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small fixes (#294)
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@manulera
manulera authored Oct 7, 2024
1 parent e86fc3c commit 26f36e2
Showing 1 changed file with 54 additions and 53 deletions.
107 changes: 54 additions & 53 deletions docs/notebooks/Example_Restriction.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -561,50 +561,31 @@
"name": "stdout",
"output_type": "stream",
"text": [
"ACCATGTCGACATGCAAACAGTAATGATGGATG\n",
"ATGGCGCGCCTAAAAGCCTTCTTCTCCC\n"
"ACCATGTCGACATGCAAACAGTAATGATGGA , Tm: 57.24061148156318\n",
"GGCGCGCCATTAAAAGCCTTCTTCTCCC , Tm: 56.64459495003314\n"
]
}
],
"source": [
"from pydna.design import primer_design\n",
"#Finding the feature containing the CDS with ase1 as a type qualifier\n",
"gene = [f for f in pombe_chromosome_I.features if f.type == \"CDS\" and \n",
" \"gene\" in f.qualifiers and \n",
" \"ase1\" in f.qualifiers[\"gene\"]][0]\n",
"gene = next(f for f in pombe_chromosome_I.features if f.type == \"CDS\" and\n",
" \"gene\" in f.qualifiers and\n",
" \"ase1\" in f.qualifiers[\"gene\"])\n",
"\n",
"#Reading off the CDS to design primers\n",
"fwd_pompe_seq = pombe_chromosome_I[min(gene):min(gene)+22]\n",
"back_pompe_seq = pombe_chromosome_I[max(gene)-18:max(gene)]\n",
"# Using the primer_design function to design primers to amplify the CDS\n",
"# `min` and `max` can be used on a SeqFeature to get the start (leftmost) and end (rightmost) positions\n",
"# this works both on feature with SimpleLocation and CompoundLocation\n",
"amplicon = primer_design(pombe_chromosome_I[min(gene):max(gene)], target_tm=55)\n",
"\n",
"fwd_primer_ase1 = Dseqrecord(\"ACCATGTCGAC\") + fwd_pompe_seq # Adding a SalI cut site\n",
"rvs_primer_ase1_3_start = back_pompe_seq + Dseqrecord(\"GGCGCGCCAT\") # Adding a AscI cut site\n",
"rvs_primer_ase1 = rvs_primer_ase1_3_start.reverse_complement()\n",
"fwd_align, rvs_align = amplicon.primers()\n",
"fwd_primer_ase1 = Dseqrecord(\"ACCATGTCGAC\") + fwd_align # Adding a SalI cut site\n",
"rvs_primer_ase1 = Dseqrecord(\"GGCGCGCCAT\") + rvs_align # Adding a AscI cut site\n",
"\n",
"# Printing out the primers\n",
"\n",
"print(fwd_primer_ase1.seq)\n",
"print(rvs_primer_ase1.seq)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"57.08651869811922\n",
"65.11883125971309\n"
]
}
],
"source": [
"# Checking that the primer Tm are matching for the genomic portion of the primer\n",
"\n",
"print(tm_default(fwd_primer_ase1.seq[-22:])) # Modify the primer sequence above retroactively here, if Tm not matching.\n",
"print(tm_default(rvs_primer_ase1.seq[:18]))"
"print(fwd_primer_ase1.seq, ', Tm: ', tm_default(fwd_align))\n",
"print(rvs_primer_ase1.seq, ', Tm: ', tm_default(rvs_align))"
]
},
{
Expand All @@ -617,7 +598,7 @@
"output_type": "stream",
"text": [
"LOCUS 2263bp_PCR_prod 2263 bp DNA linear UNK 01-JAN-1980\n",
"DEFINITION pcr_product_description_description_rc.\n",
"DEFINITION pcr_product_description_description.\n",
"ACCESSION 2263bp\n",
"VERSION 2263bp\n",
"DBLINK BioProject: PRJNA13836\n",
Expand All @@ -627,16 +608,36 @@
" ORGANISM .\n",
" .\n",
"FEATURES Location/Qualifiers\n",
" primer_bind 1..22\n",
" CDS join(1..424,472..2243)\n",
" /gene=\"ase1\"\n",
" /locus_tag=\"SPOM_SPAPB1A10.09\"\n",
" /codon_start=1\n",
" /product=\"antiparallel microtubule cross-linking factor\n",
" Ase1\"\n",
" /protein_id=\"CAC21482.1\"\n",
" /translation=\"MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIE\n",
" RLHQVLGTDGDNSSLFELFTTAMNAQLHEMEQCQKKLEDDCQQRIDSIRFLVSSLKLTD\n",
" DTSSLKIESPLIQCLNRLSMVEGQYMAQYDQKLSTIKEMYHKLESYCNRLGSPFVLPDF\n",
" ENSFLSDVSDAFTESLRGRINEAEKEIDARLEVINSFEEEILGLWSELGVEPADVPQYE\n",
" QLLESHTNRPNDVYVTQELIDQLCKQKEVFSAEKEKRSDHLKSIQSEVSNLWNKLQVSP\n",
" NEQSQFGDSSNINQENISLWETELEKLHQLKKEHLPIFLEDCRQQILQLWDSLFYSEEQ\n",
