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Pierre LINDENBAUM
Cours M2 Bioinfo
Validations
78f3e5c6
Valider
78f3e5c6
rédigé
il y a 10 ans
par
lindenb
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cont
parent
c9d64ec2
Branches
ncbi
Branches contenant la validation
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1 fichier modifié
ncbi/Makefile
+157
-13
157 ajouts, 13 suppressions
ncbi/Makefile
avec
157 ajouts
et
13 suppressions
ncbi/Makefile
+
157
−
13
Voir le fichier @
78f3e5c6
CURL
=
curl
-sLk
SHELL
=
/bin/bash
EUTILS
=
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
EFETCH
=
${
EUTILS
}
/efetch.fcgi
NCBI
=
EUTILS
=
http://eutils.ncbi.nlm.nih.gov
ENTREZ
=
${
EUTILS
}
/entrez/eutils
EFETCH
=
${
ENTREZ
}
/efetch.fcgi
ESEARCH
=
${
ENTREZ
}
/esearch.fcgi
ESUMMARY
=
${
ENTREZ
}
/esummary.fcgi
ELINK
=
${
ENTREZ
}
/elink.fcgi
HEADANDTAIL
=(
head
-n
50
;
echo
-e
'\n\n(...)\n\n'
;
head
-n
50
)
XMLFORMAT
=
xmllint
--format
-
CUT
=
awk
'{printf("%s\n",(length($$0)<100?$$0:sprintf("%s ...",substr($$0,1,100))));}'
.PHONY
:
all
all
:
@
echo
"select a specific target"
u001
:
u001
0
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=25&rettype=gb"
u002
:
u002
0
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=25"
u003
:
...
...
@@ -22,24 +30,160 @@ u003:
u004
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=25&retmode=xml"
u005
:
u005
0
:
@${
CURL
}
"http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd"
u006
:
@${
CURL
}
"
${
E
UTILS
}
/einfo.fcgi"
u006
0
:
@${
CURL
}
"
${
E
NTREZ
}
/einfo.fcgi"
u007
:
@${
CURL
}
"
${
E
UTILS
}
/einfo.fcgi?db=pubmed"
|
${
HEADANDTAIL
}
u007
0
:
@${
CURL
}
"
${
E
NTREZ
}
/einfo.fcgi?db=pubmed"
|
${
HEADANDTAIL
}
u008
:
@${
CURL
}
"
http://eutils.ncbi.nlm.nih.gov
/gquery?term=tyrannosaurus%20rex&retmode=xml"
|
\
u008
0
:
@${
CURL
}
"
${
EUTILS
}
/gquery?term=tyrannosaurus%20rex&retmode=xml"
|
\
xmllint
--format
-
gquery2html.xsl
:
${
CURL
}
-o
$@
"https://raw.githubusercontent.com/lindenb/courses/master/about.ncbi/
$@
"
trex1.html
:
gquery2html.xsl
${
CURL
}
"
http://eutils.ncbi.nlm.nih.gov
/gquery?term=tyrannosaurus%20rex&retmode=xml"
|
\
${
CURL
}
"
${
EUTILS
}
/gquery?term=tyrannosaurus%20rex&retmode=xml"
|
\
xsltproc
$<
-
>
$@
u0090
:
@${
CURL
}
"
${
ESEARCH
}
?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D"
|
${
XMLFORMAT
}
u0100
:
@${
CURL
}
"
${
ESEARCH
}
?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D&retmax=2"
|
${
XMLFORMAT
}
u0110
:
@${
CURL
}
"
${
ESEARCH
}
?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D&retmax=3&retstart=10"
|
${
XMLFORMAT
}
u0120
:
@${
CURL
}
"
${
ESUMMARY
}
?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D&rettype=count"
|
${
XMLFORMAT
}
u0130
:
@${
CURL
}
"
${
ESUMMARY
}
?db=nucleotide&id=507866428"
|
${
XMLFORMAT
}
u0140
:
@${
CURL
}
"
${
ESUMMARY
}
?db=snp&id=25"
|
${
XMLFORMAT
}
u0150
:
@${
CURL
}
"
${
ESUMMARY
}
?db=pubmed&id=7939126"
|
${
XMLFORMAT
}
u0160
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=507866428"
|
${
HEADANDTAIL
}
u0170
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=507866428&rettype=fasta"
|
${
HEADANDTAIL
}
u0180
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=507866428&rettype=fasta&retmode=xml"
|
${
XMLFORMAT
}
|
${
CUT
}
u0190
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=507866428&retmode=xml"
|
${
XMLFORMAT
}
|
${
CUT
}
u0200
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=507866428&rettype=gb&retmode=xml"
|
${
XMLFORMAT
}
|
${
CUT
}
u0210
:
@${
CURL
}
"
${
EFETCH
}
?db=nucleotide&id=KC524742&rettype=gb&retmode=xml"
|
${
XMLFORMAT
}
|
${
CUT
}
u0220
:
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=taxonomy&term=extinct%5BPROP%5D"
|
${
XMLFORMAT
}
u0230
:
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=taxonomy&term=extinct%5BPROP%5D"
|
\
xmllint
--xpath
'concat(/eSearchResult/QueryKey/text(),",",/eSearchResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
