extractfeat.txt

emboss的linux版本的源代码

                                extractfeat 



Function

   Extract features from a sequence

Description

   extractfeat is a simple utility for extracting parts of a sequence
   that have been annotated as being a specific type of feature. These
   sub-sequences are writen to the output sequence file.

   If the feature is annotated as being in the reverse sense of a nucleic
   acid sequence, then that feature's sub-sequence is
   reverse-complemented before being written out.

   It is often useful to have some information on the context of the
   feature. extractfeat allows you to specify a number of bases or
   residues before and/or after the feature to write out.

   If you are interested in extracting the sequence of the region around
   the start or end of the feature, then this can also be specified.

   'joined' features can either be extracted as individual sequences, or
   as a single concatenated sequence if the '-join' qualifier is used.

   Please remember that the output feature sequence is only as good as
   the annotation. If you rely upon other people's, or other program's
   annotation of features, then some of these will be incorrect.

Usage

   Here is a sample session with extractfeat

   To write out the exons of a sequence:


% extractfeat tembl:hsfau1 -type exon stdout 
Extract features from a sequence

>HSFAU1_408_504 [exon] H.sapiens fau 1 gene
cagtgacgtgacacgcagcccacggtctgtactgacgcgccctcgcttcttcctctttct
cgactccatcttcgcggtagctgggaccgccgttcag
>HSFAU1_774_856 [exon] H.sapiens fau 1 gene
tcgccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggcc
aggaaacggtcgcccagatcaag
>HSFAU1_951_1095 [exon] H.sapiens fau 1 gene
gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggc
gcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgactaccctg
gaagtagcaggccgcatgcttggag
>HSFAU1_1557_1612 [exon] H.sapiens fau 1 gene
gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag
>HSFAU1_1787_1912 [exon] H.sapiens fau 1 gene
gtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcggatgcagtac
aaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgccaac
tcttaa

   Go to the input files for this example

   Example 2

   To write out the exons with 10 extra bases at the start and end so
   that you can inspect the splice sites:


% extractfeat tembl:hsfau1 -type exon -before 10 -after 10 stdout 
Extract features from a sequence

>HSFAU1_408_504 [exon] H.sapiens fau 1 gene
ggtcgctcagcagtgacgtgacacgcagcccacggtctgtactgacgcgccctcgcttct
tcctctttctcgactccatcttcgcggtagctgggaccgccgttcaggtaagaatgg
>HSFAU1_774_856 [exon] H.sapiens fau 1 gene
ctttactcagtcgccaatatgcagctctttgtccgcgcccaggagctacacaccttcgag
gtgaccggccaggaaacggtcgcccagatcaaggtaaggctgc
>HSFAU1_951_1095 [exon] H.sapiens fau 1 gene
ttccctgtaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgct
cctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccct
gactaccctggaagtagcaggccgcatgcttggaggtgagtgaga
>HSFAU1_1557_1612 [exon] H.sapiens fau 1 gene
cccactacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagact
cctaaggtgagtgaga
>HSFAU1_1787_1912 [exon] H.sapiens fau 1 gene
ccttctccaggtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcg
gatgcagtacaaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccc
caatgccaactcttaagtcttttgta

   Example 3

   To write out the 10 bases around the start of all 'exon' features in
   the tembl database:


% extractfeat tembl:*  -type exon -before 5 -after -5 stdout 
Extract features from a sequence

