[med-svn] [Git][med-team/proteinortho][master] 4 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Tue Jan 12 14:27:46 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / proteinortho
Commits:
d3727ba9 by Nilesh Patra at 2021-01-12T19:47:12+05:30
routine-update: New upstream version
- - - - -
a4dc1a39 by Nilesh Patra at 2021-01-12T19:47:13+05:30
New upstream version 6.0.27+dfsg
- - - - -
d78c7b30 by Nilesh Patra at 2021-01-12T19:47:15+05:30
Update upstream source from tag 'upstream/6.0.27+dfsg'
Update to upstream version '6.0.27+dfsg'
with Debian dir c3c80d78f6e25c6f9139ec1e550c6068e3845887
- - - - -
9e6c42c3 by Nilesh Patra at 2021-01-12T19:47:35+05:30
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- .gitignore
- CHANGELOG
- CHANGEUID
- debian/changelog
- proteinortho6.pl
- src/.gitlab-ci.yml
- src/proteinortho_ffadj_mcs.py
Changes:
=====================================
.gitignore
=====================================
@@ -1,7 +1,7 @@
myproject.*
.Rhistory
old/
-remove.graph
+remove.graph*
test/*.dmnd
test/*.pin
test/*.phr
=====================================
CHANGELOG
=====================================
@@ -276,3 +276,14 @@
2. Dez (5195)
fixing proteinortho_grab_protein.pl (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/41)
and ids that are not found are printed to STDERR
+2021
+ 3. Jan (5200)
+ fixed output sorting (*.proteinortho.tsv)
+ 8. Jan (5378)
+ fixed a bug (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/42), i.e. -synteny option in combination with a -project name with a "." did let ffadj fail.
+ fixed a bug: -silent is now silent again
+ output files are overwritten instead of appended (which makes no sense)
+ selfblast option does now ignore hits between the same protein automatically (before cleanupblastgraph was used)
+ proteinortho.summary will be omitted if -nograph is set (there is no graph to generate a summary from)
+ 10. Jan (5379)
+ last update introduced a bug that removes the *.blast-graph if --step=3 is used
=====================================
CHANGEUID
=====================================
@@ -1 +1 @@
-5195
+5379
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+proteinortho (6.0.27+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Tue, 12 Jan 2021 19:47:35 +0530
+
proteinortho (6.0.25+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
proteinortho6.pl
=====================================
@@ -464,7 +464,7 @@ use POSIX;
##########################################################################################
# Variables
##########################################################################################
-our $version = "6.0.25";
+our $version = "6.0.27";
our $step = 0; # 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3
our $verbose = 1; # 0/1 -> don't / be verbose
our $debug = 0; # 0/1 -> don't / show debug data
@@ -711,7 +711,6 @@ if($gccversion_main eq "" || $gccversion_main < 5){
our $simgraph = "$project.blast-graph$run_id"; # Output file graph
our $syngraph = "$project.ffadj-graph$run_id"; # Output file synteny
-
our $csimgraph = "$project.proteinortho-graph"; # Output file graph
our $csyngraph = "$project.poff-graph"; # Output file synteny
our $simtable = "$project.proteinortho.tsv"; # Output file graph
@@ -743,23 +742,37 @@ if (-e "$project.proteinortho.tsv" && $step!=1 && ( ( scalar(@files) > 2 && $ste
print STDERR "\nWell then, proceeding...\n\n";
}
-# if($step!=1){
- if($tmp_path eq ""){$tmp_path=".";}
- if( $tmp_path !~ qr/proteinortho_cache_$project/ ){
- if(! -d $tmp_path."/proteinortho_cache_$project"){
- system("mkdir $tmp_path/proteinortho_cache_$project");
- if( -d $tmp_path."/proteinortho_cache_$project"){
- $tmp_path.="/proteinortho_cache_$project/";
- }
- }else{
+# if step=1 -> generate blast db, no need for unlinking results
+if($step!=1){
+ if($step!=3){ # if step 3 then dont destroy the blast results ...
