# HG changeset patch
# User mcharles
# Date 1421660001 18000
# Node ID 0a6c1cfe4dc8fc9b3a34a03e19c328d8e2123b73
# Parent 0e7c6fe606467159501be5e419c07e673d67761e
Uploaded
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/CreateMatrix.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/CreateMatrix.pl Mon Jan 19 04:33:21 2015 -0500
@@ -0,0 +1,20 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $input_pileup_file;
+my $input_variant_file;
+my $input_variant_unique_file;
+
+GetOptions (
+"input_pileup_file=s" => \$input_pileup_file,
+"input_variant_file=s" => \$input_variant_file,
+"input_variant_unique_file=s" => \$input_variant_unique_file
+) or die("Error in command line arguments\n");
+
+
+
+print "$input_pileup_file\n$input_variant_file\n$input_variant_unique_file\n";
+
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/CreateMatrix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/CreateMatrix.xml Mon Jan 19 04:33:21 2015 -0500
@@ -0,0 +1,21 @@
+
+Create Genotyping Matrix
+
+ CreateMatrix.pl -input_pileup_file $input_pileup_file -input_variant_file $input_variant_file -input_variant_unique_file $input_variant_unique_file > $output_file
+
+
+
+
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+
+
+
+
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/CreateMatrixMultiple.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/CreateMatrixMultiple.pl Mon Jan 19 04:33:21 2015 -0500
@@ -0,0 +1,17 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+use Getopt::Long;
+
+
+my $input_matrix_files;
+GetOptions (
+"input_matrix_files=s" => \$input_matrix_files
+) or die("Error in command line arguments\n");
+
+my @files = split(/,/,$input_matrix_files);
+for (my $i=0;$i<=$#files;$i++){
+ print $files[$i],"\n";
+}
+
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/CreateMatrixMultiple.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/CreateMatrixMultiple.xml Mon Jan 19 04:33:21 2015 -0500
@@ -0,0 +1,18 @@
+
+Create Global Genotyping Matrix
+
+ CreateMatrixMultiple.pl -input_matrix_files $input_matrix_files > $output_file
+
+
+
+
+
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+
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga Mon Oct 20 05:58:31 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,604 +0,0 @@
-{
- "a_galaxy_workflow": "true",
- "annotation": "",
- "format-version": "0.1",
- "name": "rapsosnp v1.20",
- "steps": {
- "0": {
- "annotation": "",
- "id": 0,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "ASSEMBLY"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 221
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"ASSEMBLY\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "1": {
- "annotation": "",
- "id": 1,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "READ1"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 306.76666259765625
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"READ1\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "2": {
- "annotation": "",
- "id": 2,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "READ2"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 392.5333251953125
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"READ2\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "3": {
- "annotation": "",
- "id": 3,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "DUBIOUS"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 478.29998779296875
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"DUBIOUS\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "4": {
- "annotation": "",
- "id": 4,
- "input_connections": {
- "input_fasta": {
- "id": 0,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "fastaGroomerForMakeBlastdb",
- "outputs": [
- {
- "name": "output_fasta",
- "type": "fasta"
- }
- ],
- "position": {
- "left": 427.76666259765625,
- "top": 221
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "fastaGroomerForMakeBlastdb",
- "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
- "tool_version": "1.00",
- "type": "tool",
- "user_outputs": []
- },
- "5": {
- "annotation": "",
- "id": 5,
- "input_connections": {
- "input_read1_file": {
- "id": 1,
- "output_name": "output"
- },
- "input_read2_file": {
- "id": 2,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "PrepareFastqLight",
- "outputs": [
- {
- "name": "output_read1_file",
- "type": "fastqsanger"
- },
- {
- "name": "output_read2_file",
- "type": "fastqsanger"
- },
- {
- "name": "log_file",
- "type": "txt"
- }
- ],
- "position": {
- "left": 427.76666259765625,
- "top": 351.76666259765625
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "PrepareFastqLight",
- "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
- "tool_version": "1.03",
- "type": "tool",
- "user_outputs": []
- },
- "6": {
- "annotation": "",
- "id": 6,
- "input_connections": {
- "input_file": {
- "id": 4,
- "output_name": "output_fasta"
- }
- },
- "inputs": [],
- "name": "NCBI BLAST+ makeblastdb",
- "outputs": [
- {
- "name": "outfile",
- "type": "data"
- }
- ],
- "position": {
- "left": 755.5333251953125,
- "top": 221
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
- "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}",
- "tool_version": "0.1.00",
- "type": "tool",
- "user_outputs": []
- },
- "7": {
- "annotation": "",
- "id": 7,
