AlignAndTranslatePacBioTats.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import pairwise2\n",
    "from Bio import SeqIO\n",
    "from multiprocessing import Pool, cpu_count\n",
    "import tqdm\n",
    "\n",
    "def read_fasta(file):\n",
    "    with open(file) as handle:\n",
    "        return list(SeqIO.parse(handle, 'fasta')) \n",
    "    \n",
    "def save_output(fasta, name):\n",
    "    \"\"\"\n",
    "    in:\n",
    "        > fasta: a list or XXX object containing BioRecords from a fasta file\n",
    "        > name: a string contianing the name of the file to save the fasta to\n",
    "    out:\n",
    "        > A fasta file written in the pwd containing the infromation found in\n",
    "          the fasta list\n",
    "    \"\"\"\n",
    "    \n",
    "    SeqIO.write(fasta, name, 'fasta')\n",
    "    \n",
    "def find_tat_exon_positions(seq, exon):\n",
    "        \"\"\"\n",
    "        Scans the tat sequence for the start of the exon 1 or exon 2 sequence\n",
    "        and returns its position\n",
    "        \"\"\"\n",
    "\n",
    "        if exon == 1:\n",
    "\n",
    "            # A random CARES Tat exon1 sequence used to map onto the large HIV sequence\n",
    "            exon = 'atggagccggtagatcctagactagagccctggaatcatccaggaagtcagcctaagactccttg\\\n",
    "            taccccttgctattgtaaaaggtgttgtctgcattgccaagtttgcttcataacaaaaggcttaggcatctcctatggca\\\n",
    "            ggaagaagcggagaaagcgacgaagacctcctcaagacagtgaggctcatcaggaacctctatcaaagca'.upper()\n",
    "\n",
    "            # Absurd gap penalsties to prevent any gaps from occuring\n",
    "            # Also added generous match score to encourage proper mapping\n",
    "            aln = pairwise2.align.localms(exon, seq, 7, 0, -50, -50)\n",
    "\n",
    "            start_position = aln[0][0].index('A')\n",
    "            end_position = start_position + 215\n",
    "\n",
    "        elif exon == 2:\n",
    "\n",
    "            # A random CARES Tat exon 2 sequence used to map onto the large HIV sequence\n",
    "            exon = 'atccgccccccagctccgaggggacccgacaggcccggaggaatcgaagaagaaggtggagaga\\\n",
    "            gagacagagacagatccggtggat'.upper()\n",
    "\n",
    "            # Absurd gap penalsties to prevent any gaps from occuring\n",
    "            # Also added generous match score to encourage proper mapping\n",
    "            aln = pairwise2.align.localms(exon, seq, 7, 0, -50, -50)\n",
    "\n",
    "            start_position = aln[0][0].index('A')\n",
    "\n",
    "            # Adds a large number of bps to end just so that we can get the longest exon 2 possible\n",
    "            end_position = start_position + 200\n",
    "\n",
    "        return start_position, end_position\n",
    "\n",
    "def find_tat_exon(seq, exon):\n",
    "    \"\"\"\n",
    "    Scans the Tat sequences for exon 1 or exon 2 and returns that\n",
    "    portion of the seqeunce\n",
    "    \"\"\"\n",
    "\n",
    "    start, end = find_tat_exon_positions(seq, exon)\n",
    "\n",
    "    return seq[start:end]\n",
    "\n",
    "def find_tat_cds(seq_record):\n",
    "    \"\"\"\n",
    "    Scans the seq_record seqeunce for exons 1 and 2\n",
    "    and replaces the seqeunces with the Tat CDS\n",
    "    \"\"\"\n",
    "\n",
    "    exon1 = find_tat_exon(seq_record.seq, exon = 1)\n",
    "    exon2 = find_tat_exon(seq_record.seq, exon = 2)\n",
    "\n",
    "    seq_record.seq = exon1 + exon2\n",
    "\n",
    "    return seq_record\n",
    "\n",
    "def find_mulitple_tat_cds(seq_records):\n",
    "    return [find_tat_cds(record) for record in tqdm.tqdm(seq_records)]   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from math import ceil\n",
    "\n",
    "fasta = read_fasta(\"../Data/RawData/PacBioConsensusSeqs/combined_ungapped_P100_consensus.fasta\")\n",
    "no_seq_fasta = [record for record in fasta if record.seq]\n",
    "\n",
    "# CHUNKCOUNT = 8\n",
    "# chunksize = ceil(len(no_seq_fasta) / CHUNKCOUNT)\n",
    "\n",
    "# chunks = [fasta[i:i+chunksize] for i in range(0, len(no_seq_fasta), chunksize)]\n",
    "# chunks = chunks[:CHUNKCOUNT]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def make_full_tat(record):\n",
    "    exon1 = 'atggagccggtagatcctagactagagccctggaatcatccaggaagtcagcctaagactccttg\\\n",
    "    taccccttgctattgtaaaaggtgttgtctgcattgccaagtttgcttcataacaaaaggcttaggcatctcctatggca\\\n",
    "    ggaagaagcggagaaagcgacgaagacctcctcaagacagtgaggctcatcaggaacctctatcaaagca'.upper()\n",
    "\n",
    "    exon2 = 'atccgccccccagctccgaggggacccgacaggcccggaggaatcgaagaagaaggtggagaga\\\n",
    "    gagacagagacagatccggtggat'.upper()\n",
    "    \n",
    "    #print(seq_record)\n",
    "    seq = record.seq\n",
    "\n",
    "    # Absurd gap penalsties to prevent any gaps from occuring\n",
    "    # Also added generous match score to encourage proper mapping\n",
    "    exon_one_aln = pairwise2.align.localms(exon1, seq, 7, 0, -50, -50)\n",
    "    exon_two_aln = pairwise2.align.localms(exon2, seq, 7, 0, -50, -50)\n",
    "\n",
    "    start1 = exon_one_aln[0][0].index('A')\n",
    "    end1 = start1 + 215\n",
    "\n",
    "    start2 = exon_two_aln[0][0].index('A')\n",
    "    end2 = start2 + 300\n",
    "\n",
    "    big_tat = (seq[start1:end1] + seq[start2:end2]).translate()\n",
    "\n",
    "    first_stop = big_tat.find('*')\n",
    "    tat = big_tat[:first_stop]\n",
    "    record.seq = tat\n",
    "    \n",
    "    return record\n",
    "    \n",
    "def make_full_tats(seq_records):\n",
    "    return [make_full_tat(record) for record in tqdm.tqdm(seq_records)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|          | 0/140 [00:00<?, ?it/s]/home/bobby/.local/lib/python3.8/site-packages/Bio/Seq.py:2855: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n",
      "  warnings.warn(\n",
      "100%|██████████| 140/140 [01:55<00:00,  1.21it/s]\n"
