Importing and viewing sequence files in pydna
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pydna can be used to work with FASTA, Genbank, EMBL, and snapgene files (.fasta, .gb, .embl, .dna). You can read these files into a Dseqrecord that one can view and work with. You can also instantiate Dseqrecord objects with strings.
Importing Sequence Files
To import files into pydna is simple. pydna provides the parse method to read all DNA sequences in a file into a list. As an input, parse can take:
The path to a file from your computer
A python string with the file content.
The following code shows an example of how to use the parse function to import a FASTA file.
# Install pydna (only when running on Colab)
import sys
if 'google.colab' in sys.modules:
%%capture
# Install the current development version of pydna (comment to install pip version)
!pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn
# Install pip version instead (uncomment to install)
# !pip install pydna
from pydna.parsers import parse
#Import your file into python using its path
file_path = "./U49845.fasta"
files = parse(file_path)
#Show your FASTA file in python
print(files[0].format("fasta"))
>lcl|U49845.1_cds_AAA98665.1_1 [protein=TCP1-beta] [frame=3] [protein_id=AAA98665.1] [location=<1..206] [gbkey=CDS]
TCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCC
GACATGAGACAGTTAGGTATCGTCGAGAGTTACAAGCTAAAACGAGCAGTAGTCAGCTCT
GCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGA
ACCGCCAATAGACAACATATGTAA
Note that parse returns a list object, hence requiring [0] to take the first element of the list. When you have a FASTA file that contains multiple sequences, you can index the list accordingly (e.g [0], [1], …)
The last line of code uses the format method to generate a string representation of the sequence as a FASTA file.
Another example, using a GenBank file (U49845), is shown below.
from pydna.parsers import parse
file_path = "./U49845.gb"
files = parse(file_path)
# Convert the Dseqrecord object into a formatted string in GenBank format
files[0].format("gb")
LOCUS SCU49845 5028 bp DNA linear PLN 29-OCT-2018
DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p
(AXL2) and Rev7p (REV7) genes, complete cds.
ACCESSION U49845
VERSION U49845.1
KEYWORDS .
SOURCE Saccharomyces cerevisiae (brewer's yeast)
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae;
Saccharomyces.
REFERENCE 1 (bases 1 to 5028)
AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M.
TITLE Selection of axial growth sites in yeast requires Axl2p, a novel
plasma membrane glycoprotein
JOURNAL Genes Dev. 10 (7), 777-793 (1996)
PUBMED 8846915
REFERENCE 2 (bases 1 to 5028)
AUTHORS Roemer,T.
TITLE Direct Submission
JOURNAL Submitted (22-FEB-1996) Biology, Yale University, New Haven, CT
06520, USA
FEATURES Location/Qualifiers
source 1..5028
/organism="Saccharomyces cerevisiae"
/mol_type="genomic DNA"
/db_xref="taxon:4932"
/chromosome="IX"
mRNA <1..>206
/product="TCP1-beta"
CDS <1..206
/codon_start=3
/product="TCP1-beta"
/protein_id="AAA98665.1"
/translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAA
EVLLRVDNIIRARPRTANRQHM"
gene <687..>3158
/gene="AXL2"
mRNA <687..>3158
/gene="AXL2"
/product="Axl2p"
CDS 687..3158
/gene="AXL2"
/note="plasma membrane glycoprotein"
/codon_start=1
/product="Axl2p"
/protein_id="AAA98666.1"
/translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFT
FQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVI
LEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFN
VTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYS
FVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDD
PISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFN
FEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKF
QSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSS
HHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGV
ILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSY
DDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKP
PVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKL
FDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQ
SGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQV
KDIHGRIPEML"
gene complement(<3300..>4037)
/gene="REV7"
mRNA complement(<3300..>4037)
/gene="REV7"
/product="Rev7p"
CDS complement(3300..4037)
/gene="REV7"
/codon_start=1
/product="Rev7p"
/protein_id="AAA98667.1"
/translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQF
VPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKD
DQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVD
SLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISG
DDKILNGVYSQYEEGESIFGSLF"
ORIGIN
1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg
241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa
301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa
361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat
421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga
481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc
541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga
601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta
661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag
721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa
781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata
841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga
901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac
961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg
1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc
1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa
1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca
1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac
1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa
1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag
1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct
1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac
1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa
1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc
1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata
1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca
1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc
1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc
1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca
1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc
1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg
2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt
2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc
2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg
2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca
2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata
2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg
2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga
2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt
2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat
2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt
2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc
2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag
2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta
2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa
2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact
2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt
3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa
3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag
3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct
3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt
3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact
3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa
3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg
3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt
3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc
3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca
3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc
3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc
3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat
3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa
3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga
3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat
3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc
4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc
4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa
4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg
4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc
4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt
4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg
4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg
4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt
4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt
4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat
4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc
4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct
4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta
4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac
4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct
4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct
4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc
//
Now, you can work with the sequence record using pydna, using the Dseqrecord class. Dseqrecord provides ways to highlight regions of interest on the sequence, adding new features to the record, removing features, and creating new Dseqrecord objects to store and export your changes. Please refer to the Dseq_Features notebook for more information.