+ unlink($simgraph);
+ unlink($syngraph);
+ }
+ # destroy all the *.proteinortho.tsv, *.poff, *.html results
+ unlink($csimgraph);
+ unlink($csyngraph);
+ unlink($simtable);
+ unlink($simtablehtml);
+ unlink($syntable);
+ unlink($syntablehtml);
+ unlink($desctable);
+}
+
+if($tmp_path eq ""){$tmp_path=".";}
+if( $tmp_path !~ qr/proteinortho_cache_$project/ ){
+ if(! -d $tmp_path."/proteinortho_cache_$project"){
+ system("mkdir $tmp_path/proteinortho_cache_$project");
+ if( -d $tmp_path."/proteinortho_cache_$project"){
$tmp_path.="/proteinortho_cache_$project/";
}
}else{
- if(!-d $tmp_path){
- mkdir("$tmp_path");
- }
+ $tmp_path.="/proteinortho_cache_$project/";
}
-# }
+}else{
+ if(!-d $tmp_path){
+ mkdir("$tmp_path");
+ }
+}
our $rm_simgraph = "$tmp_path$project.removed_blast-graph"; # Output remove graph
our $rm_syngraph = "$tmp_path$project.removed_ffadj-graph"; # Output remove graph
@@ -889,16 +902,38 @@ if ($step == 0 || $step == 2) {
# Check for duplicated edges if --unique or --checkblast
if($checkblast == 1){
- print STDERR "\n$GREEN**Step 2.5 Checking blast graph(s)**$NC\n";
+ if($verbose) {print STDERR "\n$GREEN**Step 2.5 Checking blast graph(s)**$NC\n"};
if($synteny){
- system("$po_path/proteinortho_cleanupblastgraph $syngraph"."* >tmp_$syngraph 2>/dev/null && mv tmp_$syngraph $syngraph"."_clean");
- $syngraph.="_clean";
- print STDERR "A clean version without any duplicated edges of $syngraph is saved to $syngraph"."_clean\n";
+ unlink($syngraph."_clean");
+ system("$po_path/proteinortho_cleanupblastgraph $syngraph"."* >tmp_$syngraph 2>$tmp_path/proteinortho_cleanupblastgraph.out && mv tmp_$syngraph $syngraph"."_clean");
+
+ my $wcl_clean = `grep "removed" $tmp_path/proteinortho_cleanupblastgraph.out | wc -l`;
+ chomp($wcl_clean);
+ $wcl_clean =~ s/[ \t]+.*$//;
+
+ if($wcl_clean > 0){
+ $syngraph.="_clean";
+ if($verbose) {print STDERR "A clean version without any duplicated edges of $syngraph is saved to $syngraph"."_clean\n";}
+ }else{
+ if($verbose) {print STDERR "$syngraph is free of duplicated edges\n";}
+ unlink($syngraph."_clean");
+ }
}else{
- system("$po_path/proteinortho_cleanupblastgraph $simgraph"."* >tmp_$simgraph 2>/dev/null && mv tmp_$simgraph $simgraph"."_clean");
- $simgraph.="_clean";
- print STDERR "A clean version without any duplicated edges of $simgraph is saved to $simgraph"."_clean\n";
+ unlink($simgraph."_clean");
+ system("$po_path/proteinortho_cleanupblastgraph $simgraph"."* >tmp_$simgraph 2>$tmp_path/proteinortho_cleanupblastgraph.out && mv tmp_$simgraph $simgraph"."_clean");
+
+ my $wcl_clean = `grep "removed" $tmp_path/proteinortho_cleanupblastgraph.out | wc -l`;
+ chomp($wcl_clean);
+ $wcl_clean =~ s/[ \t]+.*$//;
+
+ if($wcl_clean > 0){
+ $simgraph.="_clean";
+ if($verbose) {print STDERR "A clean version without any duplicated edges of $simgraph is saved to $simgraph"."_clean\n";}
+ }else{
+ if($verbose) {print STDERR "$simgraph is free of duplicated edges\n";}
+ unlink($simgraph."_clean");
+ }
}
}
@@ -973,7 +1008,7 @@ sub cluster {
my $cluster_verbose_level = "";
if($verbose == 1){ $cluster_verbose_level = "-verbose 1 "; }
if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
- system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_simgraph' $simgraph* >'$simtable'");
+ system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_simgraph' '$simgraph'* >'$simtable' ".($verbose == 2 ? "" : "2>/dev/null"));
if ($? != 0) {
&Error("'proteinortho_clustering' failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nMaybe your operating system does not support the statically compiled version, please try recompiling proteinortho with 'make clean' and 'make' (and 'make install PREFIX=...').");
}
@@ -992,7 +1027,7 @@ sub cluster {
if($verbose){print STDERR "You can extract the fasta files of each orthology group with\nproteinortho_grab_proteins.pl -tofiles $simtable '".join("' '", at files)."'\n (Careful: This will generate a file foreach line in the file $simtable).\n";}
}
