
    "  --progress \\\n",
    "  --verbose \\\n",
    "  \"${rsync_owl}${file}\" \\\n",
    "  .\n",
    "done\n",
    "\n",
    "ls -lh"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### If need to download via wget, uncomment lines in the cell below"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# %%bash\n",
    "# time \\\n",
    "# wget \"${wget_gffs}\"\n",
    "# wget \"${wget_fasta}\"\n",
    "# ls -lh ${wd}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Change scaffold names and file names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 7.9G\n",
      "-rw-rw-rw- 1 sam users 914M Jun 26 08:49 Pgenerosa_v074.fa\n",
      "-rw-rw-rw- 1 sam users 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai\n",
      "-rw-rw-r-- 1 sam users 2.5G Aug 21 11:45 Pgenerosa_v074.CpG.gff\n",
      "-rwxr--r-- 1 sam users  60M Oct 14 10:13 Panopea-generosa-vv0.74.a4.CDS.gff3\n",
      "-rwxr--r-- 1 sam users  62M Oct 14 10:13 Panopea-generosa-vv0.74.a4.exon.gff3\n",
      "-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.mRNA.gff3\n",
      "-rwxr--r-- 1 sam users 373M Oct 14 10:13 Panopea-generosa-vv0.74.a4.repeat_region.gff3\n",
      "-rwxr--r-- 1 sam users 1.5K Oct 14 10:13 Panopea-generosa-vv0.74.a4.rRNA.gff3\n",
      "-rwxr--r-- 1 sam users 2.8M Oct 14 10:13 Panopea-generosa-vv0.74.a4.tRNA.gff3\n",
      "-rw-rw-r-- 1 sam users  11M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3\n",
      "-rw-rw-r-- 1 sam users 4.5M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3\n",
      "-rw-rw-r-- 1 sam users 140K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.RC.gff3\n",
      "-rw-rw-r-- 1 sam users 735K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3\n",
      "-rw-rw-r-- 1 sam users  18M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3\n",
      "-rw-rw-r-- 1 sam users 5.4M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.DNA.gff3\n",
      "-rw-rw-r-- 1 sam users 335M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3\n",
      "-rw-rw-r-- 1 sam users 2.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.intergenic.bed\n",
      "-rw-rw-r-- 1 sam users 9.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.introns.bed\n",
      "-rw-rw-r-- 1 sam users  53M Nov  5 08:55 Panopea-generosa-v1.0.a4.CDS.gff3\n",
      "-rw-rw-r-- 1 sam users  55M Nov  5 08:55 Panopea-generosa-v1.0.a4.exon.gff3\n",
      "-rw-rw-r-- 1 sam users 9.5M Nov  5 08:55 Panopea-generosa-v1.0.a4.gene.gff3\n",
      "-rw-rw-r-- 1 sam users 9.1M Nov  5 08:55 Panopea-generosa-v1.0.a4.mRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 326M Nov  5 08:55 Panopea-generosa-v1.0.a4.repeat_region.gff3\n",
      "-rw-rw-r-- 1 sam users 1.2K Nov  5 08:55 Panopea-generosa-v1.0.a4.rRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 2.3M Nov  5 08:55 Panopea-generosa-v1.0.a4.tRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 914M Nov  5 08:56 Panopea-generosa-v1.0.fa\n",
      "-rw-rw-r-- 1 sam users  658 Nov  5 08:56 Panopea-generosa-v1.0.fa.fai\n",
      "-rw-rw-r-- 1 sam users 2.0G Nov  5 08:59 Panopea-generosa-v1.0.CpG.gff\n",
      "-rw-rw-r-- 1 sam users 996K Nov  5 08:59 Panopea-generosa-v1.0.a4.intergenic.bed\n",
      "-rw-rw-r-- 1 sam users 4.4M Nov  5 08:59 Panopea-generosa-v1.0.a4.introns.bed\n",
      "-rw-rw-r-- 1 sam users 4.7M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.DNA.gff3\n",
      "-rw-rw-r-- 1 sam users 645K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LTR.gff3\n",
      "-rw-rw-r-- 1 sam users 8.9M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.SINE.gff3\n",
      "-rw-rw-r-- 1 sam users 293M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Unknown.gff3\n",
      "-rw-rw-r-- 1 sam users  16M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LINE.gff3\n",
      "-rw-rw-r-- 1 sam users 123K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.RC.gff3\n",
      "-rw-rw-r-- 1 sam users 4.0M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Simple_repeat.gff3\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "\n",
    "files_array=(Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3)\n",
    "\n",
    "# Array of old scaffold names\n",
    "# Uses first column of FastA index file to get scaffold names\n",
    "mapfile -t orig_scaffold_names < <(awk '{print $1}' Pgenerosa_v074.fa.fai)\n",
    "\n",
    "# Array of new scaffold names\n",
    "mapfile -t new_scaffold_names < <(for number in {01..18}; do echo \"Scaffold_${number}\"; done)\n",
    "\n",
    "\n",
    "for file in \"${files_array[@]}\"\n",
    "do\n",
    "  # Set new filename, depending if FastA or GFF\n",
    "  name_check=\"${file%%.*}\"\n",
    "  if [ \"${name_check}\" = \"${fa_prefix}\" ]\n",
    "  then\n",
    "    new_name=${file/$fa_prefix/$new_prefix}\n",
    "  else\n",
    "    new_name=${file/$gff_prefix/$new_prefix}\n",
    "  fi\n",
    "  # sed substitution\n",