     ]
    }
   ],
   "source": [
    "tats = [make_full_tat(record) for record in tqdm.tqdm(no_seq_fasta)]\n",
    "\n",
    "i_tats = [record for record in tats if record.seq[0] == 'I']\n",
    "good_tats = [record for record in tats if record.seq[0] == 'M' and len(record.seq) <= 110]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A0001-R09 | MEPVDPRLEPWKHPGSQPRTPCTACYCKKCCFHCQVCFTRKGLGISYGRKKRGQRRRPPQDSEAHQVSLPKQSAPQLRGDPTGPKESKKEVERETETDPVDQ | 102\n",
      "A0002-R14 | MDPVDPRLEPWKHPGSQPKTPCTPCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPPDSQTHQAPLPKQPTAQPRGDPTGPKESKKKVERETETDPVNQ | 102\n",
      "A0004-R10 | MEPVDPSLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQDSQIHQVPLSKQPASQPRGNPTGPKEQKKKVETEAETDQFD | 101\n",
      "A0005-R05 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCLHCQVCFITKGLGISYGRKKRRKRRRAPQDSETHQVSLSKQPTSQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0005-R07 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCLHCQVCFITKGLGISYGRKKRRKRRRAPQDSETHQVSLSKQPTSQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0008-R07 | MEPVDPRLEPWKHPGSQPKTACNTCYCKRCCLHCQVCFITKGLGISYGRKKRRQRRRAAQDSETRQVPLSKQPASQRRGDPTGQKESKKKVERETETDPVH | 101\n",
      "A0008-R10 | MEPVDPRLEPWKHPGSQPKTACNTCYCKKCCLHCQVCFITKGLGISYGRKKRRQRRRASQDSETRQVPLSKQSAPQRRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0010-R08 | MEPVDPRLEPWKHPGSQPRTPCTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPPQDSETHQASLSKQPASQPRGDPTGPKE | 86\n",
      "A0010-R09 | MEPVDPRLEPWKHPGSQPKTPCTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPPQDSQTHQASLSKQPASQPRGDPTGPKE | 86\n",
      "A0013-R10 | MDPVDPRLEPWKHPGSQPKTACTPCFCKKCCYHCQVCFISKGLGISYGRKKRRQRRRPSQDNQANQASLSKQSAPQTRGNPTGPKESEKKVERETETDPIN | 101\n",
      "A0013-R11 | MDPVDPRLEPWKHPGSQPKTACTPCFCKKCCYHCQVCFISKGLGISYGRKKRRQRRRPPQDNQANQVSLSKQSAPQTRGNPTGPKESEKKVERETETDPIN | 101\n",
      "A0015-R10 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQAHQGSLPKQPASQPRGDPTGPKESKKKVETETETDPVDQWMDS | 106\n",
      "A0015-R11 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQAHQGSLPKQPASQPRGDPTGPKESKKKVERETETDPID | 101\n",
      "A0015-R13 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQAHQGSLPKQPASQPRGDPTGPKESKKKVETETETDPVDQWMDS | 106\n",
      "A0017-R11 | MELVDPKLEPWKHPGSQPKTPCTKCYCKKCCYHCQMCFTTKGLGISYGRKKRRQRRRAPQNSQTHQASLSKQPASQPRGDPTGPTESKKKVERETATDQED | 101\n",
      "A0019-R12 | MEPVDPRLEPWKHPGSQPRTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRGQRRRAPQDSETHQASLSKQPTSQPRGDPTGPKEPKKKVERETETDPEH | 101\n",
      "A0025-R09 | MDPVDPRLEPWKHPGSQPKTACTKCYCKKCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQDSKTHQDPLPKQPSSQPRGDPTGPKEQKKEVERETETDPVH | 101\n",
      "A0025-R11 | MDPVDPRLEPWKHPGSQPKTACTNCYCKKCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQDSKTHQASLSKQPSSQPRGDPTGPKEQKKKVERETETDPVH | 101\n",
      "A0026-R09 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKKCCFHCQKCFTTKGLGISYGRKKRRQRRRADQDSQTHQVSLSKQPASQPGGNPTGPKE | 86\n",
      "A0032-R05 | INPVDPSLEPWKHPGSQPKTACTKCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSKTXQNSLPKQPTSQSRGNPTGPKESKKKVKTEAETDQFN | 101\n",
      "A0032-R06 | MDPVDPSLEPWKHPGSQPKTACTKCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSQLSRFSTKAVPTSQSRGDPTGPKESKKKVETEAETDQFD | 101\n",
      "A0034-R04 | MDPVDPRLEPWQHPGSQPKTPCTNCYCKKCCFHCQSCFTRKALGISYGRKKRRQRRRAHQDSQTHQASLSKQPTSQSGGDPTGPKESEKKVERETETHPHD | 101\n",
      "A0034-R05 | MDPVDPRLEPWQHPGSQPKTPCTNCYCKKCCFHCQSCFTRKALGISYGRKKRRQRRRAPQDSQTHQASLSKQPTSQSGGDPTGPKESKEKVERETETHPYD | 101\n",
      "A0034-R06 | MDPVDPNLEPWKHPGSQPKTPCTNCYCKKCCFHCQSCFTRKALGISYGRKKRRQRRRAHQDSQTHQASLSKQPTSQSGGDPTGPKESEKKVERETETHPYD | 101\n",
      "A0036-R05 | MDPVDPKLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSKTHQTSLSKQPSSQHRGDPAGPKESKKEVERETETDPVD | 101\n",
      "A0037-R10 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPYNSQDHQDSLSKQSSPQPRGNPTGPEKQKEEVESKTETDPHD | 101\n",
      "A0037-R11 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPHNSQDHQDSLSKQSSPQPRGDPTGPEKSKKEVESETETDPHD | 101\n",
      "A0037-R12 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPHNSQDHQDSLSKQSSPQPRGDPTGQEKSKKEVESETETDPHD | 101\n",
      "A0037-R13 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPYNSQDHQDSLSKQSSPQPRGDPTGPEKQKKEVESETETDPHD | 101\n",
      "A0038-R08 | MEPVDPRLEPWKHPGSQPRTACTTCYCKRCCYHCQVCFITKGLGISYGRKKRRQRRRAPQGNQTHQVSLSKQSAPQPQRDPTGPKESEKKVERETETDPVD | 101\n",
      "A0040-R05 | MEPVDPRLEPWEHPGSQPKTACTKCYCKKCCYHCQVCFITKALGISYGRKKRRQRRRTPQDSQTHQDSLSKQPTSQSRGDPTGPKEPKKKVERETETDPYD | 101\n",
      "A0040-R06 | MEPVDHRLEPWKHPGSQPKTACTKCYCKRCCYHCQVCFITKALGISYGRKKRRQRRRTPQDSQTHQDSLPKQPTSQSRGDPTGPKEPKKKVERETETDPYD | 101\n",
      "A0044-R10 | MEPVDPRLEPWKHPGSQPKTPCTHCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPPDSEAHQVSLSKQPAAQPPGDPTGPKESKKKVERETETDPVTQ | 102\n",
      "A0044-R12 | MEPVDPRLEPWKHPGSQPKTACTHCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPPDSEAHQVSLSKQPAAQPPGDPTGPKESKKKVERETETDPVTQ | 102\n",
      "A0045-R03 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSHQNSQTHQVSLSKQPTSQPGGDPTGPKESKKKVETETETDPVH | 101\n",
      "A0045-R04 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSHQNSQTHQVSLSKQPTSQPGGDPTGPEESKKKVETETATHPID | 101\n",
      "A0045-R05 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSHQNSQTHQVSLSKQPTSQPGGDPTGPKESKKKVETETETDPVH | 101\n",
      "A0045-R06 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRSHQTVRLIKFLYQSRPTSQPGGDPTGPKESKKKVETETETHPID | 101\n",
      "A0052-R05 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQVCFMTKGLGISYGRKKRRQRRRASGQSESSSFSIKAVPASQPHGDPTGPKESKKEVERETETDPYLVNGFLAIVWVDLRSLCLFLYHRLTDLLLIVVRIVELLGRRGWEASNIVGVSYNIGVRN | 159\n",
      "A0056-R06 | MEPVDPRLEPWKHPGSRPKTDCPKCYCKRCCFHCQVCFLTKGLGISYGRKKRRQRRRPPQDSETHQASLSKQPSSQPHGDPTGPKEQKKKVESETTADPCD | 101\n",
