mbruno (7b9beb69) at 24 Nov 10:30
perf(build_bdr.sh):
mbruno (5293d0a7) at 23 Nov 14:46
feat(build_bdr.sh): add download of mitochondrial
mbruno (3db2e7f3) at 23 Nov 14:33
Move download_mitochondrion_ncbi.sh in scripts folder
mbruno (ee13c31b) at 23 Nov 12:36
perf(build_brd.sh): speed the file decompression step
wget ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/snapshot_latest/std/*
by genbank APIecoPCR
results\\
+ [empty line]
16561 atcacgatg
//
LOCUS MW172448 16569 bp DNA circular PRI 09-DEC-2020
Add separator lines at line 40064339:
sed -i '40064339 i //' ncbi_mito.gb # add '//'
sed '40064339G' ncbi_mito.gb > ncbi_mito_cleaned.gb # add empty line after lines 40064339
\\
+ [empty line]
16561 atcacgatg
//
LOCUS MW172448 16569 bp DNA circular PRI 09-DEC-2020
mbruno (71d2652a) at 02 May 15:43
feat(genbank_to_embl.py): convert genbank file into embl file (obic...
wget ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/snapshot_latest/std/*
by genbank APIecoPCR
resultsProblem during conversion with obiconvert.
Error 2 = ECO_MEM_ERROR
Related to lines 134 and 135 in https://git.metabarcoding.org/obitools/ecopcr/-/blob/master/src/libecoPCR/ecoseq.c
seq->SQ = ECOMALLOC(seqlength+1,
"Allocate sequence buffer");
Error with file embl_std_019.sdx
mbruno (8d7a739c) at 02 Mar 09:41
refactor(download_mitochrondrion_ncbi.sh): replace python script by...
mbruno (01276773) at 23 Feb 10:56
refactor(download_mitochondrion_ncbi.sh): modification of the outpu...
mbruno (a7751e01) at 23 Feb 10:43
feat: scripts to download only mitochondrial data
At the moment we use an uncurated version of NCBI Check for algorithms/methods to automatically clean some sequences identified as erroneous