    "  # creates sed script to find original scaffold names and replace them with new scafold names\n",
    "  # and passes to sed via stdin\n",
    "  for index in \"${!orig_scaffold_names[@]}\"\n",
    "  do\n",
    "    printf \"s/%s/%s/\\n\" \"${orig_scaffold_names[index]}\" \"${new_scaffold_names[index]}\"\n",
    "  done | sed --file - \"${file}\" \\\n",
    "  >> \"${new_name}\"\n",
    "done\n",
    "\n",
    "ls -ltrh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "##gff-version 3\n",
      "##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM\n",
      "##Project Name : Pgenerosa_v074\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t2\t125\t.\t+\t0\tID=PGEN_.00g000010.m01.CDS01;Name=PGEN_.00g000010.m01.CDS01;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t1995\t2095\t.\t+\t1\tID=PGEN_.00g000010.m01.CDS02;Name=PGEN_.00g000010.m01.CDS02;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t3325\t3495\t.\t+\t0\tID=PGEN_.00g000010.m01.CDS03;Name=PGEN_.00g000010.m01.CDS03;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t4651\t4719\t.\t+\t0\tID=PGEN_.00g000010.m01.CDS04;Name=PGEN_.00g000010.m01.CDS04;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t19808\t19943\t.\t-\t2\tID=PGEN_.00g000020.m01.CDS01;Name=PGEN_.00g000020.m01.CDS01;Parent=PGEN_.00g000020.m01;original_ID=cds.21510-PGEN_.00g234150.m01;Alias=cds.21510-PGEN_.00g234150.m01\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t21133\t21362\t.\t-\t0\tID=PGEN_.00g000020.m01.CDS02;Name=PGEN_.00g000020.m01.CDS02;Parent=PGEN_.00g000020.m01;original_ID=cds.21510-PGEN_.00g234150.m01;Alias=cds.21510-PGEN_.00g234150.m01\n",
      "Scaffold_01\tGenSAS_5d9637f372b5d-publish\tCDS\t22487\t22613\t.\t-\t2\tID=PGEN_.00g000020.m01.CDS03;Name=PGEN_.00g000020.m01.CDS03;Parent=PGEN_.00g000020.m01;original_ID=cds.21510-PGEN_.00g234150.m01;Alias=cds.21510-PGEN_.00g234150.m01\n",
      "\n",
      "--------------------\n",
      "##Generated\n",
      "##gff-version\n",
      "##Project\n",
      "Scaffold_01\n",
      "Scaffold_02\n",
      "Scaffold_03\n",
      "Scaffold_04\n",
      "Scaffold_05\n",
      "Scaffold_06\n",
      "Scaffold_07\n",
      "Scaffold_08\n",
      "Scaffold_09\n",
      "Scaffold_10\n",
      "Scaffold_11\n",
      "Scaffold_12\n",
      "Scaffold_13\n",
      "Scaffold_14\n",
      "Scaffold_15\n",
      "Scaffold_16\n",
      "Scaffold_17\n",
      "Scaffold_18\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "head Panopea-generosa-v1.0.a4.CDS.gff3\n",
    "\n",
    "echo \"\"\n",
    "echo \"--------------------\"\n",
    "awk '{print $1}' Panopea-generosa-v1.0.a4.CDS.gff3 | sort | uniq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 3.7G\n",
      "-rw-rw-r-- 1 sam users  53M Nov  5 08:55 Panopea-generosa-v1.0.a4.CDS.gff3\n",
      "-rw-rw-r-- 1 sam users  55M Nov  5 08:55 Panopea-generosa-v1.0.a4.exon.gff3\n",
      "-rw-rw-r-- 1 sam users 9.5M Nov  5 08:55 Panopea-generosa-v1.0.a4.gene.gff3\n",
      "-rw-rw-r-- 1 sam users 9.1M Nov  5 08:55 Panopea-generosa-v1.0.a4.mRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 326M Nov  5 08:55 Panopea-generosa-v1.0.a4.repeat_region.gff3\n",
      "-rw-rw-r-- 1 sam users 1.2K Nov  5 08:55 Panopea-generosa-v1.0.a4.rRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 2.3M Nov  5 08:55 Panopea-generosa-v1.0.a4.tRNA.gff3\n",
      "-rw-rw-r-- 1 sam users 914M Nov  5 08:56 Panopea-generosa-v1.0.fa\n",
      "-rw-rw-r-- 1 sam users  658 Nov  5 08:56 Panopea-generosa-v1.0.fa.fai\n",
      "-rw-rw-r-- 1 sam users 2.0G Nov  5 08:59 Panopea-generosa-v1.0.CpG.gff\n",
      "-rw-rw-r-- 1 sam users 996K Nov  5 08:59 Panopea-generosa-v1.0.a4.intergenic.bed\n",
      "-rw-rw-r-- 1 sam users 4.4M Nov  5 08:59 Panopea-generosa-v1.0.a4.introns.bed\n",
      "-rw-rw-r-- 1 sam users 4.7M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.DNA.gff3\n",
      "-rw-rw-r-- 1 sam users 645K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LTR.gff3\n",
      "-rw-rw-r-- 1 sam users 8.9M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.SINE.gff3\n",
      "-rw-rw-r-- 1 sam users 293M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Unknown.gff3\n",
      "-rw-rw-r-- 1 sam users  16M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LINE.gff3\n",
      "-rw-rw-r-- 1 sam users 123K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.RC.gff3\n",
      "-rw-rw-r-- 1 sam users 4.0M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Simple_repeat.gff3\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "files_array=(Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3)\n",
    "\n",
    "for file in \"${files_array[@]}\"\n",
    "do\n",
    "  rm \"${file}\"\n",
    "done\n",
    "\n",
    "ls -ltrh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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    "name": "ipython",
    "version": 3
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