>HSFAU1_408_504 [exon] H.sapiens fau 1 gene
ctcagcagtg
>HSFAU1_774_856 [exon] H.sapiens fau 1 gene
ctcagtcgcc
>HSFAU1_951_1095 [exon] H.sapiens fau 1 gene
tgtaggctca
>HSFAU1_1557_1612 [exon] H.sapiens fau 1 gene
tacaggtaaa
>HSFAU1_1787_1912 [exon] H.sapiens fau 1 gene
tccaggtggc
>HSFOS_889_1029 [exon] Human fos proto-oncogene (c-fos), complete cds.
ccacgatgat
>HSFOS_1783_2034 [exon] Human fos proto-oncogene (c-fos), complete cds.
tctaggactt
>HSFOS_2466_2573 [exon] Human fos proto-oncogene (c-fos), complete cds.
tctagttatc
>HSFOS_2688_3329 [exon] Human fos proto-oncogene (c-fos), complete cds.
tacaggagac
>HSTS1_1001_1205 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2,
 3, 4, 5, 6, 7, complete cds.
gcgccatgcc
>HSTS1_2895_2968 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2,
 3, 4, 5, 6, 7, complete cds.
ttcagatgaa
>HSTS1_5396_5570 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2,
 3, 4, 5, 6, 7, complete cds.
tccagggatc
>HSTS1_11843_11944 [exon] Homo sapiens gene for thymidylate synthase, exons 1,
2, 3, 4, 5, 6, 7, complete cds.
tacagattat
>HSTS1_13449_13624 [exon] Homo sapiens gene for thymidylate synthase, exons 1,
2, 3, 4, 5, 6, 7, complete cds.
ctcagatctt
>HSTS1_14133_14204 [exon] Homo sapiens gene for thymidylate synthase, exons 1,
2, 3, 4, 5, 6, 7, complete cds.
tatagccagg
>HSTS1_15613_15750 [exon] Homo sapiens gene for thymidylate synthase, exons 1,
2, 3, 4, 5, 6, 7, complete cds.
tttagcttca
>AB009062_75_503 [exon] Homo sapiens HERG gene, exon 6.
tgcaggtcct
>HSFERG2_50_196 [exon] Human apoferritin H gene exons 2-4
ttcagtctta
>HSFERG2_453_578 [exon] Human apoferritin H gene exons 2-4
ttcagaaacc
>HSFERG2_674_999 [exon] Human apoferritin H gene exons 2-4
tgcagttgtg
>AP000504_13_134 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class
I region, section 3/20.
ctcactgtga
>AP000504_868_930 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class
 I region, section 3/20.
gataccaaaa
>AP000504_1081_1161 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Cla
ss I region, section 3/20.
cttaccaagc
>AP000504_2752_2875 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Cla
ss I region, section 3/20.
cccacctctc
>AP000504_3425_3584 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Cla
ss I region, section 3/20.
gagacctcgg
>AP000504_3818_4038 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Cla
ss I region, section 3/20.
gttacccttt
>AP000504_7507_7763 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Cla
ss I region, section 3/20.
ccagcccggg
>AP000504_9766_9875 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Cla
ss I region, section 3/20.
ttcaggctgg
>AP000504_10068_10193 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tccaggcgga
>AP000504_10357_10463 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ttcaggtacc
>AP000504_11631_11812 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cacagatctg
>AP000504_13026_13434 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcaggtggt
>AP000504_14850_15164 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
gagggggagt
>AP000504_15284_15383 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctaaggtcga
>AP000504_15505_15578 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcaggccgg
>AP000504_15737_15856 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cctaggactt
>AP000504_16337_16486 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tctaggcaat
>AP000504_16676_16987 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tgcaggcact
>AP000504_18955_19059 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tcccttcaaa
>AP000504_19185_19264 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cttaccggtt
>AP000504_19402_19442 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcaccaaat
>AP000504_19797_19887 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcacctgtg
>AP000504_20043_20390 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cctaccatgg
>AP000504_20585_20645 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cttaccccca
>AP000504_22296_22401 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
atccttgaaa
>AP000504_23826_23936 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cccagctgac
>AP000504_24719_25381 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cctaggtaag
>AP000504_26111_26448 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
gctgtagagt
>AP000504_28403_28525 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcacggttt
>AP000504_28617_28671 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cttacccaag
>AP000504_30215_30266 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tggccatggg
>AP000504_31238_31363 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
aacaggtctc
>AP000504_31486_31691 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctgagtgaaa
>AP000504_33605_33675 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
gttcctcacc
>AP000504_33846_34001 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcacctctg
>AP000504_35893_36156 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tttacctgcc
>AP000504_36240_36569 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcacctttg
>AP000504_37069_37123 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cttacctgca
>AP000504_40724_40877 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ggaagagcag
>AP000504_41897_41953 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ggcaggatac
>AP000504_42687_42753 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tgcaggcttc
>AP000504_42999_43085 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cccaggttac
>AP000504_46996_47081 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
accaggcatt
>AP000504_50596_50669 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tgcagaggca
>AP000504_50879_51001 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcaggaagg
>AP000504_52110_52224 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cacagctacc
>AP000504_52348_52449 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcagtgtaa
>AP000504_53426_53489 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cctaggtgat
>AP000504_53901_53950 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tacagctgga
>AP000504_54324_54447 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tgcagggggt
>AP000504_54909_55013 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
accagccacg
>AP000504_55242_55305 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tctagggggc
>AP000504_55723_55779 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tgaagatacc
>AP000504_55925_55987 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cccagggttc
>AP000504_56128_56204 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cgtaggtatc
>AP000504_56288_56386 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
accagcctca
>AP000504_56484_56530 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tgcaggggag
>AP000504_56733_57055 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
ctcaggctcg
>AP000504_59988_60040 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cagagatgca
>AP000504_63714_63775 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
cacagcagcc
>AP000504_64760_64927 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA C
lass I region, section 3/20.
tctaggtaag