|
|
skipseq |
skipseq is a variant of the standard program for reading and writing sequences, seqret.
seqret has an option to allow it to only read the first sequence from a multiple set of sequences (-firstonly). seqret cannot, however, skip the first few sequences from a multiple set of sequence, writing out the rest; this is what skipseq is for.
In all other respects, skipseq is the same as seqret.
This does not skip any sequences. It is exactly equivalent to seqret:
% skipseq Reads and writes (returns) sequences, skipping first few Input (gapped) sequence(s): @eclac.list Number of sequences to skip at start [0]: output sequence(s) [j01636.fasta]: |
Go to the input files for this example
Go to the output files for this example
Example 2
This skips the first input sequence, writing out the others:
% skipseq -skip 1 Reads and writes (returns) sequences, skipping first few Input (gapped) sequence(s): @eclac.list output sequence(s) [j01636.fasta]: |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequence] seqall (Gapped) sequence(s) filename and optional
format, or reference (input USA)
-skip integer [0] Number of sequences to skip at start
(Any integer value)
[-outseq] seqoutall [
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
(Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -skip | Number of sequences to skip at start | Any integer value | 0 |
| [-outseq] (Parameter 2) |
Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -feature | Use feature information | Boolean value Yes/No | No |
#Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 |
See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.
>J01636 J01636.1 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt caattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggt gtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacg cgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaa caactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcac gcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtg gtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatctt ctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccatt gctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagaca cccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctg gtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcg cgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcg gaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaat gagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatg cgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgac gataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaacaggattttcgc ctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaag ggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacg caaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcc cgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggc accccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggata acaatttcacacaggaaacagctatgaccatgattacggattcactggccgtcgttttac aacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatcccc ctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgc gcagcctgaatggcgaatggcgctttgcctggtttccggcaccagaagcggtgccggaaa gctggctggagtgcgatcttcctgaggccgatactgtcgtcgtcccctcaaactggcaga tgcacggttacgatgcgcccatctacaccaacgtaacctatcccattacggtcaatccgc cgtttgttcccacggagaatccgacgggttgttactcgctcacatttaatgttgatgaaa gctggctacaggaaggccagacgcgaattatttttgatggcgttaactcggcgtttcatc tgtggtgcaacgggcgctgggtcggttacggccaggacagtcgtttgccgtctgaatttg acctgagcgcatttttacgcgccggagaaaaccgcctcgcggtgatggtgctgcgttgga gtgacggcagttatctggaagatcaggatatgtggcggatgagcggcattttccgtgacg tctcgttgctgcataaaccgactacacaaatcagcgatttccatgttgccactcgcttta atgatgatttcagccgcgctgtactggaggctgaagttcagatgtgcggcgagttgcgtg actacctacgggtaacagtttctttatggcagggtgaaacgcaggtcgccagcggcaccg cgcctttcggcggtgaaattatcgatgagcgtggtggttatgccgatcgcgtcacactac gtctgaacgtcgaaaacccgaaactgtggagcgccgaaatcccgaatctctatcgtgcgg tggttgaactgcacaccgccgacggcacgctgattgaagcagaagcctgcgatgtcggtt tccgcgaggtgcggattgaaaatggtctgctgctgctgaacggcaagccgttgctgattc gaggcgttaaccgtcacgagcatcatcctctgcatggtcaggtcatggatgagcagacga tggtgcaggatatcctgctgatgaagcagaacaactttaacgccgtgcgctgttcgcatt atccgaaccatccgctgtggtacacgctgtgcgaccgctacggcctgtatgtggtggatg aagccaatattgaaacccacggcatggtgccaatgaatcgtctgaccgatgatccgcgct ggctaccggcgatgagcgaacgcgtaacgcgaatggtgcagcgcgatcgtaatcacccga gtgtgatcatctggtcgctggggaatgaatcaggccacggcgctaatcacgacgcgctgt atcgctggatcaaatctgtcgatccttcccgcccggtgcagtatgaaggcggcggagccg acaccacggccaccgatattatttgcccgatgtacgcgcgcgtggatgaagaccagccct tcccggctgtgccgaaatggtccatcaaaaaatggctttcgctacctggagagacgcgcc cgctgatcctttgcgaatacgcccacgcgatgggtaacagtcttggcggtttcgctaaat [Part of this file has been deleted for brevity] gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg tgtcaaaaataataataa |
