entret |
The difference between entret and such programs as seqret which also read entries from databases or files and write them to files, is that entret reads and writes the complete sequence entry together with the heading annotation (documentation) without attempting to reformat or interpret the data in any way. seqret on the other hand will read in the entry data, determine which bit of it is the sequence, which is the description line and which is the feature table and will then write the sequence, description and features out in the way prescribed by the sequence format which has been requested for output.
entret therefore is very useful for looking at the annotation of sequences from databases, which seqret does not provide.
The other main difference is that when it writes out the sequence entry to a file, the information is treated as text, not sequence, and so options that you would normally use to change the aspects of the sequence to be written will either not be recognised and will cause an error message to be written (e.g. '-osformat') or will be quietly ignored (e.g. '-sbegin', '-send').
In previous versions of EMBOSS, entret didn't return the sequence from entries held in GCG indexed databases. This has now been fixed. entret will now return the complete sequence entries with the annotation of GCG indexed databases.
% entret tembl:hsfau Reads and writes (returns) flatfile entries Output file [hsfau.entret]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-sequence] seqall Sequence database USA [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -firstonly boolean Read one sequence and stop Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.entret |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-firstonly | Read one sequence and stop | Boolean value Yes/No | No |
ID HSFAU standard; RNA; HUM; 518 BP. XX AC X65923; XX SV X65923.1 XX DT 13-MAY-1992 (Rel. 31, Created) DT 23-SEP-1993 (Rel. 37, Last updated, Version 10) XX DE H.sapiens fau mRNA XX KW fau gene. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. XX RN [1] RP 1-518 RA Michiels L.M.R.; RT ; RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases. RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry, RL Universiteisplein 1, 2610 Wilrijk, BELGIUM XX RN [2] RP 1-518 RX MEDLINE; 93368957. RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.; RT " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as RT an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus"; RL Oncogene 8:2537-2546(1993). XX DR SWISS-PROT; P35544; UBIM_HUMAN. DR SWISS-PROT; Q05472; RS30_HUMAN. XX FH Key Location/Qualifiers FH FT source 1..518 FT /chromosome="11q" FT /db_xref="taxon:9606" FT /organism="Homo sapiens" FT /tissue_type="placenta" FT /clone_lib="cDNA" FT /clone="pUIA 631" FT /map="13" FT misc_feature 57..278 FT /note="ubiquitin like part" FT CDS 57..458 FT /db_xref="SWISS-PROT:P35544" FT /db_xref="SWISS-PROT:Q05472" FT /gene="fau" FT /protein_id="CAA46716.1" FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS" FT misc_feature 98..102 FT /note="nucleolar localization signal" FT misc_feature 279..458 FT /note="S30 part" FT polyA_signal 484..489 FT polyA_site 509 XX SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other; ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60 agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120 cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180 tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240 tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360 agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420 cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480 tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518 // |
ID HSFAU standard; RNA; HUM; 518 BP. XX AC X65923; XX SV X65923.1 XX DT 13-MAY-1992 (Rel. 31, Created) DT 23-SEP-1993 (Rel. 37, Last updated, Version 10) XX DE H.sapiens fau mRNA XX KW fau gene. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. XX RN [1] RP 1-518 RA Michiels L.M.R.; RT ; RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases. RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry, RL Universiteisplein 1, 2610 Wilrijk, BELGIUM XX RN [2] RP 1-518 RX MEDLINE; 93368957. RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.; RT " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as RT an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus"; RL Oncogene 8:2537-2546(1993). XX DR SWISS-PROT; P35544; UBIM_HUMAN. DR SWISS-PROT; Q05472; RS30_HUMAN. XX FH Key Location/Qualifiers FH FT source 1..518 FT /chromosome="11q" FT /db_xref="taxon:9606" FT /organism="Homo sapiens" FT /tissue_type="placenta" FT /clone_lib="cDNA" FT /clone="pUIA 631" FT /map="13" FT misc_feature 57..278 FT /note="ubiquitin like part" FT CDS 57..458 FT /db_xref="SWISS-PROT:P35544" FT /db_xref="SWISS-PROT:Q05472" FT /gene="fau" FT /protein_id="CAA46716.1" FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS" FT misc_feature 98..102 FT /note="nucleolar localization signal" FT misc_feature 279..458 FT /note="S30 part" FT polyA_signal 484..489 FT polyA_site 509 XX SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other; ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60 agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120 cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180 tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240 tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360 agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420 cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480 tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518 // |
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
codcopy | Reads and writes a codon usage table |
cutseq | Removes a specified section from a sequence |
degapseq | Removes gap characters from sequences |
descseq | Alter the name or description of a sequence |
extractfeat | Extract features from a sequence |
extractseq | Extract regions from a sequence |
listor | Write a list file of the logical OR of two sets of sequences |
maskfeat | Mask off features of a sequence |
maskseq | Mask off regions of a sequence |
newseq | Type in a short new sequence |
noreturn | Removes carriage return from ASCII files |
notseq | Exclude a set of sequences and write out the remaining ones |
nthseq | Writes one sequence from a multiple set of sequences |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a sequence |
seqret | Reads and writes (returns) sequences |
seqretsplit | Reads and writes (returns) sequences in individual files |
skipseq | Reads and writes (returns) sequences, skipping first few |
splitter | Split a sequence into (overlapping) smaller sequences |
trimest | Trim poly-A tails off EST sequences |
trimseq | Trim ambiguous bits off the ends of sequences |
union | Reads sequence fragments and builds one sequence |
vectorstrip | Strips out DNA between a pair of vector sequences |
yank | Reads a sequence range, appends the full USA to a list file |