4.1

wgetENAHTS.sh

@@ -4,7 +4,7 @@
 #                                                                                                            #
 #  wgetENAHTS: downloading HTS files from ENA                                                                #
 #                                                                                                            #
-   COPYRIGHT="Copyright (C) 2021 Institut Pasteur"                                                           #
+   COPYRIGHT="Copyright (C) 2021-2022 Institut Pasteur"                                                      #
 #                                                                                                            #
 #  This program  is free software:  you can  redistribute it  and/or modify it  under the terms  of the GNU  #
 #  General Public License as published by the Free Software Foundation, either version 3 of the License, or  #
@@ -33,7 +33,10 @@
 # = VERSIONS =                                                                                               #
 # ============                                                                                               #
 #                                                                                                            #
-  VERSION=4.0.211129acjg                                                                                     #
+  VERSION=4.1.220307acjg                                                                                     #
+# + fixed bugs with option -p                                                                                #
+#                                                                                                            #
+# VERSION=4.0.211129acjg                                                                                     #
 # + for better download, adding automatic selection step between ftp and https protocols                     #
 # + faster repository checking                                                                               #
 # + downloading accessions sorted according to the decreasing total file size                                #
@@ -102,7 +105,7 @@ chrono() {
 #   prints the doc                                                                                           #
 #                                                                                                            #
 mandoc() {
-  echo -e "\n\033[1m wgetENAHTS v$VERSION                  $COPYRIGHT\033[0m";
+  echo -e "\n\033[1m wgetENAHTS v$VERSION              $COPYRIGHT\033[0m";
   cat <<EOF
 
  USAGE:  wgetENAHTS.sh  [[-o <dir>]  [-f <infile>]  [-t <nthreads>]  
@@ -275,21 +278,37 @@ echo ;
 URL="ftp.sra.ebi.ac.uk/vol1/fastq";
 if [ "$PROTOCOL" == "auto" ]
 then
-  echo -n -e "$(chrono)\t\tassessing transfer protocol " ;
-  PROTOCOL="ftp://";   time_ftp=$SECONDS;
-  for i in {1..5} ; do echo -n "." ; timeout 2 $WGET_TEST "$PROTOCOL$URL/DRR00$i/" &>/dev/null ; rm -f wget-log ; done
-  time_ftp=$(( $SECONDS - $time_ftp ));
-  PROTOCOL="https://"; time_https=$SECONDS;
-  for i in {1..5} ; do echo -n "." ; timeout 2 $WGET_TEST "$PROTOCOL$URL/DRR00$i/" &>/dev/null ; rm -f wget-log ; done
-  time_https=$(( $SECONDS - $time_https ));
-  echo " [ok]" ;
+  echo -n -e "$(chrono)\t\tassessing transfer protocol ." ;
+  PROTOCOL="ftp";
+  if $WGET_TEST "$PROTOCOL""://""$URL/DRR001/"
+  then
+    time_ftp=$SECONDS;
+    for i in {2..5} ; do echo -n "." ; timeout 2 $WGET_TEST "$PROTOCOL""://""$URL/DRR00$i/" &>/dev/null ; rm -f wget-log ; done
+    time_ftp=$(( $SECONDS - $time_ftp ));
+  else
+    rm -f wget-log ;
+    echo -n "...." ;
+    time_ftp=10;
+  fi
+  PROTOCOL="https";
+  if $WGET_TEST "$PROTOCOL""://""$URL/DRR001/"
+  then
+    time_https=$SECONDS;
+    for i in {2..5} ; do echo -n "." ; timeout 2 $WGET_TEST "$PROTOCOL""://""$URL/DRR00$i/" &>/dev/null ; rm -f wget-log ; done
+    time_https=$(( $SECONDS - $time_https ));
+  else
+    rm -f wget-log ;
+    echo -n "...." ;
+    time_https=10;
+  fi
+  echo ". [ok]" ;
   if [ $time_ftp -lt $time_https ]
-  then PROTOCOL="ftp://";   echo -e "$(chrono)\t\tselected protocol: ftp ($time_ftp<$time_https)" ;
-  else PROTOCOL="https://"; echo -e "$(chrono)\t\tselected protocol: https ($time_https<$time_ftp)" ;
+  then PROTOCOL="ftp";   echo -e "$(chrono)\t\tselected protocol: ftp ($time_ftp<$time_https)" ;
+  else PROTOCOL="https"; echo -e "$(chrono)\t\tselected protocol: https ($time_https<$time_ftp)" ;
   fi
   echo ;
 fi
-FTPENA="$PROTOCOL$URL" ;
+FTPENA="$PROTOCOL""://""$URL" ;
 
 
 ##############################################################################################################
@@ -380,47 +399,6 @@ echo ;
 ACCNSORT="$(for ACCN in $ACCNLIST ; do [ -s $OUTDIR/$ACCN.weh ] && echo -e "$(sed 's/   /\t/g' $OUTDIR/$ACCN.weh | cut -f2 | paste -sd+ | bc -l)\t$ACCN" ; done | sort -gr | cut -f2 | tr '\n' ' ')";
 
 
-##############################################################################################################
-####                                                                                                      ####
-#### MEASURING DOWNLOAD SPEED                                                                             ####
-####                                                                                                      ####
-##############################################################################################################
-
-# if [ "$MAXRATE" == "NA" ]
-# then
-#   echo -e -n "$(chrono)\t\testimating download speed " ;
-#   for ACCN in $ACCNSORT
-#   do
-#     echo -n "." ;
-#     if [ ! -s $OUTDIR/$ACCN.weh ]; then continue ; fi
-#     nc=${#ACCN};
-#     if   [ $nc -eq 9 ];  then URL="$FTPENA/${ACCN:0:6}/$ACCN/";
-#     elif [ $nc -eq 10 ]; then URL="$FTPENA/${ACCN:0:6}/00${ACCN:9:1}/$ACCN/";
-#     else                      URL="$FTPENA/${ACCN:0:6}/0${ACCN:9:2}/$ACCN/";
-#     fi
-#     echo -n "." ;
-#     for FQGZ in $(sed "s/.*$ACCN/$ACCN/g" $OUTDIR/$ACCN.weh)
-#     do
-#       echo -n "." ;
-#       timeout 30 $WGET_DWNL $URL$FQGZ &>/dev/null ;
-#       bytes=$(du -b $OUTDIR/$FQGZ | tail -1 | cut -f1);
-#       RATE=$(( $bytes / 30 ));
-#       rm -f wget-log ;
-#       break ;
-#     done
-#     break ;
-#   done
-#   echo " [ok]" ;
-#   if [ $N -lt $NTHREADS ]; then RATE=$(( $RATE / $N )); else RATE=$(( $RATE / $NTHREADS )); fi
-#   if [ $RATE -gt 10000 ]
-#   then
-#     WGET_DWNL="$WGET_DWNL --limit-rate=$RATE"
-#     echo -e "$(chrono)\t\tdownload speed per file: $RATE bytes/seconds" ;
-#   fi
-#   echo ;
-# fi
-
-
 ##############################################################################################################
 ####                                                                                                      ####
 #### DOWNLOADING FASTQ FILES                                                                              ####