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Change IMGT urls to https #10

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18 changes: 9 additions & 9 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -236,13 +236,13 @@ For the command line tools change to directory data/IgL


Now to create a model from scratch,
download gene templates and anchors from IMGT website [IMGT](http://www.imgt.org/)
download gene templates and anchors from IMGT website [IMGT](https://www.imgt.org/)
A list of available species to download from IMGT can be queried with imgt-get-genomes command and option --info.

```console
(statbiophys) $ pygor imgt-get-genomes --info
--------------------------------
http://www.imgt.org
https://www.imgt.org
Downloading data from ...
List of IMGT available species:

Expand Down Expand Up @@ -278,21 +278,21 @@ Papio+anubis+anubis
Mus+spretus
Rattus+norvegicus
For more details access:
http://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList
https://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList
```

1. Download genomic templates using VJ or VDJ corresponding to the type of chain.

```console
(statbiophys) $ pygor imgt-get-genomes --imgt-species Homo+sapiens --imgt-chain IGL -t VJ
--------------------------------
http://www.imgt.org
https://www.imgt.org
get_ref_genome
Homo+sapiens IGLV http://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
Homo+sapiens IGLJ http://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=8.1+IGLV&species=Homo+sapiens&IMGTlabel=2nd-CYS
Homo+sapiens IGLV https://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
https://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
Homo+sapiens IGLJ https://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
https://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
https://www.imgt.org/genedb/GENElect?query=8.1+IGLV&species=Homo+sapiens&IMGTlabel=2nd-CYS
No anchor is found for : AC279423|IGLV(I)-11-1*01|Homo sapiens|P|V-REGION|22452..22620|169 nt|1| | | | |169+0=169|partial in 5'| |
No anchor is found for : D87007|IGLV(I)-20*01|Homo sapiens|P|V-REGION|15573..15858|286 nt|1| | | | |286+0=286| | |
No anchor is found for : AC279208|IGLV(I)-20*02|Homo sapiens|P|V-REGION|19943..20228|286 nt|1| | | | |286+0=286| | |
Expand Down
2 changes: 1 addition & 1 deletion docs/make.bat
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Expand Up @@ -21,7 +21,7 @@ if errorlevel 9009 (
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
echo.https://sphinx-doc.org/
exit /b 1
)

Expand Down
18 changes: 9 additions & 9 deletions docs/source/LEEME.md
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Expand Up @@ -211,13 +211,13 @@ For the command line tools change to directory data/IgL


Now to create a model from scratch,
download gene templates and anchors from IMGT website [IMGT](http://www.imgt.org/)
download gene templates and anchors from IMGT website [IMGT](https://www.imgt.org/)
A list of available species to download from IMGT can be queried with imgt-get-genomes command and option --info.

```console
(statbiophys) $ pygor imgt-get-genomes --info
--------------------------------
http://www.imgt.org
https://www.imgt.org
Downloading data from ...
List of IMGT available species:

Expand Down Expand Up @@ -253,21 +253,21 @@ Papio+anubis+anubis
Mus+spretus
Rattus+norvegicus
For more details access:
http://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList
https://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList
```

1. Download genomic templates using VJ or VDJ corresponding to the type of chain.

```console
(statbiophys) $ pygor imgt-get-genomes --imgt-species Homo+sapiens --imgt-chain IGL -t VJ
--------------------------------
http://www.imgt.org
https://www.imgt.org
get_ref_genome
Homo+sapiens IGLV http://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
Homo+sapiens IGLJ http://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=8.1+IGLV&species=Homo+sapiens&IMGTlabel=2nd-CYS
Homo+sapiens IGLV https://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
https://www.imgt.org/genedb/GENElect?query=7.2+IGLV&species=Homo+sapiens
Homo+sapiens IGLJ https://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
https://www.imgt.org/genedb/GENElect?query=7.2+IGLJ&species=Homo+sapiens
https://www.imgt.org/genedb/GENElect?query=8.1+IGLV&species=Homo+sapiens&IMGTlabel=2nd-CYS
No anchor is found for : AC279423|IGLV(I)-11-1*01|Homo sapiens|P|V-REGION|22452..22620|169 nt|1| | | | |169+0=169|partial in 5'| |
No anchor is found for : D87007|IGLV(I)-20*01|Homo sapiens|P|V-REGION|15573..15858|286 nt|1| | | | |286+0=286| | |
No anchor is found for : AC279208|IGLV(I)-20*02|Homo sapiens|P|V-REGION|19943..20228|286 nt|1| | | | |286+0=286| | |
Expand Down
4 changes: 2 additions & 2 deletions pygor3/IgorIO.py
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Expand Up @@ -78,7 +78,7 @@ def command_from_dict_options(dicto: dict):


def run_command(cmd):
"""from http://blog.kagesenshi.org/2008/02/teeing-python-subprocesspopen-output.html
"""from https://blog.kagesenshi.org/2008/02/teeing-python-subprocesspopen-output.html
"""
# print(cmd)
# p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
Expand Down Expand Up @@ -128,7 +128,7 @@ def run_command_print(cmd):


def run_command_no_output(cmd):
"""from http://blog.kagesenshi.org/2008/02/teeing-python-subprocesspopen-output.html
"""from https://blog.kagesenshi.org/2008/02/teeing-python-subprocesspopen-output.html
"""
# p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
try:
Expand Down
10 changes: 5 additions & 5 deletions pygor3/imgt.py
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Expand Up @@ -15,11 +15,11 @@
from io import StringIO # Python 3

imgt_params={
'url.home' : "http://www.imgt.org",
'url.genelist' : "http://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList",
'url.genedb' : "http://www.imgt.org/genedb/GENElect?",
'url.release' : "http://www.imgt.org/download/GENE-DB/RELEASE",
'url.readme' : "http://www.imgt.org/download/GENE-DB/README.txt",
'url.home' : "https://www.imgt.org",
'url.genelist' : "https://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList",
'url.genedb' : "https://www.imgt.org/genedb/GENElect?",
'url.release' : "https://www.imgt.org/download/GENE-DB/RELEASE",
'url.readme' : "https://www.imgt.org/download/GENE-DB/README.txt",
'Genesymbol' : [],
'data.chainlist' : ['TRA', 'TRB', 'BCR']
}
Expand Down