seqretsetall |
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% seqretsetall -osf phylip Reads and writes (returns) many sets of sequences Input sequence set(s): globins-all.phy output sequence(s) [globins-all.phylip]: |
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Go to the output files for this example
Reads and writes (returns) many sets of sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqsetall Sequence set(s) filename and optional format, or reference (input USA) [-outseq] seqoutall [ |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequence] (Parameter 1) |
seqsetall | Sequence set(s) filename and optional format, or reference (input USA) | Readable sets of sequences | Required |
[-outseq] (Parameter 2) |
seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-feature | boolean | Use feature information | Boolean value Yes/No | No |
Associated qualifiers | ||||
"-sequence" associated seqsetall qualifiers | ||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |
-sid1 -sid_sequence |
string | Entryname | Any string | |
-ufo1 -ufo_sequence |
string | UFO features | Any string | |
-fformat1 -fformat_sequence |
string | Features format | Any string | |
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
"-outseq" associated seqoutall qualifiers | ||||
-osformat2 -osformat_outseq |
string | Output seq format | Any string | |
-osextension2 -osextension_outseq |
string | File name extension | Any string | |
-osname2 -osname_outseq |
string | Base file name | Any string | |
-osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |
-osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |
-ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
-oufo2 -oufo_outseq |
string | UFO features | Any string | |
-offormat2 -offormat_outseq |
string | Features format | Any string | |
-ofname2 -ofname_outseq |
string | Features file name | Any string | |
-ofdirectory2 -ofdirectory_outseq |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
7 164 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN-VD EVGGEALGR- LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN-EE EVGGEALGR- LLVVYPWTQR HBA_HUMAN ---------- ----VLSPAD KTNVKAA-WG KVGAHAGEYG AEALERMFLS HBA_HORSE ---------- ----VLSAAD KTNVKAA-WS KVGGHAGEYG AEALERMFLG MYG_PHYCA -------VLS EGEWQLVLHV WAKVEAD-VA GHGQDILIR- LFKSHPETLE GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN LKGTFAALSE FPTTKTYFPH FDLSHGSAQV KGHGKKVADA LTNAVAHVDD MPNALSALSD FPTTKTYFPH FDLSHGSAQV KAHGKKVGDA LTLAVGHLDD LPGALSNLSD KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD LFSFLKGTSE VPQNNPELQA HAGKVFKLVY EAAIQLQVTG VVVTDATLKN LHCDKLH--V DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA LHCDKLH--V DPENFRLLGN VLVVVLARHF GKDFTPELQA SYQKVVAGVA LHAHKLR--V DPVNFKLLSH CLLVTLAAHL PAEFTPAVHA SLDKFLASVS LHAHKLR--V DPVNFKLLSH CLLSTLAVHL PNDFTPAVHA SLDKFLSSVS SHATKHK--I PIKYLEFISE AIIHVLHSRH PGDFGADAQG AMNKALELFR LSGKHAK--S FQVDPQYFKV LAAVIADTVA AGDAGFEKLM SMICILLRSA LGSVHVSKGV ADAHFPVVKE AILKTIKEVV GAKWSEELNS AWTIAYDELA NALAHKYH-- ---- NALAHKYH-- ---- TVLTSKYR-- ---- TVLTSKYR-- ---- KDIAAKYKEL GYQG Y--------- ---- IVIKKEMNDA A--- 7 167 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN--V DEVGGEALGR LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN--E EEVGGEALGR LLVVYPWTQR HBA_HUMAN ---------V LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT HBA_HORSE ---------V LSAADKTNVK AAWSKVGGHA GEYGAEALER MFLGFPTTKT GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE MYG_PHYCA ---------V LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN -----LKGTF YFPHF-DLS- ----HGSAQV KGHGKKVADA LTNAVAHVDD -----MPNAL YFPHF-DLS- ----HGSAQV KAHGKKVGDA LTLAVGHLDD -----LPGAL FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD T--EKMSMKL KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH -----HEAEL LFSFLKGTSE VP--QNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL ATLSELHCDK LHVDPENFRL LGNVLVCVLA HHFGKEFTPP VQAAYQKVVA AALSELHCDK LHVDPENFRL LGNVLVVVLA RHFGKDFTPE LQASYQKVVA SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA VHASLDKFLS RDLSGKHAKS FQVDPQYFKV LAAVIADTVA AG-------- -DAGFEKLMS KPLAQSHATK HKIPIKYLEF ISEAIIHVLH SRHPGDFGAD AQGAMNKALE KNLGSVHVSK G-VADAHFPV VKEAILKTIK EVVGAKWSEE LNSAWTIAYD GVANALAHKY H------ GVANALAHKY H------ SVSTVLTSKY R------ SVSTVLTSKY R------ MICILLRSAY ------- LFRKDIAAKY KELGYQG ELAIVIKKEM NDAA--- |
