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Imgt url fix #274

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merged 2 commits into from
Jul 8, 2023
Merged

Imgt url fix #274

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6963132
Fixed imgt download url
mdeboth Jul 6, 2023
385fb59
Bug fix
mdeboth Jul 6, 2023
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19 changes: 9 additions & 10 deletions bin/fetch_imgt.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -68,15 +68,14 @@ do
echo "|---- Ig"
for CHAIN in IGHV IGHD IGHJ IGKV IGKJ IGLV IGLJ
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=7.14+${CHAIN}&species=${VALUE}"
URL="https://www.imgt.org/genedb/GENElect?query=7.14+${CHAIN}&species=${VALUE}"
FILE_NAME="${FILE_PATH}/${REPERTOIRE}_${KEY}_${CHAIN}.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
wget $URL -O $TMP_FILE -q
awk '/<pre>/{i++}/<\/pre>/{j++}{if(j==2){exit}}{if(i==2 && j==1 && $0!~"^<pre>"){print}}' $TMP_FILE > $FILE_NAME

# Checking once that file exists and is not empty (checks IMGT server is online)
read file
if [ -s "$FILE_NAME" ]
then
echo "IMGT Fasta file exists and is not empty"
Expand All @@ -93,7 +92,7 @@ do
# V amino acid for Ig
for CHAIN in IGHV IGKV IGLV
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=7.3+${CHAIN}&species=${VALUE}"
URL="https://www.imgt.org/genedb/GENElect?query=7.3+${CHAIN}&species=${VALUE}"
FILE_NAME="${FILE_PATH_AA}/${REPERTOIRE}_aa_${KEY}_${CHAIN}.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -108,7 +107,7 @@ do
echo "|---- TCR"
for CHAIN in TRAV TRAJ TRBV TRBD TRBJ TRDV TRDD TRDJ TRGV TRGJ
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=7.14+${CHAIN}&species=${VALUE}"
URL="https://www.imgt.org/genedb/GENElect?query=7.14+${CHAIN}&species=${VALUE}"
FILE_NAME="${FILE_PATH}/${REPERTOIRE}_${KEY}_${CHAIN}.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -121,7 +120,7 @@ do
# V amino acid for TCR
for CHAIN in TRAV TRBV TRDV TRGV
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=7.3+${CHAIN}&species=${VALUE}"
URL="https://www.imgt.org/genedb/GENElect?query=7.3+${CHAIN}&species=${VALUE}"
FILE_NAME="${FILE_PATH_AA}/${REPERTOIRE}_aa_${KEY}_${CHAIN}.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -140,7 +139,7 @@ do
echo "|---- Ig"
for CHAIN in IGH IGK IGL
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=8.1+${CHAIN}V&species=${VALUE}&IMGTlabel=L-PART1+L-PART2"
URL="https://www.imgt.org/genedb/GENElect?query=8.1+${CHAIN}V&species=${VALUE}&IMGTlabel=L-PART1+L-PART2"
FILE_NAME="${FILE_PATH}/${REPERTOIRE}_${KEY}_${CHAIN}L.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -154,7 +153,7 @@ do
echo "|---- TCR"
for CHAIN in TRA TRB TRG TRD
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=8.1+${CHAIN}V&species=${VALUE}&IMGTlabel=L-PART1+L-PART2"
URL="https://www.imgt.org/genedb/GENElect?query=8.1+${CHAIN}V&species=${VALUE}&IMGTlabel=L-PART1+L-PART2"
FILE_NAME="${FILE_PATH}/${REPERTOIRE}_${KEY}_${CHAIN}L.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -179,7 +178,7 @@ do
QUERY=7.5
fi

URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=${QUERY}+${CHAIN}&species=${VALUE}"
URL="https://www.imgt.org/genedb/GENElect?query=${QUERY}+${CHAIN}&species=${VALUE}"
FILE_NAME="${FILE_PATH}/${REPERTOIRE}_${KEY}_${CHAIN}.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -193,7 +192,7 @@ do
echo "|---- TCR"
for CHAIN in TRAC TRBC TRGC TRDC
do
URL="http://www.imgt.org/IMGT_GENE-DB/GENElect?query=14.1+${CHAIN}&species=${VALUE}"
URL="https://www.imgt.org/genedb/GENElect?query=14.1+${CHAIN}&species=${VALUE}"
FILE_NAME="${FILE_PATH}/${REPERTOIRE}_${KEY}_${CHAIN}.fasta"
TMP_FILE="${FILE_NAME}.tmp"
#echo $URL
Expand All @@ -209,7 +208,7 @@ done

# Write download info
INFO_FILE=${OUTDIR}/IMGT.yaml
echo -e "source: http://www.imgt.org/IMGT_GENE-DB" > $INFO_FILE
echo -e "source: https://www.imgt.org/genedb" > $INFO_FILE
echo -e "date: ${DATE}" >> $INFO_FILE
echo -e "species:" >> $INFO_FILE
for Q in ${SPECIES_QUERY[@]}
Expand Down
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