Is there any way to retrieve a list of start and end positions of tuberculosis genome genes automatically?
I have a list of TB drug resistance genes:
ebmB
embR
Rv3124
Rv3125c
Rv3126
Rv0340
iniA
iniB
iniC
rmlA2
rmlD
inhA
ethA
gyrA
gyrB
tlyA
thyA
rss
katG
kasA
ndh
oxyR
ahpC
mabA
inhA
furA
Rv0340
Rv1592c
Rv1772
srmR
fabD
accD6
fbpC
fadE24
efpA
nhoA
gid
rpsL
pncA
embC
embB
embA
rpoB
katG
Want to get a respective columns of Start and End nucleotide numbers automatically
Thx
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written
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bioinformatics_bel •
for i in `cat ./gene`; do esearch -db gene -query "$i[gene] AND Mycobacterium tuberculosis[orgn]" | efetch -format docsum | xtract -pattern DocumentSummary -element ScientificName -element Name -element ChrStart -element ChrStart | sed 's/999999999//g';done
Should produce.
Mycobacterium tuberculosis H37Rv embR 1417346 1417346
Mycobacterium tuberculosis str. Erdman = ATCC 35801 embR 1415864 1415864
Mycobacterium tuberculosis UT205 embR 1420011 1420011
Mycobacterium tuberculosis CTRI-2 embR 1417710 1417710
Mycobacterium tuberculosis H37Ra embR 1418656 1418656
Mycobacterium tuberculosis H37Rv moaR1 3489505 3489505
Mycobacterium tuberculosis H37Rv PPE49 3491650 3491650
Mycobacterium tuberculosis H37Rv Rv0340 408633 408633
Mycobacterium tuberculosis H37Rv iniA 410837 410837
Mycobacterium tuberculosis CCDC5079 iniA 409232 409232
Mycobacterium tuberculosis str. Erdman = ATCC 35801 iniA 411274 411274
Mycobacterium tuberculosis UT205 iniA 412048 412048
Mycobacterium tuberculosis CTRI-2 iniA 413184 413184
Mycobacterium tuberculosis H37Ra iniA 412199 412199
Mycobacterium tuberculosis H37Rv iniB 409361 409361
Mycobacterium tuberculosis CCDC5079 iniB 407756 407756
Mycobacterium tuberculosis str. Erdman = ATCC 35801 iniB 409723 409723
Mycobacterium tuberculosis UT205 iniB 410572 410572
Mycobacterium tuberculosis CTRI-2 iniB 411708 411708
Mycobacterium tuberculosis H37Ra iniB 410723 410723
what package to download and where to put these codes? I have tried lInux shell terminal and it does not work for list of genes, thx.
Download eutils from NCBI. This absolutely works, the results are in the post above.
Maybe you could try:
It should give you the coordinates you are after in the annotation attribute.
esearch -db genome -query "Mycobacterium tuberculosis[Organism]"|elink -target gene|efilter -query "embR[gene]"|efetch -format ft_na
Or the following command that should give you coordinates for each genome:
esearch -db gene -query "embR[gene]"|efilter -query "Mycobacterium tuberculosis[Organism]"|efetch -format ft_na
what package to download and where to put these codes? I have tried lInux shell terminal and it does not work for list of genes, thx.
what package to download and where to put these codes? I have tried lInux shell terminal and it does not work for a list of genes, thx.
it does not work
That's not very informative. You could at least tell us what went wrong.
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Are you after a specific strain or genome? I could suggest efetch/eutils solution if you could please provide more info.
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