- system("(head -n 1 '$simtable' && tail -n +2 '$simtable' | sort -k1,2nr -k3,3gr ) > '$simtable.sort'; mv '$simtable.sort' '$simtable'");
+ system("(head -n 1 '$simtable' && tail -n +2 '$simtable' | LC_ALL=C sort -k1,1nr -k2,2nr -k3,3nr ) > '$simtable.sort'; mv '$simtable.sort' '$simtable'");
if ($singles) {
if($verbose){print STDERR "Adding singles...\n";}
@@ -1009,10 +1044,10 @@ sub cluster {
if($verbose){print STDERR "[OUTPUT] -> Orthologous pairs are written to $csimgraph\n";}
}
- if(-x "$po_path/proteinortho_summary.pl"){
+ if(!$nograph && (-x "$po_path/proteinortho_summary.pl")){
system("$po_path/proteinortho_summary.pl '$csimgraph' >>'$csimgraph.summary' 2>/dev/null");
+ if($verbose){print STDERR "[OUTPUT] -> Summary is written to $csimgraph.summary\n";}
}
- if($verbose){print STDERR "[OUTPUT] -> Summary is written to $csimgraph.summary\n";}
if(scalar @files < 10){
@@ -1037,7 +1072,7 @@ sub cluster {
my $cluster_verbose_level = "";
if($verbose == 1){ $cluster_verbose_level = "-verbose 1 "; }
if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
- system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level $clusterOptions -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_syngraph' $syngraph* >'$syntable'");
+ system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level $clusterOptions -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_syngraph' '$syngraph'* >'$syntable' ".($verbose == 2 ? "" : "2>/dev/null"));
if ($? != 0) {
&Error("proteinortho_clustering failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nDid you use a static version? Maybe your operating system does not support the static compiled version, please recompile 'make clean' and 'make' or 'make USEPRECOMPILEDLAPACK=FALSE'.");
}
@@ -1047,7 +1082,7 @@ sub cluster {
system("mv mcl.proteinortho-graph $csyngraph");
}
- system("(head -n 1 '$syntable' && tail -n +2 '$syntable' | sort -k1,2nr -k3,3gr ) > '$syntable.sort'; mv '$syntable.sort' '$syntable'");
+ system("(head -n 1 '$syntable' && tail -n +2 '$syntable' | LC_ALL=C sort -k1,1nr -k2,2nr -k3,3nr ) > '$syntable.sort'; mv '$syntable.sort' '$syntable'");
if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $syntable\nYou can extract the fasta files of each orthology group with\nproteinortho_grab_proteins.pl -tofiles $syntable '".join("' '", at files)."'\n(Careful: This will generate a file foreach line in the file $syntable).\n";}
@@ -1064,10 +1099,10 @@ sub cluster {
}elsif($useMcl){
if($verbose){print STDERR "[OUTPUT] -> Orthologous pairs are written to $csyngraph\n";}
}
- if(-x "$po_path/proteinortho_summary.pl"){
+ if(!$nograph && (-x "$po_path/proteinortho_summary.pl")){
system("$po_path/proteinortho_summary.pl '$csyngraph' >>'$csyngraph.summary'");
+ if($verbose){print STDERR "[OUTPUT] -> Summary is written to $csyngraph.summary\n";}
}
- if($verbose){print STDERR "[OUTPUT] -> Summary is written to $csyngraph.summary\n";}
system("perl $po_path/proteinortho2html.pl $syntable '".join("' '", at files)."' >$syntablehtml");
if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $syntablehtml\n";}
@@ -1342,7 +1377,7 @@ sub workerthread {
# Clean up, just to be safe
unlink("$temp_file.tmp");
unlink("$temp_file.log");
- unlink("$temp_file.matching");
+ unlink("$temp_file.tmp.matching");
while (1) {
my ($i, $j);
@@ -1406,6 +1441,17 @@ sub workerthread {
# Remove secondary hits if better exist (test here instead of later)
%reciprocal_matches = %{&adaptive_best_blast_matches(\%reciprocal_matches)};
+ if($selfblast && $file_i eq $file_j){
+ my %seen_selfblast_edge;
+ foreach (keys %reciprocal_matches) {
+ my ($a,$b) = split(" ",$_);
+ my $key = ($a lt $b ? "$a $b" : "$b $a" );
+ if(!exists $seen_selfblast_edge{$key}){$seen_selfblast_edge{$key}=1}else{
+ delete $reciprocal_matches{$_};
+ }
+ }
+ }
+
if ($synteny) {
my ($ordered_matches, $track_pointer, $close_copies_pointer) = &synteny_matches(\%reciprocal_matches,$file_i,$file_j);
open(PREGRAPH,">>$temp_file.tmp") || &Error("Could not open temp file '$temp_file.tmp': $!");
@@ -1440,13 +1486,13 @@ sub workerthread {
# Generate hash for synteny hits
my %synteny;