      "A0056-R07 | MEPVDPRLEPWKHPGSRPKTVCTKCYCKKCCFHCQVCFITKGLGISYGRKKRKQRRRTPQDSETHQASLSKQPSSQPHGDPTGPKEQKKKVESETKADPCD | 101\n",
      "A0059-R08 | MEPVDPSLEPWKHPGSQPKTACNNCFCKKCCFHCQKCFVTKGLGISYGRKKRRQRRRAHQGNQSHQSSLPKQPPSQSRGNPTGPEEQKKKVEKEAETDPFA | 101\n",
      "A0059-R09 | MEPVDPSLEPWKHPGSQPKTACNNCFCKKCCFHCQKCFVTKGLGISYGRKKRRQRRRAHQGNQSHQSSLPKQPPSQSRGNPTGPEEQKKKVEKEAETDPFA | 101\n",
      "A0067-R11 | MEPIDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPDSQTHQASLSKQ | 71\n",
      "A0068-R03 | MEPVDPKLEPWKHPGSQPKTACTNCYCKICCFHCQVCFTRKGLGISYGRKKRRQRRRAPQDSQTHQDSLPKQPASQPRGDPTGPKESKKKVERETETDPEDQWRAS | 106\n",
      "A0075-R07 | MDPVDPRLEPWKHPGSQPRTACTNCYCKQCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQGGQAHQGSLSKQPSSQQRGDPTGPKEQKEKVERETETDPDH | 101\n",
      "A0075-R09 | MDPVDPRLEPWKHPGSQPRTACTNCYCKRCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQGGQAHQDSLSKQPSSQQRGDPTGPKEQKEKVERETETDPDH | 101\n",
      "A0075-R10 | MDPVDPRLEPWKHPGSQPRTACTNCYCKRCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQGGQAHQDSLSKQPSSQQRGDPTGPKEQKEKVERETETDPDH | 101\n",
      "A0076-R04 | MDPVDPRLEPWNHPGSQPKTACTKCYCKKCCLHCQVCFIKKGLGISYGRKKRRQRRRTPQGGQTHQVSLPKQPSSQPRGDPTGPKESKEKVERETETHPVN | 101\n",
      "A0076-R05 | MDPVDPRLEPWNHPGSQPKTACTKCYCKKCCLHCQVCFIKKGLGISYGRKKRRQRRRTPQGGQTHQVSLSKQPSSQPRGDPTGPKESKEKVERETETHPVN | 101\n",
      "A0083-R06 | MDPVDPRLEPWKHPGSRPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPPQTVRLIKFLYQSRPSSQHPGDPTGPKESKKEVERETETDPVH | 101\n",
      "A0086-R04 | MEPVDPRLEPWKHPGSQPKTACTRCYCKQCCFHCQVCFITKALGISYGRKKRRQRRRAPQDSENHQVSPPKQPASQPRGDPTGPKESKKKVERETETDPDH | 101\n",
      "A0086-R05 | MEPVDPRLEPWKHPGSQPKTACTRCYCKQCCFHCQVCFITKALGISYGRKKRRQRRRAPQDSENHQVSPPKQPASQLRGDPTGPKKSKKEVERETETDPDH | 101\n",
      "A0091-R04 | MDPVDPRLEPWKHPGSQPKTACSPCHCKVCCFHCQVCFIRKALGISYGRKKRRQRRRAPQDSQTHQASLSEQPAPQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0095-R09 | MEPVDPRLEPWNHPGSQPKTPCTPCYCKRCCLHCQVCFITKGLGISYGRKKRRKRRRSPQDSETHQEPLSKQPTSQPRGDPTGPEESKKKVERETETHPRA | 101\n",
      "A0095-R10 | MEPVDPRLEPWNHPGSQPKTPCTPCYCKRCCLHCQVCFITKGLGISYGRKKRRKRRRSPQDSEAHQEPLSKQPTSQPRGDPTGPEESKKTVERETETHPRD | 101\n",
      "A0095-R11 | MEPVDPRLEPWNHPGSQPKTPCTPCYCKRCCLHCQVCFITKGLGISYGRKKRRKRRRSPQDSETHQGPLSKQPTSQPRGDPTGPEKSKKKVERETETHPRD | 101\n",
      "A0096-R08 | MEPVDPRLEPWKHPGSQPRTPCTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRPPQDNQTHQVPLSKQPASQTGGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0103-R06 | MEPVDPRLEPWKHPGSQPETACTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSQTHQVSLSKQSAPQQRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0103-R07 | MEPVDPRLEPWKHPGSQPETACTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSQTHQVSLSKQSAPQQRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0107-R09 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPSPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0107-R10 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPSPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0107-R11 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPGPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0107-R12 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPGPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0109-R11 | MDPVDPRLEPWKHPGSQPKTACTNCYCKQCCFHCQVCFITKGLGISYGRKKRRQRRRINQDNQNHQVPLPKQPTTQPRGDQTGPKE | 86\n",
      "A0111-R05 | MEPIDPSLEPWKHPGSQPKTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRSKRRRAPQDSQTHQVSLSKQPTSQSRGDPTGPKESKKKVETETETDPDH | 101\n",
      "A0111-R07 | MEPVDPKLEPWKHPGSQPKTACTPCYCKQCCFHCQVCFITKGLGISYGRKKRSKRRRAPQTIRLIKSLYQSRPTSQPRGDPTGPKESKKKVERETETDQDN | 101\n",
      "A0113-R11 | MEPVDPRLEPWKHPGSQPRTPCTSCYCKQCCFHCQKCFITKGLGISYGRKKRRQRRRAPQGSQTHQVSLPKQPASQPGGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0113-R12 | MEPVDPRLEPWKHPGSQPSTPCTSCYCKQCCFHCQKCFVTKGLGISYGRKKRRQRRRAPQGSQTHQVSLPKQPASQPGGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0127-R08 | MEPVDPSLEPWKHPGSQPRTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQTHQEALSKQPASQPRGDPTGPKESTKKVERETETNPDD | 101\n",
      "A0132-R11 | MEPIDPRLEPWQHPGSQPKTPCTSCYCKKCCFHCQVFHDKRLRHLLWQEEAETATKSSSSRQSDSSSVSIKAPTSQPRGDPTGPKESKKKVERETETDPED | 101\n",
      "A0133-R05 | MEPVDPRLEPWKHPGSQPKTPCNKCYCKRCCFHCQMFHNKRLRHLLWQEEAETATKSSSEQSDSSRSSTKAVPASQPRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0143-R06 | MEPVDPRLEPWKHPGSQPKTACTKCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRTSQDSQDHQVPLSKQPASQPGGDPTGPKESKKKVERETETDPVDQWMDS | 106\n",
      "A0145-R08 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSPQDSQTHQVPLPKQPASQPRGDQTGPKESKKKVAKETEMDPVS | 101\n",
      "A0145-R11 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSPQDSQTHQVPLPKQPASQPRGDQTGPKESKKKVAKETEMDPVS | 101\n",
      "A0145-R12 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSPQDSQTHQVPLPKQPASQPRGDQTGPKESKKKVAKETEMDPVS | 101\n",
      "A0152-R03 | INPVDPRLEP | 10\n",
      "A0156-R06 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKKCCFHCQVCFMTKGLGISYGRKKRGQRRRTPQGGQSHQVPLPKQPTSQPGGDPTGPKEQKKKVERETETDPYA | 101\n",
      "A0208-R05 | MEPVDPRLEPWKHPGSQPKTACTNAIVKSVAFIAKFVS | 38\n",
      "A0209-R07 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSKTHQASLSKQPTSQPRGDPTGPKEPKKKVEREAETDPVD | 101\n",
      "A0213-R04 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKECCFHCQVCFTKKGLGISYGRKKRRQRRGTHQSSETHQVSLPKQKGLRHLLWQEEAETATRNSSKQ | 94\n",
      "A0215-R09 | MEPVDHKLEPWKHPGSQPKTPCTNCYCKKCCFHCQVCFTKKGLGISYGRKKRRQRRRTSQDSETHQASLSKQPTSQQRGDPTGPKESKEKVERETAADPFD | 101\n",
      "A0218-R04 | MEPVDPSLEPWKHPGSQPKTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPHQDSQTHQDSLPKQPSSQPRGDQTGPKESQKKVERETETDPVA | 101\n",
      "A0223-R04 | MDPVDPRLEPWKHPGSQPKTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQSRQVSLSKQPTAQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0227-R04 | MEPVDPRLEPWKHPGSQPQTPCTPCYCKKCCFHCQVCFTKKALGISYGRKKRSKRRRAPQDSETRQASLPEQPTSQHRGDPTGPEEQKKKVERETEADPILVDGFLALFWVDLRSLFLFSYHRLRDLLLIVVRTVEILGHRGWELLKYWWSILQYWSQELKNSAVSLLNA | 170\n",
