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read_embl
Martin Asser Hansen edited this page Oct 2, 2015
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read_embl read in entries from EMBL files. A EMBL entry consists of three main parts:
- Generic info (such as accession number, species, references, taxonimy, version, etc.)
- Feature table (containing info on features within each EMBL entry)
- Sequence
read_embl per default read all these informations, but it is possible to specify which parts of the Generic info, Feature table, and Sequence that is read - which results in great speed improvements.
A Biopiece record is output per feature from the Feature table. The sequence for each feature is included.
Based on the Location of each feature S_BEG, S_END, and STRAND keys are added to the biopiece
record.
For each feature the qualifiers are seperated with semi-colon per qualifier.
The EMBL format is notoriously evil to parse and read_embl uses a couple of compromises in order to focus on parsing information from the Feature table. E.g. the parsing of references from the Generic info section is crude.
read_embl [options] -i <EMBL file(s)>
[-? | --help] # Print full usage description.
[-i <files!> | --data_in=<files!>] # Comma separated list of files or glob expression to read.
[-n <uint> | --num=<uint>] # Limit number of records to read.
[-k <list> | --keys=<list>] # Match a subset of record keys only.
[-f <list> | --features=<list>] # Match a subset of features only.
[-q <list> | --qualifiers=<list>] # Match a subset of qualifiers only.
[-I <file!> | --stream_in=<file!>] # Read input stream from file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following EMBL record in the file test.embl:
ID U49845; SV 1; linear; genomic DNA; STD; FUN; 5028 BP.
XX
AC U49845;
XX
DT 07-MAY-1996 (Rel. 47, Created)
DT 25-MAR-2010 (Rel. 104, Last updated, Version 5)
XX
DE Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p (AXL2) and
DE Rev7p (REV7) genes, complete cds.
XX
KW .
XX
OS Saccharomyces cerevisiae (baker's yeast)
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
XX
RN [1]
RP 1-5028
RX PUBMED; 8846915.
RA Roemer T., Madden K., Chang J., Snyder M.;
RT "Selection of axial growth sites in yeast requires Axl2p, a novel plasma
RT membrane glycoprotein";
RL Genes Dev. 10(7):777-793(1996).
XX
RN [2]
RP 1-5028
RA Roemer T.;
RT ;
RL Submitted (22-FEB-1996) to the INSDC.
RL Biology, Yale University, New Haven, CT 06520, USA
XX
DR Ensembl-Gn; YIL139C; Saccharomyces_cerevisiae.
DR Ensembl-Gn; YIL140W; Saccharomyces_cerevisiae.
DR Ensembl-Gn; YIL142W; Saccharomyces_cerevisiae.
DR Ensembl-Tr; YIL139C; Saccharomyces_cerevisiae.
DR Ensembl-Tr; YIL140W; Saccharomyces_cerevisiae.
DR Ensembl-Tr; YIL142W; Saccharomyces_cerevisiae.
DR EnsemblGenomes; YIL139C; Saccharomyces_cerevisiae.
DR EnsemblGenomes; YIL140W; Saccharomyces_cerevisiae.
DR EnsemblGenomes; YIL142W; Saccharomyces_cerevisiae.