- "input_connections": {
- "genomeSource|ownFile": {
- "id": 0,
- "output_name": "output"
- },
- "paired|input1": {
- "id": 5,
- "output_name": "output_read1_file"
- },
- "paired|input2": {
- "id": 5,
- "output_name": "output_read2_file"
- }
- },
- "inputs": [],
- "name": "Map with BWA for Illumina",
- "outputs": [
- {
- "name": "output",
- "type": "sam"
- }
- ],
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- "top": 378.76666259765625
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
- "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
- "tool_version": "1.2.3",
- "type": "tool",
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- "id": 8,
- "input_connections": {
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- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "filtersam_mapped_and_unique",
- "outputs": [
- {
- "name": "output_sam_file",
- "type": "sam"
- },
- {
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- "type": "txt"
- }
- ],
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- "post_job_actions": {},
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- "9": {
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- "id": 9,
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- "output_name": "output_sam_file"
- },
- "source|ref_file": {
- "id": 0,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "SAM-to-BAM",
- "outputs": [
- {
- "name": "output1",
- "type": "bam"
- }
- ],
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- "10": {
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- },
- "reference_source|ref_file": {
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- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "MPileup",
- "outputs": [
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- "name": "output_mpileup",
- "type": "pileup"
- },
- {
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\ No newline at end of file
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga Mon Oct 20 05:58:31 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2967 +0,0 @@
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- "id": 74,
- "output_name": "output_file"
- }
- },
- "inputs": [],
- "name": "mpileupfilterandstat",
- "outputs": [
- {
- "name": "output_file",
- "type": "pileup"
- },
- {
- "name": "log_file",
- "type": "txt"
- }
- ],
- "position": {
- "left": 7105.75,
- "top": 903.75
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "mpileupfilterandstat",
- "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"4\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"200\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.2\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.0\\\"\", \"min_depth\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"500\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
- "tool_version": "1.00",
- "type": "tool",
- "user_outputs": []
- },
- "76": {
- "annotation": "",
- "id": 76,
- "input_connections": {
- "input_files": [
- {
- "id": 75,
- "output_name": "log_file"
- },
- {
- "id": 69,
- "output_name": "log_file"
- },
- {
- "id": 73,
- "output_name": "log_file"
- },
- {
- "id": 72,
- "output_name": "log_file"
- },
- {
- "id": 71,
- "output_name": "log_file"
- },
- {
- "id": 70,
- "output_name": "log_file"
- },
- {
- "id": 68,
- "output_name": "log_file"
- },
- {
- "id": 67,
- "output_name": "log_file"
- },
- {
- "id": 66,
- "output_name": "log_file"
- },
- {
- "id": 65,
- "output_name": "log_file"
- },
- {
- "id": 64,
- "output_name": "log_file"
- },
- {
- "id": 42,
- "output_name": "log_file"
- },
- {
- "id": 41,
- "output_name": "log_file"
- },
- {
- "id": 37,
- "output_name": "log_file"
- },
- {
- "id": 36,
- "output_name": "log_file"
- },
- {
- "id": 34,
- "output_name": "log_file"
- },
- {
- "id": 32,
- "output_name": "log_file"
- },
- {
- "id": 31,
- "output_name": "log_file"
- },
- {
- "id": 35,
- "output_name": "log_file"
- },
- {
- "id": 33,
- "output_name": "log_file"
- },
- {
- "id": 30,
- "output_name": "log_file"
- },
- {
- "id": 29,
- "output_name": "log_file"
- },
- {
- "id": 28,
- "output_name": "log_file"
- },
- {
- "id": 16,
- "output_name": "log_file"
- },
- {
- "id": 15,
- "output_name": "log_file"
- },
- {
- "id": 13,
- "output_name": "log_file"
- },
- {
- "id": 11,
- "output_name": "log_file"
- },
- {
- "id": 10,
- "output_name": "log_file"
- },
- {
- "id": 14,
- "output_name": "log_file"
- },
- {
- "id": 12,
- "output_name": "log_file"
- },
- {
- "id": 9,
- "output_name": "log_file"
- },
- {
- "id": 8,
- "output_name": "log_file"
- },
- {
- "id": 7,
- "output_name": "log_file"
- }
- ]
- },
- "inputs": [],
- "name": "MergeMultiFile",
- "outputs": [
- {
- "name": "output_file",
- "type": "txt"
- }
- ],
- "position": {
- "left": 7458.25,
- "top": 1140.75
- },
- "post_job_actions": {
- "RenameDatasetActionoutput_file": {
- "action_arguments": {
- "newname": "LOGS"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output_file"
- }
- },
- "tool_errors": null,
- "tool_id": "MergeMultiFile",
- "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}",
- "tool_version": "1.00",
- "type": "tool",
- "user_outputs": []
- }
- }
-}
\ No newline at end of file
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/MergeLogFiles.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeLogFiles.pl Mon Jan 19 04:33:21 2015 -0500