      "A0239-R05 | MDPVDPKLEPWKHPGSQPNTPCTNCYCKKCCFHCQVCFTKKALGISYGRKKRIKRRRPSQDSQTHQGPLPKQPTTQPRGDPTGPKESKKKVERETETDPED | 101\n",
      "A0241-R03 | MEPVDPNLEPWKHPGSQPKTACTPCYCKKCCFHCQKCFTTKGLGISYGRKKRGQRRRPPQDSKTHQVSLSKQSAPQPRGDPTGPKESKKKVERETETDPKD | 101\n",
      "A0255-R02 | MEPVDPRLEPWQHPGSQPTTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQGSEIHQVSLSKQPSSQSQGDPTGPKESKEKVESKTETDLVDQ | 102\n",
      "A0257-R05 | MEPVDPRLEPWKHPGSQPKTVCTACYCKKCCYHCPVCFVSKGLGISYGRKKRRRRRRADQGSQTHQVSLSKQPTSQLRGDPTGPKESKKKVERETETDQVD | 101\n",
      "A0264-R03 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCLHCQVCFITKGLGISNGRKKRRQRRRASQTVRLIKLLYQSRPASQPRGDPTGPKESKKKVERETEADPDH | 101\n",
      "A0274-R06 | MDPVDPRLEPWKHPGSQPRTPCTKCYCKKCCLHCQVCFITKGLGISYGRKKRRQRRRTPQDSQTNQVPASEQPSSQSRGDPTGPKESKEKVERETETDPCD | 101\n",
      "A0278-R05 | MEPVDPKLEPWKHPGSQPRTACTNCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQNSQIDQVSPSKQPSSQPRGDPTGPKESEKKVERETEKDQGH | 101\n",
      "A0285-R04 | MEPVDPRLEP | 10\n",
      "A0310-R04 | MEPVDPRLEPWKHPGSQPETPCNACYCKKCCFHCQWCFTRKGLGISYGRKKRGQRRRPPQDSQAHQVPLPKQSAPQPRGDQTGPKESKKKVERETETDPDN | 101\n",
      "A0318-R03 | MEPVDPRLEPWKHPGSQPKTACNNCYCKRCCFHCQVCFTRKGLGISYGRKKRRQRRRPAQDSQAHQVSLSKQPSSQLRGDPKGPKESKKKVERETETDPYD | 101\n",
      "A0325-R03 | MEPVDPKLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQDSETHQANLSKQPASQPRGDPTGPEESKKKVERETETDQLD | 101\n",
      "A0338-R01 | MEPVDSRLEPWKHPGSQPQTPCTSCYCKKCCFHCQVCFIKKALGISYGRKKRSKRRRASHDSPNHQDSLPKQPSSQLGGDPTGPKKQKKEVERETETHPDN | 101\n",
      "A0342-R03 | MEPVDPRLEPWKHPGSQPATACTSCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQNSQTHQDSLSKQPASQQRGDPTGPKESKKKVEREAETDPDH | 101\n",
      "A0357-R04 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSKAHQASLPKQPASQPRGDPTGPKESTKKVERETETDPNH | 101\n",
      "A0359-R07 | MEPVDPRLEPWKHPGSQPKTPCTPCYCKKCCYHCQIAS | 38\n",
      "A0379-R06 | MEPVDPSLEPWKHPGSQPKTACNSCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRASQDSQTDQVSLSKQPATQRRGDPTGPKESKKKVERETETDPNH | 101\n",
      "A0380-R03 | MDPVDPRLEPWKHPGSQPKTACNNCYCKKCCWHCQLCFLKKGLGISYGRKKRRQRRRTNQVXQTHQGDLSKQPASQLRGDPTGPKEQKKKVESKTETDP | 99\n",
      "A0384-R03 | MEPVDPRLEPWKHPGSQPRTPCNKCYCKKCCLHCQVCFISKGLGISYGRKKRRQRRRPPHDSQTHQDSLPKQPSSQDRGDPKGPKEQKEKVERETATDPCD | 101\n",
      "A0389-R07 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSQTHQDSLSKQPASQSGGNPTGPKESKKKVESKTETDPDD | 101\n",
      "A0401-R03 | MEPVDPRLEPWKHPGSQPKTACNKCYCKRCCLHCQVCFVTKGLGISYGRKKRRPRRRPPQHSQTHQASLSEQPASQPRGDPTGPKESKEKVESKTETDPDH | 101\n",
      "A0408-R02 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKKCCYHCQVCFITKGLGISYGRKKRRQRRRAPQDSQNHQVPLSKQPTSQPGGDPTGPKESKKKVETETETDPVH | 101\n",
      "A0413-R07 | MDPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFMQKGLGISYGRKKRRQRRRAPQGSKTRQASLSKQPTSQPGGDPTGPKESKKKVERKTETDPXISEWILSTYLGRPTEPVPLQLPPLERLNLDCSEDCGTSGTQGVGNPQVLGEHPPILESGTKE | 162\n",
      "A0417-R01 | MEPVDPSLEPWKHPGSQPKTACTPCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRPPRTVRIIKLLYQSRPASQPGGDPTGPKESKKKVEGTTETHPLD | 101\n",
      "A0417-R03 | MEPVDPSLEPWKHPGSQPKTACTPCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRPPRTVRIIKLLYQSRPASQPGGDPTGPKESKKKVEGTTETHPLD | 101\n",
      "A0429-R04 | MEPVDHNLDPWKHPGSQPKTPCNKCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRSPQGSQTHQVSPSKQPASQPRGDPTGPKEPKKKVERETETDPVH | 101\n",
      "A0430-R01 | MEPVDPRLEPWKHPGSQPRTPCTACYCKKCCYHCQVCFITKGLGISYGRKKRRQRRRTPQDSQTHQASLSKQPSSQPRRDQTGPKESKKKVERETETDPED | 101\n",
      "A0433-R04 | MDPVDPRLEPWKHPGSQPKTACTPCFCKRCCYHCQVCFISKGLGISYGRKKRRQRRRPPQDSQIHQVSLSKQSASQLRGNPTGPKESEKKVERETETDPVH | 101\n",
      "A0439-R01 | MEPVDPKLEPWNHPGSQPRTACTNCYCKKCCLHCQVCFITKGLGISYGRKKRRQRRRAHQDSETHQGDLSQQPASQPRGDPTGPKESKEKVERETEADPGH | 101\n",
      "A0440-R02 | MEPVDPRLEPWKHPGSQPRTPCTACYCKKCCYHCQVCFITKGLGISYGRKKRRQRRRSPQGSQTHQDSLSKQPPSQPRGDQTGPKESTKKVERETKTDPKD | 101\n",
      "A0446-R04 | MEPVDPRLAPWQHPGSQPRTACTSCYCKKCCFHCQKCFTTKGLGISYGRKKRRQRRTAPGDSQIHQVSLSKQPATQARGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0447-R01 | MEPVDPRLEPWKHPGSQPRTPCTSCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRPHQTVKFIKILYQSRPDSQPRGDPTGPKESKKKVESETETDQFA | 101\n",
      "A0448-R04 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRGQRRRPPHGSETRPDSLSKQPSSQPRGNPTGPTEPEKKVERETEAHPS | 100\n",
      "A0449-R01 | MEPVDPRIEPWKHPGSQPKTACTTCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQTHQASLSKQSAPQLRGDPTGPKESKKTVERETETDPVN | 101\n",
      "A0451-R03 | MEPVDPRLEPWKHPGSQPRTACNNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPRQSKSSRFSIKAVPSSQLRGDPTGPKKQKKEVERETETDPVN | 101\n",
      "A0471-R02 | MEPVDPRLEPWKHPGSQPRTACTSCYCKKCCFHCQVCFTKKGLGISYGRKKRGQRRRSPQSSETHQAALPEQPTSQPGGDPTGPKESKKKVETETETDPLH | 101\n",
      "A0474-R03 | MDPVDPRLEPWKHPGSQPKTACTPCFCKKCCYHCQVCFISKGLGISYGRKKRRQRRRSPHDSQNNQVSLSKQSAPQPRGDPTGPKESEKKVERETETDPVT | 101\n",
      "A0477-R03 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKICCFHCQVCFTQKGLGISYGRKKRRQRRRAPQDSQTHQVSLPKQPTSQSGGDPTGPKESEKKVERETETDPAVSERILATYLGGPAEPVPLQLPPLERLTLDCSEDCGTSGTQGVGTPQIFVESHTVLESGTKE | 162\n",
      "A0490-R02 | MEPVDPNLEPWKHPGSQPKTACTKCYCKRCCFHCQVCFITKGLGISYGRKKWRQRRRASQDSQTRQVSLSKQPTSQPGGDPTGPKESKKKVERETEADPVY | 101\n",
      "A0500-R03 | MEPVDPRLEPWKHPGSQPKTACTPCFCKVCCYHCQVCFISKGLGISYGRKKRRQRRRAPQDSETHQVSLPKQPTTQPRGDKKGPEESKKKVERETETHPGR | 101\n",
      "A0501-R02 | MEPVDPRLEPWKHPGSQPKTACNNCFCKKCCYHCQGCFISKGLGISYGRKKRRQRRRAPQDSEDHQVSLPKQPTSQTRGDPTGPEEPQKKVESKTETHPGD | 101\n",
      "A0503-R04 | MEPVDPRLEPWKHPGSQPRTACTTCYCKKCCFHCQVCFMTKGLGISYGRKKRRQRRRATQDSQAHQAPLSKQPASQHRGDPTGPEESKKKVERETETDPVH | 101\n",
      "A0523-R03 | MEPVDPRLEPWNHPGSQPKTACTPCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRTPQDSKDHQVSLSKQPSSQLQGDPTGPKESKKKVEKEAGTDPGH | 101\n",