- unless (-s "$temp_file.matching") {
+ unless (-s "$temp_file.tmp.matching") {
print STDERR "\n$RED [Error] Failed to run $po_path/proteinortho_ffadj_mcs.py for\n$file_i vs $file_j\nMoving source to $temp_file.err for debugging\nI will continue, but results may be insufficient.$NC \n\n";
system("mv $temp_file.tmp $temp_file.err");
next;
}
- open(OSYNGRAPH,"<$temp_file.matching") || &Error("Could not open temp file $temp_file.matching: $!'");
+ open(OSYNGRAPH,"<$temp_file.tmp.matching") || &Error("Could not open temp file $temp_file.tmp.matching: $!'");
while(<OSYNGRAPH>) {
$_=~s/[\r\n]+$//;
my ($i, $j, $score) = split(/\s+/,$_,3);
@@ -1480,7 +1526,7 @@ sub workerthread {
close(OSYNGRAPH);
unlink("$temp_file.tmp");
unlink("$temp_file.log");
- unlink("$temp_file.matching");
+ unlink("$temp_file.tmp.matching");
{
lock($syn_lock);
@@ -2288,6 +2334,13 @@ sub blast {
if(!$keep){unlink $bla}
}
+ if($selfblast){
+ @data = map {
+ my @a = split("\t",$_);
+ ($a[0] ne $a[1]) ? ($_) : ()
+ } @data;
+ }
+
return \@data;
}
=====================================
src/.gitlab-ci.yml
=====================================
@@ -8,16 +8,52 @@ stages:
- test-precompiled-bins
- recompile-and-test
-gcc-latest-alloptions:
+gcc-latest-manyoptions-together:
image: gcc
stage: test-precompiled-bins
script:
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- - mkdir ~/bin
- - cp diamond ~/bin
- - perl proteinortho*pl -project=testasd -cpus=1 -ram=100 -verbose=2 -selfblast -silent -force -desc -checkfasta -cleanblast -debug -binpath=~/bin -tmp='~/' -e=0.000001 -sim=0.9 -identity=20 -cov=30 -subparaBlast='--more-sensitive' -synteny -dups=1 -cs=4 -alpha=0.4 -conn=0.01 -purity=0.00001 -minspecies=2 -subparaCluster='-cpus 1 -seed 1' -nograph -singles -xml -exactstep3 test/*faa >/dev/null 2>&1 && rm testasd*poff* && rm testasd*fadj* && rm testasd*info* && export LC_NUMERIC="C" && export LC_ALL="C" && rm *descriptions* && rm *proteinortho.html* && rm *summary* && for f in testasd.*; do sort $f >$f.testasd; done; sha256sum -b *testasd | tr -d '\n' | awk '{if($0 == "fa18e9a0530f5a5754f045cfe97deaf818bdb5eb725619952633f1da0641cf7b *testasd.proteinortho.tsv.testasdb62d47f47bd68c8b8cfdbb4aacfd820cfd40b220622fe96a414fc207ade2668e *testasd.proteinortho.tsv.xml.testasd"){print $0." -> OK"; exit 0}else{print $0." -> failed"; exit 1}}'
+ - cp diamond $HOME
+ - export PATH="$PATH:$HOME"
+ - perl proteinortho*pl -project=testasd -cpus=1 -ram=1 -verbose=1 -force -desc -checkfasta -cleanblast -e=0.000001 -sim=0.98 -identity=20 -cov=30 -subparaBlast='--more-sensitive' -synteny -dups=1 -cs=4 -alpha=0.4 -conn=0.01 -purity=0.00001 -minspecies=2 -subparaCluster='-cpus 1 -seed 1 -powLapD 10' -nograph -singles -xml -exactstep3 test/*faa || exit 1
+ - rm *info;
+ - for f in testasd.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+ - rm *descriptions *html *xml;
+
+gcc-latest-someoptions-one-by-one:
+ image: gcc
+ stage: test-precompiled-bins
+ script:
+ - echo "installing diamond"
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
+ - tar xzf diamond-linux64.tar.gz
+ - cp diamond $HOME
+ - export PATH="$PATH:$HOME"
+ - perl proteinortho*pl -synteny test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+ - rm myproject*;
+ - perl proteinortho*pl -selfblast test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+ - rm myproject*;
+ - perl proteinortho*pl -conn=1 test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+ - rm myproject*;
+ - perl proteinortho*pl -sim=1 test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+ - rm myproject*;
+ - perl proteinortho*pl -singles test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+ - rm myproject*;
+ - perl proteinortho*pl -project="weirdname.,:_+#*\$ ?.,($&)" test/*faa || exit 1
+ - rm *info;
+ - for f in weirdname.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
gcc-latest-all-p:
image: gcc
@@ -35,33 +71,39 @@ gcc-latest-all-p:
- cd $CWD && echo "installing topaz"
- git clone https://github.com/ajm/topaz && cd topaz/src && make && cp topaz $HOME && cd ../..