@@ -0,0 +1,16 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+use Getopt::Long;
+
+
+my $input_log_files;
+GetOptions (
+"input_log_files=s" => \$input_log_files
+) or die("Error in command line arguments\n");
+
+my @files = split(/,/,$input_log_files);
+for (my $i=0;$i<=$#files;$i++){
+ print $files[$i],"\n";
+}
\ No newline at end of file
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/MergeLogFiles.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeLogFiles.xml Mon Jan 19 04:33:21 2015 -0500
@@ -0,0 +1,18 @@
+
+Merge multiple log files
+
+ MergeLogFiles.pl -input_log_files $input_log_files > $output_file
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/ParseBlastForUniqueMatch.pl
--- a/rapsodyn/ParseBlastForUniqueMatch.pl Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/ParseBlastForUniqueMatch.pl Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,5 @@
#!/usr/bin/perl
+#V1.1.0 manage empty files
#V1.0.1 added log, option parameters
use strict;
use warnings;
@@ -24,6 +25,10 @@
my %hash_name;
open(INB, $input_blast_file) or die ("Can't open $input_blast_file\n");
+if ( -z INB){
+ exit(0);
+}
+
while (my $line =){
my @fields = split (/\s+/,$line);
# print $#fields,"\n";
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/ParseBlastForUniqueMatch.xml
--- a/rapsodyn/ParseBlastForUniqueMatch.xml Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/ParseBlastForUniqueMatch.xml Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,4 @@
-
+
Filter mpileup with blast results
ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/PileupVariant.pl
--- a/rapsodyn/PileupVariant.pl Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/PileupVariant.pl Mon Jan 19 04:33:21 2015 -0500
@@ -3,39 +3,94 @@
use strict;
use warnings;
use Getopt::Long;
+#v1.1.0 choose exclusion file
+#v1.0.2 manage empty files
+#v1.0.1 bug correction
+#V1.0.1 added log, option parameters
my $input_pileup_file;
my $output_pileup_file;
+my $input_exclusion_file;
my $log_file;
my $nb_base_covered=0;
my $nb_variant=0;
+my $nb_variant_conserved=0;
+my $do_exclusion=0;
+my $nb_exclusion=0;
+my $nb_excluded=0;
+my %exclusion;
GetOptions (
"input_pileup_file=s" => \$input_pileup_file,
+"input_exclusion_file=s" => \$input_exclusion_file,
"log_file=s" => \$log_file
) or die("Error in command line arguments\n");
open(IN, $input_pileup_file) or die ("Can't open $input_pileup_file\n");
+if ( -z IN){
+ exit(0);
+}
+
+if ($input_exclusion_file){
+ open (EX,$input_exclusion_file) or die ("Can't open $input_exclusion_file\n");
+ if ( -z EX){
+
+ }
+ else {
+ $do_exclusion=1;
+ while (my $line=){
+ $nb_exclusion++;
+ chomp($line);
+ my @fields = split(/\s+/,$line);
+ if (($fields[0])&&($fields[1])){
+ $exclusion{"$fields[0]\t$fields[1]"}=1;
+ }
+ else {
+ print STDERR "Error formatting in Exclusion File\nExclusion file lines should be 'chromosome number' TAB 'position'\n$line\n",$fields[0],"\n",$fields[1],"\n";
+ }
+ }
+
+ }
+ close (EX);
+}
#Extraction des variants
my $nb_line=0;
while (my $line=){
#print $line;
- $nb_base_covered++;
- $line =~ s/\$//g; #the read start at this position
- $line =~ s/\^.//g; #the read end at this position followed by quality char
+ if ($line !~ /^\s*$/){
+ my @fields = split(/\s+/,$line);
+ if ($fields[4]){
+ $nb_base_covered++;
+ my $pile = $fields[4];
+ $pile =~ s/\$//g; #the read start at this position
+ $pile =~ s/\^.//g; #the read end at this position followed by quality char
+ if ($fields[4]=~/[ATGCN]/i){ #Indel are +/-\d[ATGCatgc]+ and SNP are [ATGCatgc]+ so [ATGCN]/i detection cover indel and snp
+ $nb_variant++;
+ if (($do_exclusion==1)&&($exclusion{"$fields[0]\t$fields[1]"})){
+
+ }
+ else {
+ print $line;
+ $nb_variant_conserved++;
+ }
+ }
+ }
+ elsif ($fields[3]==0){
+ }
+ else {
+ print STDERR "Error in pileup format\nPileup result expected at column 5\n$line\n";
+ }
+ }
#print $line;
- my @field = split(/\s+/,$line);
- if ($field[4]=~/[ATGCN]/i){
- print $line;
- $nb_variant++;
- }
+
}
close(IN);
open (LF,">$log_file") or die("Can't open $log_file\n");
print LF "\n####\t Variant extraction \n";
-print LF "Position covered :\t$nb_base_covered\n";
-print LF "Variant detected :\t$nb_variant\n";
+print LF "Position covered\t:\t$nb_base_covered\n";
+print LF "Variant detected\t:\t$nb_variant\n";
+print LF "Variant conserved\t:\t$nb_variant_conserved\n";
close (LF);
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/PileupVariant.xml
--- a/rapsodyn/PileupVariant.xml Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/PileupVariant.xml Mon Jan 19 04:33:21 2015 -0500
@@ -1,10 +1,27 @@
-
+
Keep only mpileup line with variant
- PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file
+ #if $exclude.do=="YES"
+ PileupVariant.pl -input_pileup_file $input_pileup_file -input_exclusion_file $input_exclusion_file -log_file $log_file > $output_pileup_file
+ #else
+ PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/PrepareFastqLight.pl
--- a/rapsodyn/PrepareFastqLight.pl Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/PrepareFastqLight.pl Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,6 @@
#!/usr/bin/perl
+#v1.1.0 manage empty files
+#v1.0.4 bug correction, last read not considered
#v1.0.3 support rapsodyn header (.... 1:... / .... 2:...)