      "B0037-R01 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCSFHCQVCFITKGLGISYGRKKRRQRRRAPHNSQDHQDSLSKQSSPQPRGDPTGPEKSKKEVEIETETDPHD | 101\n",
      "B0044-R02 | MEPVDPRLEPWKHPGSQPKTACTHCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPPDSEAHQVSLSKQPAAQPPGDPTGPKESKKKVERETETDPVTQ | 102\n",
      "B0076-R00 | MEPVDPRLEPWKHPGSQPKTACTKCYCKKCCLHCQVCFIKKGLGISYGRKKRRQRRRTPQGGQTHQVSLSKQPSSQPRGDPTGPKESKEKVERETETHPVD | 101\n",
      "B0146-R00 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQTHQASLSKQPASQPRGDPTGPKESKKKVERETETDPRD | 101\n",
      "B0147-R00 | MEPVDPRLEPWKHPGSQPKTDCTNCYCKRCCFHCQVCFMKKGLGISYGRKKRRQRRRTPQGSEAHQGPLSKQPASQHRGDPTGPKESKKKVERETETDQDN | 101\n",
      "B0303-R02 | MDPVDPKLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRTPQDGQTHQTSLSKQPSSQPRGDPTGPKESKKKVEREAETHPAD | 101\n",
      "B0325-R00 | MEPVDPKLEPWKHPGSQPKTACTPCYCKKCCFHCQTCFITKGLGISYGRKKRRQRRRAHQDSETHQANLSKQPASQPRGDPTGPEESKKKVERETETDQLD | 101\n",
      "B0325-R01 | MEPVDPKLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQDSETHQANLSKQPASQPRGDPTGPEESKKKVERETETDQLD | 101\n",
      "B0477-R00 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKICCFHCQVCFTQKGLGISYGRKKRRQRRRPPQDSQTHQVSLPKQPTSQPGGDPTGPKESEKKVERETETDPAVSERILATYLGGPAEPVPLQLPPLERLTLDCSEDCGTSGTQGVGTPQILVESHTVLESGTKEQCC | 165\n",
      "B0485-R00 | MEPIDPRLEPWKHPGSQPRTACTKCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRASENNQTHQASLPKQPASQPGGDPTGPKESKKKVESKTETDPVD | 101\n",
      "B0522-R00 | MEPVDPSLEPWKHPGSQPRTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSQTHQVSLSKQPASQPGGNPTGPKESKKKVERETETYPVD | 101\n",
      "B0522-R01 | MEPVDPSLEPWKHPGSQPRTPCTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAPQGSQTHQVSLSKQPASQPGGNPTGPKESKKKVERETETHPVD | 101\n",
      "B0538-R01 | MEPIDPRLEPWKHPGSQPKTPCTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSQTHQASLSKQPTSQPGGDPTGPKESKKKVERETETGPND | 101\n"
     ]
    }
   ],
   "source": [
    "#######################################################################\n",
    "# Conclusion: There are some insanly long Tats that I can't just ignore\n",
    "# but are too long to fit in the model. I'll keep them for safe keeping\n",
    "# in case I want to revisit these later on. \n",
    "#######################################################################\n",
    "\n",
    "for i in tats: print(f\"{i.id[:9]} | {i.seq} | {len(i)}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ORIGINAL SEQUENCE COUNTS: 157\n",
      "PATIENT COUNTS CONTAINING SEQS: 140\n",
      "TAT <= 110 RESIDUES AND FIRST RESIDUE == 'M': 133\n",
      "---\n",
      "TOTAL PATIENT COUNT: 97\n",
      "PATIENTS:\n",
      "{'A0032', 'B0147', 'A0257', 'A0408', 'A0451', 'A0004', 'A0075', 'A0439', 'A0001', 'A0040', 'A0127', 'A0380', 'B0076', 'A0447', 'B0485', 'A0037', 'A0056', 'A0310', 'A0010', 'A0325', 'A0145', 'A0143', 'A0264', 'A0036', 'A0111', 'A0008', 'A0096', 'A0241', 'A0430', 'A0433', 'A0026', 'A0107', 'A0448', 'A0133', 'A0013', 'A0086', 'A0067', 'A0038', 'A0440', 'A0342', 'A0034', 'A0501', 'A0215', 'A0025', 'A0017', 'A0002', 'A0471', 'A0095', 'A0103', 'A0278', 'B0044', 'B0522', 'A0338', 'A0132', 'A0417', 'A0005', 'A0318', 'B0146', 'A0474', 'A0091', 'A0223', 'A0239', 'A0019', 'A0357', 'A0208', 'A0359', 'A0446', 'A0449', 'A0490', 'B0303', 'A0076', 'A0500', 'A0274', 'A0083', 'A0218', 'B0037', 'B0325', 'A0045', 'A0389', 'A0068', 'A0113', 'A0109', 'A0209', 'A0059', 'A0015', 'A0213', 'A0156', 'A0255', 'A0285', 'A0401', 'A0429', 'A0379', 'A0523', 'B0538', 'A0384', 'A0503', 'A0044'}\n",
      "---\n",
      "A0001-R09 | MEPVDPRLEPWKHPGSQPRTPCTACYCKKCCFHCQVCFTRKGLGISYGRKKRGQRRRPPQDSEAHQVSLPKQSAPQLRGDPTGPKESKKEVERETETDPVDQ | 102\n",
      "A0002-R14 | MDPVDPRLEPWKHPGSQPKTPCTPCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPPDSQTHQAPLPKQPTAQPRGDPTGPKESKKKVERETETDPVNQ | 102\n",
      "A0004-R10 | MEPVDPSLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQDSQIHQVPLSKQPASQPRGNPTGPKEQKKKVETEAETDQFD | 101\n",
      "A0005-R05 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCLHCQVCFITKGLGISYGRKKRRKRRRAPQDSETHQVSLSKQPTSQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0005-R07 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCLHCQVCFITKGLGISYGRKKRRKRRRAPQDSETHQVSLSKQPTSQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0008-R07 | MEPVDPRLEPWKHPGSQPKTACNTCYCKRCCLHCQVCFITKGLGISYGRKKRRQRRRAAQDSETRQVPLSKQPASQRRGDPTGQKESKKKVERETETDPVH | 101\n",
      "A0008-R10 | MEPVDPRLEPWKHPGSQPKTACNTCYCKKCCLHCQVCFITKGLGISYGRKKRRQRRRASQDSETRQVPLSKQSAPQRRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0010-R08 | MEPVDPRLEPWKHPGSQPRTPCTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPPQDSETHQASLSKQPASQPRGDPTGPKE | 86\n",
      "A0010-R09 | MEPVDPRLEPWKHPGSQPKTPCTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPPQDSQTHQASLSKQPASQPRGDPTGPKE | 86\n",
      "A0013-R10 | MDPVDPRLEPWKHPGSQPKTACTPCFCKKCCYHCQVCFISKGLGISYGRKKRRQRRRPSQDNQANQASLSKQSAPQTRGNPTGPKESEKKVERETETDPIN | 101\n",
      "A0013-R11 | MDPVDPRLEPWKHPGSQPKTACTPCFCKKCCYHCQVCFISKGLGISYGRKKRRQRRRPPQDNQANQVSLSKQSAPQTRGNPTGPKESEKKVERETETDPIN | 101\n",
      "A0015-R10 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQAHQGSLPKQPASQPRGDPTGPKESKKKVETETETDPVDQWMDS | 106\n",
      "A0015-R11 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQAHQGSLPKQPASQPRGDPTGPKESKKKVERETETDPID | 101\n",
      "A0015-R13 | MDPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQAHQGSLPKQPASQPRGDPTGPKESKKKVETETETDPVDQWMDS | 106\n",
      "A0017-R11 | MELVDPKLEPWKHPGSQPKTPCTKCYCKKCCYHCQMCFTTKGLGISYGRKKRRQRRRAPQNSQTHQASLSKQPASQPRGDPTGPTESKKKVERETATDQED | 101\n",
      "A0019-R12 | MEPVDPRLEPWKHPGSQPRTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRGQRRRAPQDSETHQASLSKQPTSQPRGDPTGPKEPKKKVERETETDPEH | 101\n",
      "A0025-R09 | MDPVDPRLEPWKHPGSQPKTACTKCYCKKCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQDSKTHQDPLPKQPSSQPRGDPTGPKEQKKEVERETETDPVH | 101\n",