- cd $CWD && echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz && tar xzf diamond-linux64.tar.gz && cp diamond $HOME
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz && tar xzf diamond-linux64.tar.gz && cp diamond $HOME
- export PATH="$PATH:$HOME"
- echo "start proteinortho tests"
- gcc --version
- make clean
- make all
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
gcc-latest-diamond:
image: gcc
stage: test-precompiled-bins
script:
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- cp diamond $HOME
- export PATH="$PATH:$HOME"
- echo "start proteinortho tests"
- gcc --version
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
nolapack-gcc-latest:
image: gcc
stage: recompile-and-test
script:
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- cp diamond $HOME
- export PATH="$PATH:$HOME"
@@ -70,6 +112,9 @@ nolapack-gcc-latest:
- make clean
- make LAPACK=FALSE
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
#gcc5:
# image: gcc:5
@@ -81,7 +126,7 @@ nolapack-gcc-latest:
# - make
# - cp topaz $HOME
# - echo "installing diamond"
-# - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+# - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
# - tar xzf diamond-linux64.tar.gz
# - cp diamond $HOME
# - export PATH="$PATH:$HOME"
@@ -104,12 +149,15 @@ ubuntu-latest0:
- cp topaz $HOME
- cd ../..
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- cp diamond $HOME
- export PATH="$PATH:$HOME"
- echo "start proteinortho tests"
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
ubuntu-latest:
image: ubuntu
@@ -123,7 +171,7 @@ ubuntu-latest:
- cp topaz $HOME
- cd ../..
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- cp diamond $HOME
- export PATH="$PATH:$HOME"
@@ -131,6 +179,9 @@ ubuntu-latest:
- make clean
- make all
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
debian-latest:
image: debian
@@ -143,7 +194,7 @@ debian-latest:
- make
- cp topaz $HOME
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- cp diamond $HOME
- export PATH="$PATH:$HOME"
@@ -152,6 +203,9 @@ debian-latest:
- make clean
- make all
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
#fedora-latest:
# image: fedora
@@ -175,7 +229,7 @@ debian-latest:
# - cp ncbi-blast*/bin/blastp $HOME
# - cp ncbi-blast*/bin/makeblastdb $HOME
# - echo "installing diamond"
-# - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+# - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
# - tar xzf diamond-linux64.tar.gz
# - cp diamond $HOME
# - export PATH="$PATH:$HOME"
@@ -198,7 +252,7 @@ centos-latest:
- cp ncbi-blast*/bin/blastp $HOME
- cp ncbi-blast*/bin/makeblastdb $HOME
- echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+ - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- tar xzf diamond-linux64.tar.gz
- cp diamond $HOME
- export PATH="$PATH:$HOME"
@@ -206,6 +260,9 @@ centos-latest:
- make clean
- make
- make test
+ - perl proteinortho*pl test/*faa || exit 1
+ - rm *info;
+ - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
#code_quality:
# image: docker:stable
=====================================
src/proteinortho_ffadj_mcs.py
=====================================
@@ -820,7 +820,7 @@ if __name__ == '__main__':
edg = sum(map(len, selectedRuns))
- matchfile = args.dist_file.rsplit('.')[0]+'.matching'
+ matchfile = args.dist_file+'.matching'
printMatching(g1_mod, g2_mod, g1_runs, multiChrom, matchfile)
#
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/625ddb2a8fe50a736115943ed43db4138aa3a386...9e6c42c356a281fb5b32f95587dd63adfe0178e4
--
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/625ddb2a8fe50a736115943ed43db4138aa3a386...9e6c42c356a281fb5b32f95587dd63adfe0178e4
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