" RKSFTPMYEDIITEQVLTAHENYIKQLEAEVSANKSFLSLINRYASLIEGKKELEASSN\n",
" DASRLTQRGRRDPGLLLREEKIRKRLSRELPKVQSLLIPEITAWEERNGRTFLFYDEPL\n",
" LKICQEATQPKSLYRSASAAANRPKTATTTDSVNRTPSQRGRVAVPSTPSVRSASRAMT\n",
" SPRTPLPRVKNTQNPSRSISAEPPSATSTANRRHPTANRIDINARLNSASRSRSANMIR\n",
" QGANGSDSNMSSSPVSGNSNTPFNKFPNSVSRNTHFESKSPHPNYSRTPHETYSKASSK\n",
" NVPLSPPKQRVVNEHALNIMSEKLQRTNLKEQTPEMDIENSSQNLPFSPMKISPIRASP\n",
" VKTIPSSPSPTTNIFSAPLNNITNCTPMEDEWGEEGF\"\n",
" primer_bind 1..20\n",
" /label=\"name\"\n",
" /PCR_conditions=\"primer\n",
" sequence:ACCATGTCGACATGCAAACAGTAATGATGGATG\"\n",
" sequence:ACCATGTCGACATGCAAACAGTAATGATGGA\"\n",
" /ApEinfo_fwdcolor=\"#baffa3\"\n",
" /ApEinfo_revcolor=\"#ffbaba\"\n",
" primer_bind complement(2225..2242)\n",
" /label=\"name_rc\"\n",
" primer_bind complement(2225..2243)\n",
" /label=\"name\"\n",
" /PCR_conditions=\"primer\n",
" sequence:ATGGCGCGCCTAAAAGCCTTCTTCTCCC\"\n",
" sequence:GGCGCGCCATTAAAAGCCTTCTTCTCCC\"\n",
" /ApEinfo_fwdcolor=\"#baffa3\"\n",
" /ApEinfo_revcolor=\"#ffbaba\"\n",
"ORIGIN\n",
Expand Down Expand Up @@ -677,7 +678,7 @@
" 2041 aactaatctg aaagaacaaa cacccgagat ggacattgaa aacagctcgc agaaccttcc\n",
" 2101 tttttctcct atgaagatat cccccataag agcatcaccc gtaaagacaa ttccatcatc\n",
" 2161 accgtccccc actaccaaca ttttttctgc tccactcaac aatattacaa attgtacacc\n",
" 2221 gatggaggat gaatggggag aagaaggctt ttaggcgcgc cat\n",
" 2221 gatggaggat gaatggggag aagaaggctt ttaatggcgc gcc\n",
"//\n"
]
}
Expand All @@ -702,21 +703,21 @@
"output_type": "stream",
"text": [
"(Dseqrecord(-30), Dseqrecord(-3916))\n",
"(Dseqrecord(-10), Dseqrecord(-2253), Dseqrecord(-8))\n"
"(Dseqrecord(-10), Dseqrecord(-2255), Dseqrecord(-6))\n"
]
}
],
"source": [
"# Cleaving the cloning vector with restriction enzymes\n",
"\n",
"plamsid_digests = vector.cut(SalI, AscI)\n",
"plasmid_digests = vector.cut(SalI, AscI)\n",
"\n",
"# Cleaving the gene fragment with restriction enzymes\n",
"\n",
"gene_digests = Dseqrecord(pcr_product).cut(SalI, AscI)\n",
"\n",
"# Printing out the digests\n",
"print(plamsid_digests) \n",
"print(plasmid_digests) \n",
"print(gene_digests)"
]
},
Expand All @@ -729,7 +730,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"LOCUS name 6161 bp DNA circular UNK 01-JAN-1980\n",
"LOCUS name 6163 bp DNA circular UNK 01-JAN-1980\n",
"DEFINITION description.\n",
"ACCESSION id\n",
"VERSION id\n",
Expand Down Expand Up @@ -815,10 +816,10 @@
" primer_bind 3859..3876\n",
" /label=\"SP6\"\n",
" /note=\"SP6 promoter, forward primer\"\n",
" primer_bind complement(6131..6148)\n",
" /label=\"name_rc\"\n",
" primer_bind complement(6131..6149)\n",
" /label=\"name\"\n",
" /PCR_conditions=\"primer\n",
" sequence:ATGGCGCGCCTAAAAGCCTTCTTCTCCC\"\n",
" sequence:GGCGCGCCATTAAAAGCCTTCTTCTCCC\"\n",
" /ApEinfo_fwdcolor=\"#baffa3\"\n",
" /ApEinfo_revcolor=\"#ffbaba\"\n",
"ORIGIN\n",
Expand Down Expand Up @@ -924,20 +925,20 @@
" 5941 gcaaagaact aatctgaaag aacaaacacc cgagatggac attgaaaaca gctcgcagaa\n",
" 6001 ccttcctttt tctcctatga agatatcccc cataagagca tcacccgtaa agacaattcc\n",
" 6061 atcatcaccg tcccccacta ccaacatttt ttctgctcca ctcaacaata ttacaaattg\n",
" 6121 tacaccgatg gaggatgaat ggggagaaga aggcttttag g\n",
" 6121 tacaccgatg gaggatgaat ggggagaaga aggcttttaa tgg\n",
"//\n"
]
}
],
"source": [
"# Ligating, then circularising the synthetic plasmid\n",
"\n",
"Synthetic_Vector = plamsid_digests[1] + gene_digests [1]\n",
"Synthetic_Vector = Synthetic_Vector.looped()\n",
"synthetic_vector = plasmid_digests[1] + gene_digests [1]\n",
"synthetic_vector = synthetic_vector.looped()\n",
"\n",
"# Printing out the completed cloning vector\n",
"\n",
"print(Synthetic_Vector.format(\"gb\"))"
"print(synthetic_vector.format(\"gb\"))"
]
}
],
Expand All @@ -957,7 +958,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down

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