XX
FH Key Location/Qualifiers
FH
FT source 1..5028
FT /organism="Saccharomyces cerevisiae"
FT /chromosome="IX"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:4932"
FT mRNA <1..>206
FT /product="TCP1-beta"
FT CDS <1..206
FT /codon_start=3
FT /product="TCP1-beta"
FT /db_xref="GOA:P39076"
FT /db_xref="InterPro:IPR002194"
FT /db_xref="InterPro:IPR002423"
FT /db_xref="InterPro:IPR012716"
FT /db_xref="InterPro:IPR017998"
FT /db_xref="PDB:3P9D"
FT /db_xref="UniProtKB/Swiss-Prot:P39076"
FT /protein_id="AAA98665.1"
FT /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAA
FT EVLLRVDNIIRARPRTANRQHM"
FT gene <687..>3158
FT /gene="AXL2"
FT mRNA <687..>3158
FT /gene="AXL2"
FT /product="Axl2p"
FT CDS 687..3158
FT /codon_start=1
FT /gene="AXL2"
FT /product="Axl2p"
FT /note="plasma membrane glycoprotein"
FT /db_xref="GOA:P38928"
FT /db_xref="InterPro:IPR006644"
FT /db_xref="InterPro:IPR008009"
FT /db_xref="InterPro:IPR013783"
FT /db_xref="InterPro:IPR014805"
FT /db_xref="InterPro:IPR015919"
FT /db_xref="SGD:S000001402"
FT /db_xref="UniProtKB/Swiss-Prot:P38928"
FT /protein_id="AAA98666.1"
FT /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFT
FT FQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVI
FT LEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFN
FT VTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYS
FT FVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDD
FT PISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFN
FT FEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKF
FT QSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSS
FT HHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGV
FT ILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSY
FT DDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKP
FT PVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKL
FT FDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQ
FT SGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQV
FT KDIHGRIPEML"
FT gene complement(<3300..>4037)
FT /gene="REV7"
FT mRNA complement(<3300..>4037)
FT /gene="REV7"
FT /product="Rev7p"
FT CDS complement(3300..4037)
FT /codon_start=1
FT /gene="REV7"
FT /product="Rev7p"
FT /db_xref="GOA:P38927"
FT /db_xref="InterPro:IPR003511"
FT /db_xref="SGD:S000001401"
FT /db_xref="UniProtKB/Swiss-Prot:P38927"
FT /protein_id="AAA98667.1"
FT /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQF
FT VPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKD
FT DQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVD
FT SLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISG
FT DDKILNGVYSQYEEGESIFGSLF"
XX
SQ Sequence 5028 BP; 1510 A; 1074 C; 835 G; 1609 T; 0 other;
gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 60
ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 120
ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 180
gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg 240
ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa 300
agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa 360
attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat 420
aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga 480
gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc 540
tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga 600
acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta 660
cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag 720
ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa 780
aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata 840
cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga 900
gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac 960
tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg 1020
acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc 1080
tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa 1140
acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca 1200
ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac 1260
ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa 1320
actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag 1380
gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct 1440
ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac 1500
ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa 1560
acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc 1620
cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata 1680
cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca 1740
ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc 1800
cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc 1860
aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca 1920
agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc 1980
tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg 2040
caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt 2100
acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc 2160
cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg 2220
ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca 2280
gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata 2340
atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg 2400
atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga 2460
aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt 2520
ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat 2580
tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt 2640
cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc 2700
tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag 2760
aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta 2820
tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa 2880
caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact 2940
ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt 3000
ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa 3060
gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag 3120
ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct 3180
taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt 3240
agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact 3300
taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa 3360
attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg 3420
tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt 3480
aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc 3540
tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca 3600
ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc 3660
ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc 3720
tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat 3780
aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa 3840
agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga 3900
acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat 3960
acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc 4020
tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc 4080
tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa 4140
gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg 4200
atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc 4260
ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt 4320
tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg 4380
cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg 4440
ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt 4500
agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt 4560
tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat 4620
tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc 4680
atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct 4740
tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta 4800
gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac 4860
ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct 4920
ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct 4980
tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc 5028
//
Now, reading in the entire entry with read_embl yields:
read_embl -i test.embl
<6 records output - one for each feature>
To limit parsing of the Generic info section specify which keys
you are interested in with the -k switch (using the first two
letters in upper case):
read_embl -i test.embl -k AC
<6 records output - one for each feature>
To limit parsing of the Feature table specify which features
you are interested in with the -f switch:
read_embl -i test.embl -k AC -f CDS
<3 records output - one for each CDS feature>
To limit parsing of the qualifiers specify which to parse using
the -q switch:
read_embl -i test.embl -k AC -f CDS -q translation
<3 records output - one for each CDS feature>
Martin Asser Hansen - Copyright (C) - All rights reserved.
December 2011
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_embl is part of the Biopieces framework.