      "A0025-R11 | MDPVDPRLEPWKHPGSQPKTACTNCYCKKCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQDSKTHQASLSKQPSSQPRGDPTGPKEQKKKVERETETDPVH | 101\n",
      "A0026-R09 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKKCCFHCQKCFTTKGLGISYGRKKRRQRRRADQDSQTHQVSLSKQPASQPGGNPTGPKE | 86\n",
      "A0032-R06 | MDPVDPSLEPWKHPGSQPKTACTKCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSQLSRFSTKAVPTSQSRGDPTGPKESKKKVETEAETDQFD | 101\n",
      "A0034-R04 | MDPVDPRLEPWQHPGSQPKTPCTNCYCKKCCFHCQSCFTRKALGISYGRKKRRQRRRAHQDSQTHQASLSKQPTSQSGGDPTGPKESEKKVERETETHPHD | 101\n",
      "A0034-R05 | MDPVDPRLEPWQHPGSQPKTPCTNCYCKKCCFHCQSCFTRKALGISYGRKKRRQRRRAPQDSQTHQASLSKQPTSQSGGDPTGPKESKEKVERETETHPYD | 101\n",
      "A0034-R06 | MDPVDPNLEPWKHPGSQPKTPCTNCYCKKCCFHCQSCFTRKALGISYGRKKRRQRRRAHQDSQTHQASLSKQPTSQSGGDPTGPKESEKKVERETETHPYD | 101\n",
      "A0036-R05 | MDPVDPKLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSKTHQTSLSKQPSSQHRGDPAGPKESKKEVERETETDPVD | 101\n",
      "A0037-R10 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPYNSQDHQDSLSKQSSPQPRGNPTGPEKQKEEVESKTETDPHD | 101\n",
      "A0037-R11 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPHNSQDHQDSLSKQSSPQPRGDPTGPEKSKKEVESETETDPHD | 101\n",
      "A0037-R12 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPHNSQDHQDSLSKQSSPQPRGDPTGQEKSKKEVESETETDPHD | 101\n",
      "A0037-R13 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRAPYNSQDHQDSLSKQSSPQPRGDPTGPEKQKKEVESETETDPHD | 101\n",
      "A0038-R08 | MEPVDPRLEPWKHPGSQPRTACTTCYCKRCCYHCQVCFITKGLGISYGRKKRRQRRRAPQGNQTHQVSLSKQSAPQPQRDPTGPKESEKKVERETETDPVD | 101\n",
      "A0040-R05 | MEPVDPRLEPWEHPGSQPKTACTKCYCKKCCYHCQVCFITKALGISYGRKKRRQRRRTPQDSQTHQDSLSKQPTSQSRGDPTGPKEPKKKVERETETDPYD | 101\n",
      "A0040-R06 | MEPVDHRLEPWKHPGSQPKTACTKCYCKRCCYHCQVCFITKALGISYGRKKRRQRRRTPQDSQTHQDSLPKQPTSQSRGDPTGPKEPKKKVERETETDPYD | 101\n",
      "A0044-R10 | MEPVDPRLEPWKHPGSQPKTPCTHCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPPDSEAHQVSLSKQPAAQPPGDPTGPKESKKKVERETETDPVTQ | 102\n",
      "A0044-R12 | MEPVDPRLEPWKHPGSQPKTACTHCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPPDSEAHQVSLSKQPAAQPPGDPTGPKESKKKVERETETDPVTQ | 102\n",
      "A0045-R03 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSHQNSQTHQVSLSKQPTSQPGGDPTGPKESKKKVETETETDPVH | 101\n",
      "A0045-R04 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSHQNSQTHQVSLSKQPTSQPGGDPTGPEESKKKVETETATHPID | 101\n",
      "A0045-R05 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSHQNSQTHQVSLSKQPTSQPGGDPTGPKESKKKVETETETDPVH | 101\n",
      "A0045-R06 | MEPVDPRLEPWKHPGSQPMTPCTNCYCKKCCFHCQACFITKGLGISYGRKKRRQRRRSHQTVRLIKFLYQSRPTSQPGGDPTGPKESKKKVETETETHPID | 101\n",
      "A0056-R06 | MEPVDPRLEPWKHPGSRPKTDCPKCYCKRCCFHCQVCFLTKGLGISYGRKKRRQRRRPPQDSETHQASLSKQPSSQPHGDPTGPKEQKKKVESETTADPCD | 101\n",
      "A0056-R07 | MEPVDPRLEPWKHPGSRPKTVCTKCYCKKCCFHCQVCFITKGLGISYGRKKRKQRRRTPQDSETHQASLSKQPSSQPHGDPTGPKEQKKKVESETKADPCD | 101\n",
      "A0059-R08 | MEPVDPSLEPWKHPGSQPKTACNNCFCKKCCFHCQKCFVTKGLGISYGRKKRRQRRRAHQGNQSHQSSLPKQPPSQSRGNPTGPEEQKKKVEKEAETDPFA | 101\n",
      "A0059-R09 | MEPVDPSLEPWKHPGSQPKTACNNCFCKKCCFHCQKCFVTKGLGISYGRKKRRQRRRAHQGNQSHQSSLPKQPPSQSRGNPTGPEEQKKKVEKEAETDPFA | 101\n",
      "A0067-R11 | MEPIDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPDSQTHQASLSKQ | 71\n",
      "A0068-R03 | MEPVDPKLEPWKHPGSQPKTACTNCYCKICCFHCQVCFTRKGLGISYGRKKRRQRRRAPQDSQTHQDSLPKQPASQPRGDPTGPKESKKKVERETETDPEDQWRAS | 106\n",
      "A0075-R07 | MDPVDPRLEPWKHPGSQPRTACTNCYCKQCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQGGQAHQGSLSKQPSSQQRGDPTGPKEQKEKVERETETDPDH | 101\n",
      "A0075-R09 | MDPVDPRLEPWKHPGSQPRTACTNCYCKRCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQGGQAHQDSLSKQPSSQQRGDPTGPKEQKEKVERETETDPDH | 101\n",
      "A0075-R10 | MDPVDPRLEPWKHPGSQPRTACTNCYCKRCCWHCQVCFLTKGLGISYGRKKRRQRRRAPQGGQAHQDSLSKQPSSQQRGDPTGPKEQKEKVERETETDPDH | 101\n",
      "A0076-R04 | MDPVDPRLEPWNHPGSQPKTACTKCYCKKCCLHCQVCFIKKGLGISYGRKKRRQRRRTPQGGQTHQVSLPKQPSSQPRGDPTGPKESKEKVERETETHPVN | 101\n",
      "A0076-R05 | MDPVDPRLEPWNHPGSQPKTACTKCYCKKCCLHCQVCFIKKGLGISYGRKKRRQRRRTPQGGQTHQVSLSKQPSSQPRGDPTGPKESKEKVERETETHPVN | 101\n",
      "A0083-R06 | MDPVDPRLEPWKHPGSRPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPPQTVRLIKFLYQSRPSSQHPGDPTGPKESKKEVERETETDPVH | 101\n",
      "A0086-R04 | MEPVDPRLEPWKHPGSQPKTACTRCYCKQCCFHCQVCFITKALGISYGRKKRRQRRRAPQDSENHQVSPPKQPASQPRGDPTGPKESKKKVERETETDPDH | 101\n",
      "A0086-R05 | MEPVDPRLEPWKHPGSQPKTACTRCYCKQCCFHCQVCFITKALGISYGRKKRRQRRRAPQDSENHQVSPPKQPASQLRGDPTGPKKSKKEVERETETDPDH | 101\n",
      "A0091-R04 | MDPVDPRLEPWKHPGSQPKTACSPCHCKVCCFHCQVCFIRKALGISYGRKKRRQRRRAPQDSQTHQASLSEQPAPQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0095-R09 | MEPVDPRLEPWNHPGSQPKTPCTPCYCKRCCLHCQVCFITKGLGISYGRKKRRKRRRSPQDSETHQEPLSKQPTSQPRGDPTGPEESKKKVERETETHPRA | 101\n",
      "A0095-R10 | MEPVDPRLEPWNHPGSQPKTPCTPCYCKRCCLHCQVCFITKGLGISYGRKKRRKRRRSPQDSEAHQEPLSKQPTSQPRGDPTGPEESKKTVERETETHPRD | 101\n",
      "A0095-R11 | MEPVDPRLEPWNHPGSQPKTPCTPCYCKRCCLHCQVCFITKGLGISYGRKKRRKRRRSPQDSETHQGPLSKQPTSQPRGDPTGPEKSKKKVERETETHPRD | 101\n",
      "A0096-R08 | MEPVDPRLEPWKHPGSQPRTPCTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRPPQDNQTHQVPLSKQPASQTGGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0103-R06 | MEPVDPRLEPWKHPGSQPETACTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSQTHQVSLSKQSAPQQRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0103-R07 | MEPVDPRLEPWKHPGSQPETACTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSQTHQVSLSKQSAPQQRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0107-R09 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPSPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0107-R10 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPSPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0107-R11 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPGPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0107-R12 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQDSQTDQGYLPKQPGPQHRGDPTGPKESKKKVERETEAGPKD | 101\n",
