Dear EMBOSS developers,
I have used extractfeats in EMBOSS 6.4 to extract some features of GenBank
files with commands like the following.
$ extractfeat TRG@.gb -filter -join TRUE -tag 'standard_name' -value
"TRGC1" -describe standard_name -osformat2 fasta
>NG_007033_36562_39077 [C_region] (standard_name="TRGC1") Mus musculus T
cell receptor gamma chain (Tcrg) on chromosome 13.
acaaaaggcttgatgcagacatttcccccaagcccactattttccttccttctgttgctg
aaacaaatctccataagactgggacatacctttgtctccttgaaaagttctttccagatg
ttataagggtgtattggaaagaaaaggatggcaatactatcctggactcccaggaagggg
atacgctgaagactaacgacacatacatgaagtttagctggcttacagtgcctgaaaggg
caatggggaaagagcacagatgtattgtcaaacatgagaacaacaaaggaggagcagatc
aagagattttctttccttcaataaagaaagttgctgtgagtaccaagcctacaacttgct
ggcaagataaaaatgatgtgctgcagctccagttcacgatcacctctgcctactacacct
accttctcctgctcctcaagagtgtgatctacttggccatcatcagcttctctctgctta
gaagaacatctgtctgtggcaatgagaagaaatcctaa
However, with EMBOSS 6.6, there is no output anymore.
$ extractfeat TRG@.gb -filter -join TRUE -tag 'standard_name' -value
"TRGC1" -describe standard_name -osformat2 fasta
Warning: No sequences written to output file 'stdout'
The TRG@.gb file was downloaded from NCBI's website and a copy is available at
the following URL.
http://source.clonotyper.branchable.com/?p=source.git;a=blob;f=references/TRG@.gb;h=9d48fafbb7e4209a462dbb1ab552195c00e920e3;hb=HEAD
The commands ran on a Debian system with the Debian packages 6.4.0-2 or
6.6.0-1.
Is that a bug in EMBOSS > 6.4 ?
Have a nice day,
Charles Plessy
--
Charles Plessy, Ph.D. – RIKEN Center for Life Science Technologies
Division of Genomic Technologies – Genomics Miniaturization Technology Unit
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
http://population-transcriptomics.org/
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