EFETCH
}
?db=taxonomy&retmode=xml&usehistory=y&query_key=%s&WebEnv=%s\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
ncbi2epost.xsl
:
${
CURL
}
-o
$@
"https://raw.githubusercontent.com/lindenb/courses/master/about.ncbi/
$@
"
u0240
:
ncbi2epost.xsl
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=taxonomy&term=extinct%5BPROP%5D"
|
\
xmllint
--xpath
'concat(/eSearchResult/QueryKey/text(),",",/eSearchResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
EFETCH
}
?db=taxonomy&retmode=xml&usehistory=y&query_key=%s&WebEnv=%s\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
xsltproc
$<
-
u0241
:
ncbi2epost.xsl
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=taxonomy&term=extinct%5BPROP%5D"
|
\
xmllint
--xpath
'concat(/eSearchResult/QueryKey/text(),",",/eSearchResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
EFETCH
}
?db=taxonomy&retmode=xml&usehistory=y&query_key=%s&WebEnv=%s\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
xsltproc
$<
- |
\
/bin/bash
u0242
:
ncbi2epost.xsl
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=taxonomy&term=extinct%5BPROP%5D"
|
\
xmllint
--xpath
'concat(/eSearchResult/QueryKey/text(),",",/eSearchResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
EFETCH
}
?db=taxonomy&retmode=xml&usehistory=y&query_key=%s&WebEnv=%s\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
xsltproc
$<
- |
\
/bin/bash |
\
xmllint
--xpath
'concat(/ePostResult/QueryKey/text(),",",/ePostResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
ESEARCH
}
?db=taxonomy&query_key=%s&usehistory=y&WebEnv=%s&term=Homo%20Sapiens\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
${
XMLFORMAT
}
u0243
:
ncbi2epost.xsl
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=taxonomy&term=extinct%5BPROP%5D"
|
\
xmllint
--xpath
'concat(/eSearchResult/QueryKey/text(),",",/eSearchResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
EFETCH
}
?db=taxonomy&retmode=xml&usehistory=y&query_key=%s&WebEnv=%s\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
xsltproc
$<
- |
\
/bin/bash |
\
xmllint
--xpath
'concat(/ePostResult/QueryKey/text(),",",/ePostResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
ESEARCH
}
?db=taxonomy&query_key=%s&usehistory=y&WebEnv=%s&term=Tyrannosaurus\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
${
XMLFORMAT
}
u0250
:
${
CURL
}
"
${
ELINK
}
?dbfrom=nucleotide&db=pubmed&id=507866428&cmd=neighbor_score"
u0251
:
${
CURL
}
"
${
ELINK
}
?dbfrom=nucleotide&db=pubmed&id=507866428&cmd=neighbor_score"
|
\
xmllint
--xpath
'/eLinkResult/LinkSet/LinkSetDb[1]/Link[1]/Id[1]/text()'
- |
\
awk
-F
,
'{printf("\"
${
EFETCH
}
?db=pubmed&rettype=medline&id=%s\"\n",$$0);}'
|
\
xargs
${
CURL
}
u0260
:
xsltproc <
(
${
CURL
}
"https://raw.github.com/lindenb/xslt-sandbox/master/stylesheets/bio/ncbi/gb2svg.xsl"
)
\
"
${
EFETCH
}
?db=nucleotide&id=14971102&retmode=xml&rettype=gbc"
>
$(
addsuffix .svg,
$@
)
pubmed2rstats.xsl
:
${
CURL
}
-o
$@
"https://raw.githubusercontent.com/lindenb/courses/master/about.ncbi/
$@
"
u0270
:
pubmed2rstats.xsl
${
CURL
}
"
${
ESEARCH
}
?usehistory=y&db=pubmed&term=tyrannosaurus"
|
\
xmllint
--xpath
'concat(/eSearchResult/QueryKey/text(),",",/eSearchResult/WebEnv/text())'
- |
\
awk
-F
,
'{printf("
${
EFETCH
}
?db=pubmed&retmode=xml&usehistory=y&query_key=%s&WebEnv=%s\n",$$1,$$2);}'
|
\
xargs
${
CURL
}
|
\
xsltproc
$<
- | R
--no-save
--quiet
docsum_3.3.xsd
:
${
CURL
}
-o
$@
"ftp://ftp.ncbi.nlm.nih.gov/snp/specs/
$@
"
u0280
:
docsum_3.3.xsd
xjc
-d
.
$<
ParseDbSnp.java
:
${
CURL
}
-o
$@
"https://raw.githubusercontent.com/lindenb/courses/master/about.ncbi/
$@
"
u0290
:
ParseDbSnp.java u0280
javac
$<
gov/nih/nlm/ncbi/snp/docsum/
*
.java
&&
\
${
CURL
}
"ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/XML/ds_ch1.xml.gz"
|
\
gunzip
-c
| java ParseDbSnp
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