Importing Sequences from Strings
parse also allows sequences to be read from a string alone. This could be useful to read FASTA sequences obtained from GenBank APIs.
from pydna.parsers import parse
my_record = parse(
'''
>lcl|U49845.1_cds_AAA98667.1_3 [gene=REV7] [protein=Rev7p] [protein_id=AAA98667.1] [location=complement(3300..4037)] [gbkey=CDS]
ATGAATAGATGGGTAGAGAAGTGGCTGAGGGTATACTTAAAATGCTACATTAATTTGATTTTATTTTATA
GAAATGTATACCCACCTCAGTCATTCGACTACACTACTTACCAGTCATTCAACTTGCCGCAGTTCGTTCC
CATTAATAGGCATCCTGCTTTAATTGACTATATAGAAGAACTTATACTGGATGTTCTTTCTAAATTAACG
CACGTTTACAGATTTTCCATCTGCATTATTAATAAAAAGAACGATTTATGCATTGAAAAATACGTTTTAG
ATTTTAGTGAATTACAACATGTGGATAAAGACGATCAGATCATTACGGAAACTGAAGTGTTCGACGAATT
CCGATCTTCCTTAAATAGTTTGATTATGCATTTGGAGAAATTACCTAAAGTCAACGATGACACAATAACA
TTTGAAGCAGTTATTAATGCGATCGAATTGGAACTAGGACATAAGTTGGACAGAAACAGGAGGGTCGATA
GTTTGGAGGAAAAAGCAGAAATTGAAAGGGATTCAAACTGGGTTAAATGTCAAGAAGATGAAAATTTACC
AGACAATAATGGTTTTCAACCTCCTAAAATAAAACTCACTTCTTTAGTCGGTTCTGACGTGGGGCCTTTG
ATTATTCATCAGTTTAGTGAAAAATTAATCAGCGGTGACGACAAAATTTTGAATGGAGTGTATTCTCAAT
ATGAAGAGGGCGAGAGCATTTTTGGATCTTTGTTTTAA
'''
)
print(my_record[0].format("fasta"))
>lcl|U49845.1_cds_AAA98667.1_3 [gene=REV7] [protein=Rev7p] [protein_id=AAA98667.1] [location=complement(3300..4037)] [gbkey=CDS]
ATGAATAGATGGGTAGAGAAGTGGCTGAGGGTATACTTAAAATGCTACATTAATTTGATT
TTATTTTATAGAAATGTATACCCACCTCAGTCATTCGACTACACTACTTACCAGTCATTC
AACTTGCCGCAGTTCGTTCCCATTAATAGGCATCCTGCTTTAATTGACTATATAGAAGAA
CTTATACTGGATGTTCTTTCTAAATTAACGCACGTTTACAGATTTTCCATCTGCATTATT
AATAAAAAGAACGATTTATGCATTGAAAAATACGTTTTAGATTTTAGTGAATTACAACAT
GTGGATAAAGACGATCAGATCATTACGGAAACTGAAGTGTTCGACGAATTCCGATCTTCC
TTAAATAGTTTGATTATGCATTTGGAGAAATTACCTAAAGTCAACGATGACACAATAACA
TTTGAAGCAGTTATTAATGCGATCGAATTGGAACTAGGACATAAGTTGGACAGAAACAGG
AGGGTCGATAGTTTGGAGGAAAAAGCAGAAATTGAAAGGGATTCAAACTGGGTTAAATGT
CAAGAAGATGAAAATTTACCAGACAATAATGGTTTTCAACCTCCTAAAATAAAACTCACT
TCTTTAGTCGGTTCTGACGTGGGGCCTTTGATTATTCATCAGTTTAGTGAAAAATTAATC
AGCGGTGACGACAAAATTTTGAATGGAGTGTATTCTCAATATGAAGAGGGCGAGAGCATT
TTTGGATCTTTGTTTTAA
Extra info
Note that pydna’s parse guesses whether the argument passed is a file path or a string, and also guesses the file type based on the content, so it can give unexpected behaviour if your files are not well formatted. To have more control over the parsing of sequences, you can use biopython’s parse from Bio.SeqIO, and then instantiate a Dseqrecord from the biopython’s SeqRecord
from Bio.SeqIO import parse as seqio_parse
from pydna.dseqrecord import Dseqrecord
file_path = './U49845.gb'
# Extract the first Seqrecord of the SeqIO.parse iterator
seq_record = next(seqio_parse(file_path, 'genbank'))
# This is how circularity is stored in biopython's seqrecord
is_circular = 'topology' in seq_record.annotations.keys() and seq_record.annotations['topology'] == 'circular'
# Convert into Dseqrecord
dseq_record = Dseqrecord(seq_record, circular=is_circular)
dseq_record
Dseqrecord(-5028)