      "A0109-R11 | MDPVDPRLEPWKHPGSQPKTACTNCYCKQCCFHCQVCFITKGLGISYGRKKRRQRRRINQDNQNHQVPLPKQPTTQPRGDQTGPKE | 86\n",
      "A0111-R05 | MEPIDPSLEPWKHPGSQPKTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRSKRRRAPQDSQTHQVSLSKQPTSQSRGDPTGPKESKKKVETETETDPDH | 101\n",
      "A0111-R07 | MEPVDPKLEPWKHPGSQPKTACTPCYCKQCCFHCQVCFITKGLGISYGRKKRSKRRRAPQTIRLIKSLYQSRPTSQPRGDPTGPKESKKKVERETETDQDN | 101\n",
      "A0113-R11 | MEPVDPRLEPWKHPGSQPRTPCTSCYCKQCCFHCQKCFITKGLGISYGRKKRRQRRRAPQGSQTHQVSLPKQPASQPGGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0113-R12 | MEPVDPRLEPWKHPGSQPSTPCTSCYCKQCCFHCQKCFVTKGLGISYGRKKRRQRRRAPQGSQTHQVSLPKQPASQPGGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0127-R08 | MEPVDPSLEPWKHPGSQPRTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQTHQEALSKQPASQPRGDPTGPKESTKKVERETETNPDD | 101\n",
      "A0132-R11 | MEPIDPRLEPWQHPGSQPKTPCTSCYCKKCCFHCQVFHDKRLRHLLWQEEAETATKSSSSRQSDSSSVSIKAPTSQPRGDPTGPKESKKKVERETETDPED | 101\n",
      "A0133-R05 | MEPVDPRLEPWKHPGSQPKTPCNKCYCKRCCFHCQMFHNKRLRHLLWQEEAETATKSSSEQSDSSRSSTKAVPASQPRGDPTGPKESKKKVERETETDPVH | 101\n",
      "A0143-R06 | MEPVDPRLEPWKHPGSQPKTACTKCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRTSQDSQDHQVPLSKQPASQPGGDPTGPKESKKKVERETETDPVDQWMDS | 106\n",
      "A0145-R08 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSPQDSQTHQVPLPKQPASQPRGDQTGPKESKKKVAKETEMDPVS | 101\n",
      "A0145-R11 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSPQDSQTHQVPLPKQPASQPRGDQTGPKESKKKVAKETEMDPVS | 101\n",
      "A0145-R12 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRSPQDSQTHQVPLPKQPASQPRGDQTGPKESKKKVAKETEMDPVS | 101\n",
      "A0156-R06 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKKCCFHCQVCFMTKGLGISYGRKKRGQRRRTPQGGQSHQVPLPKQPTSQPGGDPTGPKEQKKKVERETETDPYA | 101\n",
      "A0208-R05 | MEPVDPRLEPWKHPGSQPKTACTNAIVKSVAFIAKFVS | 38\n",
      "A0209-R07 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSKTHQASLSKQPTSQPRGDPTGPKEPKKKVEREAETDPVD | 101\n",
      "A0213-R04 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKECCFHCQVCFTKKGLGISYGRKKRRQRRGTHQSSETHQVSLPKQKGLRHLLWQEEAETATRNSSKQ | 94\n",
      "A0215-R09 | MEPVDHKLEPWKHPGSQPKTPCTNCYCKKCCFHCQVCFTKKGLGISYGRKKRRQRRRTSQDSETHQASLSKQPTSQQRGDPTGPKESKEKVERETAADPFD | 101\n",
      "A0218-R04 | MEPVDPSLEPWKHPGSQPKTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRPHQDSQTHQDSLPKQPSSQPRGDQTGPKESQKKVERETETDPVA | 101\n",
      "A0223-R04 | MDPVDPRLEPWKHPGSQPKTACTSCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQSRQVSLSKQPTAQLRGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0239-R05 | MDPVDPKLEPWKHPGSQPNTPCTNCYCKKCCFHCQVCFTKKALGISYGRKKRIKRRRPSQDSQTHQGPLPKQPTTQPRGDPTGPKESKKKVERETETDPED | 101\n",
      "A0241-R03 | MEPVDPNLEPWKHPGSQPKTACTPCYCKKCCFHCQKCFTTKGLGISYGRKKRGQRRRPPQDSKTHQVSLSKQSAPQPRGDPTGPKESKKKVERETETDPKD | 101\n",
      "A0255-R02 | MEPVDPRLEPWQHPGSQPTTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQGSEIHQVSLSKQPSSQSQGDPTGPKESKEKVESKTETDLVDQ | 102\n",
      "A0257-R05 | MEPVDPRLEPWKHPGSQPKTVCTACYCKKCCYHCPVCFVSKGLGISYGRKKRRRRRRADQGSQTHQVSLSKQPTSQLRGDPTGPKESKKKVERETETDQVD | 101\n",
      "A0264-R03 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCLHCQVCFITKGLGISNGRKKRRQRRRASQTVRLIKLLYQSRPASQPRGDPTGPKESKKKVERETEADPDH | 101\n",
      "A0274-R06 | MDPVDPRLEPWKHPGSQPRTPCTKCYCKKCCLHCQVCFITKGLGISYGRKKRRQRRRTPQDSQTNQVPASEQPSSQSRGDPTGPKESKEKVERETETDPCD | 101\n",
      "A0278-R05 | MEPVDPKLEPWKHPGSQPRTACTNCYCKKCCFHCQVCFTKKALGISYGRKKRRQRRRAPQNSQIDQVSPSKQPSSQPRGDPTGPKESEKKVERETEKDQGH | 101\n",
      "A0285-R04 | MEPVDPRLEP | 10\n",
      "A0310-R04 | MEPVDPRLEPWKHPGSQPETPCNACYCKKCCFHCQWCFTRKGLGISYGRKKRGQRRRPPQDSQAHQVPLPKQSAPQPRGDQTGPKESKKKVERETETDPDN | 101\n",
      "A0318-R03 | MEPVDPRLEPWKHPGSQPKTACNNCYCKRCCFHCQVCFTRKGLGISYGRKKRRQRRRPAQDSQAHQVSLSKQPSSQLRGDPKGPKESKKKVERETETDPYD | 101\n",
      "A0325-R03 | MEPVDPKLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQDSETHQANLSKQPASQPRGDPTGPEESKKKVERETETDQLD | 101\n",
      "A0338-R01 | MEPVDSRLEPWKHPGSQPQTPCTSCYCKKCCFHCQVCFIKKALGISYGRKKRSKRRRASHDSPNHQDSLPKQPSSQLGGDPTGPKKQKKEVERETETHPDN | 101\n",
      "A0342-R03 | MEPVDPRLEPWKHPGSQPATACTSCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQNSQTHQDSLSKQPASQQRGDPTGPKESKKKVEREAETDPDH | 101\n",
      "A0357-R04 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSKAHQASLPKQPASQPRGDPTGPKESTKKVERETETDPNH | 101\n",
      "A0359-R07 | MEPVDPRLEPWKHPGSQPKTPCTPCYCKKCCYHCQIAS | 38\n",
      "A0379-R06 | MEPVDPSLEPWKHPGSQPKTACNSCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRASQDSQTDQVSLSKQPATQRRGDPTGPKESKKKVERETETDPNH | 101\n",
      "A0380-R03 | MDPVDPRLEPWKHPGSQPKTACNNCYCKKCCWHCQLCFLKKGLGISYGRKKRRQRRRTNQVXQTHQGDLSKQPASQLRGDPTGPKEQKKKVESKTETDP | 99\n",
      "A0384-R03 | MEPVDPRLEPWKHPGSQPRTPCNKCYCKKCCLHCQVCFISKGLGISYGRKKRRQRRRPPHDSQTHQDSLPKQPSSQDRGDPKGPKEQKEKVERETATDPCD | 101\n",
      "A0389-R07 | MEPVDPRLEPWKHPGSQPRTPCTTCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSQTHQDSLSKQPASQSGGNPTGPKESKKKVESKTETDPDD | 101\n",
      "A0401-R03 | MEPVDPRLEPWKHPGSQPKTACNKCYCKRCCLHCQVCFVTKGLGISYGRKKRRPRRRPPQHSQTHQASLSEQPASQPRGDPTGPKESKEKVESKTETDPDH | 101\n",
      "A0408-R02 | MEPVDPRLEPWKHPGSQPKTPCTNCYCKKCCYHCQVCFITKGLGISYGRKKRRQRRRAPQDSQNHQVPLSKQPTSQPGGDPTGPKESKKKVETETETDPVH | 101\n",
      "A0417-R01 | MEPVDPSLEPWKHPGSQPKTACTPCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRPPRTVRIIKLLYQSRPASQPGGDPTGPKESKKKVEGTTETHPLD | 101\n",
      "A0417-R03 | MEPVDPSLEPWKHPGSQPKTACTPCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRPPRTVRIIKLLYQSRPASQPGGDPTGPKESKKKVEGTTETHPLD | 101\n",
      "A0429-R04 | MEPVDHNLDPWKHPGSQPKTPCNKCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRSPQGSQTHQVSPSKQPASQPRGDPTGPKEPKKKVERETETDPVH | 101\n",
      "A0430-R01 | MEPVDPRLEPWKHPGSQPRTPCTACYCKKCCYHCQVCFITKGLGISYGRKKRRQRRRTPQDSQTHQASLSKQPSSQPRRDQTGPKESKKKVERETETDPED | 101\n",