>X51872 X51872.1 Escherichia coli lacA gene for thiogalactoside transacetylase gtgaatgaagtcgcttaagcaatcaatgtcggatgcggcgcgacgcttatccgaccaaca tatcataacggagtgatcgcattgaacatgccaatgaccgaaagaataagagcaggcaag ctatttaccgatatgtgcgaaggcttaccggaaaaaagacttcgtgggaaaacgttaatg tatgagtttaatcactcgcatccatcagaagttgaaaaaagagaaagcctgattaaagaa atgtttgccacggtaggggaaaacgcctgggtagaaccgcctgtctatttctcttacggt tccaacatccatataggccgcaatttttatgcaaatttcaatttaaccattgtcgatgac tacacggtaacaatcggtgataacgtactgattgcacccaacgttactctttccgttacg ggacaccctgtacaccatgaattgagaaaaaacggcgagatgtactcttttccgataacg attggcaataacgtctggatcggaagtcatgtggttattaatccaggcgtcaccatcggg gataattctgttattggcgcgggtagtatcgtcacaaaagacattccaccaaacgtcgtg gcggctggcgttccttgtcgggttattcgcgaaataaacgaccgggataagcactattat ttcaaagattataaagttgaatcgtcagtttaaattataaaaattgcctgatacgctgcg cttatcaggcctacaagttcagcgatctacattagccgcatccggcatgaacaaagcgca ggaacaagcgtcgcatcatgcctctttgacccacagctgcggaaaacgtactggtgcaaa acgcagggttatgatcatcagcccaacgacgcacagcgcatgaaatgcccagtccatcag gtaattgccgctgatactacgcagcacgccagaaaaccacggggcaagcccggcgatgat aaaaccgattccctgcataaacgccaccagcttgccagcaatagccggttgcacagagtg atcgagcgccagcagcaaacagagcggaaacgcgccgcccagacctaacccacacaccat cgcccacaataccggcaattgcatcggcagccagataaagccgcagaaccccaccagttg taacaccagcgccagcattaacagtttgcgccgatcctgatggcgagccatagcaggcat cagcaaagctcctgcggcttgcccaagcgtcatcaatgccagtaaggaaccgctgtactg cgcgctggcaccaatctcaatatagaaagcgggtaaccaggcaatcaggctggcgtaacc gccgttaatcagaccgaagtaaacacccagcgtccacgcgcggggagtgaataccacgcg aaccggagtggttgttgtcttgtgggaagaggcgacctcgcgggcgctttgccaccacca ggcaaagagcgcaacaacggcaggcagcgccaccaggcgagtgtttgataccaggtttcg ctatgttgaactaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagcc gcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtttaatcaccgaa gcatcaccgcctgaatgatgccgatccccaccccaccaagcagtgcgctgctaagcagca gcgcactttgcgggtaaagctcacgcatcaatgcaccgacggcaatcagcaacagactga tggcgacactgcgacgttcgctgacatgctgatgaagccagcttccggccagcgccagcc cgcccatggtaaccaccggcagagcggtcgac >V00294 V00294.1 E. coli laci gene (codes for the lac repressor). ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca gagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtt tctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaac cgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagt ctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactg ggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcg gtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgac caggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtc tctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggc gtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagt tctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaatt cagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatg caaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcg ctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggta gtgggatacgacgataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaa caggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggc caggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctg [Part of this file has been deleted for brevity] gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg tgtcaaaaataataataa |
See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.
| 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 |
| entret | Reads and writes (returns) flatfile entries |
| extractalign | Extract regions from a sequence alignment |
| 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 |
| makenucseq | Creates random nucleotide sequences |
| makeprotseq | Creates random protein 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 |
| 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 |
skipseq is a variant of the standard program for reading and writing sequences, seqret.