7 164 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN-VD EVGGEALGR- LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN-EE EVGGEALGR- LLVVYPWTQR HBA_HUMAN ---------- ----VLSPAD KTNVKAA-WG KVGAHAGEYG AEALERMFLS HBA_HORSE ---------- ----VLSAAD KTNVKAA-WS KVGGHAGEYG AEALERMFLG MYG_PHYCA -------VLS EGEWQLVLHV WAKVEAD-VA GHGQDILIR- LFKSHPETLE GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN LKGTFAALSE FPTTKTYFPH FDLSHGSAQV KGHGKKVADA LTNAVAHVDD MPNALSALSD FPTTKTYFPH FDLSHGSAQV KAHGKKVGDA LTLAVGHLDD LPGALSNLSD KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD LFSFLKGTSE VPQNNPELQA HAGKVFKLVY EAAIQLQVTG VVVTDATLKN LHCDKLH--V DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA LHCDKLH--V DPENFRLLGN VLVVVLARHF GKDFTPELQA SYQKVVAGVA LHAHKLR--V DPVNFKLLSH CLLVTLAAHL PAEFTPAVHA SLDKFLASVS LHAHKLR--V DPVNFKLLSH CLLSTLAVHL PNDFTPAVHA SLDKFLSSVS SHATKHK--I PIKYLEFISE AIIHVLHSRH PGDFGADAQG AMNKALELFR LSGKHAK--S FQVDPQYFKV LAAVIADTVA AGDAGFEKLM SMICILLRSA LGSVHVSKGV ADAHFPVVKE AILKTIKEVV GAKWSEELNS AWTIAYDELA NALAHKYH-- ---- NALAHKYH-- ---- TVLTSKYR-- ---- TVLTSKYR-- ---- KDIAAKYKEL GYQG Y--------- ---- IVIKKEMNDA A--- 7 167 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN--V DEVGGEALGR LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN--E EEVGGEALGR LLVVYPWTQR HBA_HUMAN ---------V LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT HBA_HORSE ---------V LSAADKTNVK AAWSKVGGHA GEYGAEALER MFLGFPTTKT GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE MYG_PHYCA ---------V LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN -----LKGTF YFPHF-DLS- ----HGSAQV KGHGKKVADA LTNAVAHVDD -----MPNAL YFPHF-DLS- ----HGSAQV KAHGKKVGDA LTLAVGHLDD -----LPGAL FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD T--EKMSMKL KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH -----HEAEL LFSFLKGTSE VP--QNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL ATLSELHCDK LHVDPENFRL LGNVLVCVLA HHFGKEFTPP VQAAYQKVVA AALSELHCDK LHVDPENFRL LGNVLVVVLA RHFGKDFTPE LQASYQKVVA SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA VHASLDKFLS RDLSGKHAKS FQVDPQYFKV LAAVIADTVA AG-------- -DAGFEKLMS KPLAQSHATK HKIPIKYLEF ISEAIIHVLH SRHPGDFGAD AQGAMNKALE KNLGSVHVSK G-VADAHFPV VKEAILKTIK EVVGAKWSEE LNSAWTIAYD GVANALAHKY H------ GVANALAHKY H------ SVSTVLTSKY R------ SVSTVLTSKY R------ MICILLRSAY ------- LFRKDIAAKY KELGYQG ELAIVIKKEM NDAA--- |
Program name | Description |
---|---|
aligncopy | Reads and writes alignments |
aligncopypair | Reads and writes pairs from alignments |
biosed | Replace or delete sequence sections |
codcopy | Copy and reformat a codon usage table |
cutseq | Removes a section from a sequence |
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
descseq | Alter the name or description of a sequence |
entret | Retrieves sequence entries from flatfile databases and files |
extractalign | Extract regions from a sequence alignment |
extractfeat | Extract features from sequence(s) |
extractseq | Extract regions from a sequence |
featcopy | Reads and writes a feature table |
featreport | Reads and writes a feature table |
feattext | Return a feature table original text |
listor | Write a list file of the logical OR of two sets of sequences |
makenucseq | Create random nucleotide sequences |
makeprotseq | Create random protein sequences |
maskambignuc | Masks all ambiguity characters in nucleotide sequences with N |
maskambigprot | Masks all ambiguity characters in protein sequences with X |
maskfeat | Write a sequence with masked features |
maskseq | Write a sequence with masked regions |
newseq | Create a sequence file from a typed-in sequence |
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file |
noreturn | Remove carriage return from ASCII files |
nospace | Remove whitespace from an ASCII text file |
notab | Replace tabs with spaces in an ASCII text file |
notseq | Write to file a subset of an input stream of sequences |
nthseq | Write to file a single sequence from an input stream of sequences |
nthseqset | Reads and writes (returns) one set of sequences from many |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a nucleotide sequence |
seqcount | Reads and counts sequences |
seqret | Reads and writes (returns) sequences |
seqretsplit | Reads sequences and writes them to individual files |
sizeseq | Sort sequences by size |
skipredundant | Remove redundant sequences from an input set |
skipseq | Reads and writes (returns) sequences, skipping first few |
splitsource | Split sequence(s) into original source sequences |
splitter | Split sequence(s) into smaller sequences |
trimest | Remove poly-A tails from nucleotide sequences |
trimseq | Remove unwanted characters from start and end of sequence(s) |
trimspace | Remove extra whitespace from an ASCII text file |
union | Concatenate multiple sequences into a single sequence |
vectorstrip | Removes vectors from the ends of nucleotide sequence(s) |
yank | Add a sequence reference (a full USA) to a list file |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.