      "A0433-R04 | MDPVDPRLEPWKHPGSQPKTACTPCFCKRCCYHCQVCFISKGLGISYGRKKRRQRRRPPQDSQIHQVSLSKQSASQLRGNPTGPKESEKKVERETETDPVH | 101\n",
      "A0439-R01 | MEPVDPKLEPWNHPGSQPRTACTNCYCKKCCLHCQVCFITKGLGISYGRKKRRQRRRAHQDSETHQGDLSQQPASQPRGDPTGPKESKEKVERETEADPGH | 101\n",
      "A0440-R02 | MEPVDPRLEPWKHPGSQPRTPCTACYCKKCCYHCQVCFITKGLGISYGRKKRRQRRRSPQGSQTHQDSLSKQPPSQPRGDQTGPKESTKKVERETKTDPKD | 101\n",
      "A0446-R04 | MEPVDPRLAPWQHPGSQPRTACTSCYCKKCCFHCQKCFTTKGLGISYGRKKRRQRRTAPGDSQIHQVSLSKQPATQARGDPTGPKESKKKVERETETDPVN | 101\n",
      "A0447-R01 | MEPVDPRLEPWKHPGSQPRTPCTSCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRPHQTVKFIKILYQSRPDSQPRGDPTGPKESKKKVESETETDQFA | 101\n",
      "A0448-R04 | MEPVDPRLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRGQRRRPPHGSETRPDSLSKQPSSQPRGNPTGPTEPEKKVERETEAHPS | 100\n",
      "A0449-R01 | MEPVDPRIEPWKHPGSQPKTACTTCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQTHQASLSKQSAPQLRGDPTGPKESKKTVERETETDPVN | 101\n",
      "A0451-R03 | MEPVDPRLEPWKHPGSQPRTACNNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPRQSKSSRFSIKAVPSSQLRGDPTGPKKQKKEVERETETDPVN | 101\n",
      "A0471-R02 | MEPVDPRLEPWKHPGSQPRTACTSCYCKKCCFHCQVCFTKKGLGISYGRKKRGQRRRSPQSSETHQAALPEQPTSQPGGDPTGPKESKKKVETETETDPLH | 101\n",
      "A0474-R03 | MDPVDPRLEPWKHPGSQPKTACTPCFCKKCCYHCQVCFISKGLGISYGRKKRRQRRRSPHDSQNNQVSLSKQSAPQPRGDPTGPKESEKKVERETETDPVT | 101\n",
      "A0490-R02 | MEPVDPNLEPWKHPGSQPKTACTKCYCKRCCFHCQVCFITKGLGISYGRKKWRQRRRASQDSQTRQVSLSKQPTSQPGGDPTGPKESKKKVERETEADPVY | 101\n",
      "A0500-R03 | MEPVDPRLEPWKHPGSQPKTACTPCFCKVCCYHCQVCFISKGLGISYGRKKRRQRRRAPQDSETHQVSLPKQPTTQPRGDKKGPEESKKKVERETETHPGR | 101\n",
      "A0501-R02 | MEPVDPRLEPWKHPGSQPKTACNNCFCKKCCYHCQGCFISKGLGISYGRKKRRQRRRAPQDSEDHQVSLPKQPTSQTRGDPTGPEEPQKKVESKTETHPGD | 101\n",
      "A0503-R04 | MEPVDPRLEPWKHPGSQPRTACTTCYCKKCCFHCQVCFMTKGLGISYGRKKRRQRRRATQDSQAHQAPLSKQPASQHRGDPTGPEESKKKVERETETDPVH | 101\n",
      "A0523-R03 | MEPVDPRLEPWNHPGSQPKTACTPCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRTPQDSKDHQVSLSKQPSSQLQGDPTGPKESKKKVEKEAGTDPGH | 101\n",
      "B0037-R01 | MEPVDPRLEPWKHPGSQPKTPCTKCYCKKCSFHCQVCFITKGLGISYGRKKRRQRRRAPHNSQDHQDSLSKQSSPQPRGDPTGPEKSKKEVEIETETDPHD | 101\n",
      "B0044-R02 | MEPVDPRLEPWKHPGSQPKTACTHCYCKRCCFHCQVCFITKGLGISYGRKKRRQRRRAPPDSEAHQVSLSKQPAAQPPGDPTGPKESKKKVERETETDPVTQ | 102\n",
      "B0076-R00 | MEPVDPRLEPWKHPGSQPKTACTKCYCKKCCLHCQVCFIKKGLGISYGRKKRRQRRRTPQGGQTHQVSLSKQPSSQPRGDPTGPKESKEKVERETETHPVD | 101\n",
      "B0146-R00 | MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQDSQTHQASLSKQPASQPRGDPTGPKESKKKVERETETDPRD | 101\n",
      "B0147-R00 | MEPVDPRLEPWKHPGSQPKTDCTNCYCKRCCFHCQVCFMKKGLGISYGRKKRRQRRRTPQGSEAHQGPLSKQPASQHRGDPTGPKESKKKVERETETDQDN | 101\n",
      "B0303-R02 | MDPVDPKLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRTPQDGQTHQTSLSKQPSSQPRGDPTGPKESKKKVEREAETHPAD | 101\n",
      "B0325-R00 | MEPVDPKLEPWKHPGSQPKTACTPCYCKKCCFHCQTCFITKGLGISYGRKKRRQRRRAHQDSETHQANLSKQPASQPRGDPTGPEESKKKVERETETDQLD | 101\n",
      "B0325-R01 | MEPVDPKLEPWKHPGSQPKTACTPCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAHQDSETHQANLSKQPASQPRGDPTGPEESKKKVERETETDQLD | 101\n",
      "B0485-R00 | MEPIDPRLEPWKHPGSQPRTACTKCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRASENNQTHQASLPKQPASQPGGDPTGPKESKKKVESKTETDPVD | 101\n",
      "B0522-R00 | MEPVDPSLEPWKHPGSQPRTPCTNCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSQTHQVSLSKQPASQPGGNPTGPKESKKKVERETETYPVD | 101\n",
      "B0522-R01 | MEPVDPSLEPWKHPGSQPRTPCTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAPQGSQTHQVSLSKQPASQPGGNPTGPKESKKKVERETETHPVD | 101\n",
      "B0538-R01 | MEPIDPRLEPWKHPGSQPKTPCTNCYCKKCCFHCQVCFTTKGLGISYGRKKRRQRRRAPQDSQTHQASLSKQPTSQPGGDPTGPKESKKKVERETETGPND | 101\n"
     ]
    }
   ],
   "source": [
    "print(f\"\"\"ORIGINAL SEQUENCE COUNTS: {len(fasta)}\n",
    "PATIENT COUNTS CONTAINING SEQS: {len(no_seq_fasta)}\n",
    "TAT <= 110 RESIDUES AND FIRST RESIDUE == 'M': {len(good_tats)}\n",
    "---\n",
    "TOTAL PATIENT COUNT: {len(set([tat.id[:5] for tat in good_tats]))}\n",
    "PATIENTS:\n",
    "{set([tat.id[:5] for tat in good_tats])}\n",
    "---\"\"\")\n",
    "\n",
    "for i in good_tats: print(f\"{i.id[:9]} | {i.seq} | {len(i)}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TOTAL TATS WHERE FIRST RESIDUE == 'I' : 2\n",
      "'I' TAT PATIENT COUNT: 2\n",
      "'I' TAT PATIENTS:\n",
      "{'A0032', 'A0152'}\n",
      "---\n",
      "A0032-R05 | INPVDPSLEPWKHPGSQPKTACTKCYCKKCCFHCQVCFITKGLGISYGRKKRRQRRRAPQGSKTXQNSLPKQPTSQSRGNPTGPKESKKKVKTEAETDQFN | 101\n",
      "A0152-R03 | INPVDPRLEP | 10\n"
     ]
    }
   ],
   "source": [
    "#######################################################################\n",
    "# Conclusion: 'I' Tats cannot be salvaged. The rest of the\n",
    "# exon just fits too cleanly for it to be a misalignment. But\n",
    "# This seems interesting all things considered. Maybe it's\n",
    "# A blessing in disguiase. Saving these Tats for later investigation\n",
    "#######################################################################\n",
    "\n",
    "print(f\"\"\"TOTAL TATS WHERE FIRST RESIDUE == 'I' : {len(i_tats)}\n",
    "'I' TAT PATIENT COUNT: {len(set([tat.id[:5] for tat in i_tats]))}\n",
    "'I' TAT PATIENTS:\n",
    "{set([tat.id[:5] for tat in i_tats])}\n",
    "---\"\"\")\n",
    "\n",
    "for i in i_tats: print(f\"{i.id[:9]} | {i.seq} | {len(i)}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "save = True\n",
    "\n",
    "if save:\n",
    "    save_output(tats, '../Data/CohortTats/PacBio/PacBio_All_Tats.fasta')\n",
    "    save_output(good_tats, '../Data/CohortTats/PacBio/PacBio_Trimmed_Normal_Tats.fasta')\n",
    "    save_output(i_tats, '../Data/CohortTats/PacBio/PacBio_Trimmed_I_Tats.fasta')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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