#V1.0.2 added auto type detection
#V1.0.1 added log, option parameters
@@ -49,6 +51,14 @@
open(OUT2, ">$output2_file") or die ("Can't open $output2_file\n");
open (LF,">$log_file") or die("Can't open $log_file\n");
+if (( -z READ1)&&( -z READ2)){
+ exit(0);
+}
+elsif (( -z READ1)||( -z READ2)){
+ print STDERR "One empty File\n";
+ exit(0);
+}
+
my $error1=0;
my $error2=0;
@@ -113,7 +123,7 @@
-
+my $compt=0;
while (my $ligne1_r1 =){
my $ligne2_r1 =;
my $ligne3_r1 =;
@@ -122,7 +132,13 @@
my $ligne2_r2 =;
my $ligne3_r2 =;
my $ligne4_r2 =;
-
+ # chomp($ligne1_r1);
+ # chomp($ligne2_r1);
+ # chomp($ligne3_r1);
+ # chomp($ligne4_r1);
+ # chomp($ligne2_r1);
+
+ $compt++;
$nb_read1++;
$nb_read2++;
@@ -160,13 +176,13 @@
#@ 1 - 2 sec
else {
- my $length_seq1 = length($ligne2_r1);
- my $length_qual1 =length($ligne4_r1);
+ my $length_seq1 = length(chomp($ligne2_r1));
+ my $length_qual1 =length(chomp($ligne4_r1));
my $seq1;
my $qual1;
- my $length_seq2 = length($ligne2_r2);
- my $length_qual2 =length($ligne4_r2);
+ my $length_seq2 = length(chomp($ligne2_r2));
+ my $length_qual2 =length(chomp($ligne4_r2));
my $seq2;
my $qual2;
my $header1="";
@@ -210,7 +226,7 @@
}
elsif (($TYPE eq "sanger")&&((!$header1)||(!$header2))){
if ($VERBOSE eq "ON"){
- print "Error in header refgsd : empty\n";
+ print "Error in header ref : empty\n";
print $ligne1_r1;
print $ligne2_r1;
print $ligne3_r1;
@@ -256,10 +272,12 @@
elsif (($length_seq1 != $length_qual1)||($length_seq2 != $length_qual2)){
if ($VERBOSE eq "ON"){
print "Error in seq/qual length\n";
+ print "$length_seq1 / $length_qual1 \t $length_seq2 / $length_qual2\n";
print $ligne1_r1;
print $ligne2_r1;
print $ligne3_r1;
print $ligne4_r1;
+ print "\n";
print $ligne1_r2;
print $ligne2_r2;
print $ligne3_r2;
@@ -270,6 +288,7 @@
}
#@ 1 - 2 sec
else {
+ #print "TEST : $compt\n";
### Parsing sequence & qualité
if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){
$seq1 = $1;
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/PrepareFastqLight.xml
--- a/rapsodyn/PrepareFastqLight.xml Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/PrepareFastqLight.xml Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,4 @@
-
+
Fastq preparation
PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/extractseq.pl
--- a/rapsodyn/extractseq.pl Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/extractseq.pl Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,6 @@
#!/usr/bin/perl
+#V1.10 manage empty files
+#V1.02 Trop de pb avec nbci blast+, changment du header des fasta
#V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+
use strict;
@@ -16,6 +18,12 @@
) or die("Error in command line arguments\n");
open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n");
+
+if ( -z INV){
+ print ">empty\nAAAAA";
+ exit(0);
+}
+
open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n");
my @variant_list;
@@ -89,11 +97,13 @@
}
$variant{"desc"}=$descriptor;
- print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n";
+ #print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n";
+ #V1.02 : changement du header
#print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n";
+ print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n";
push(@variant_list,\%variant);
}
diff -r 0e7c6fe60646 -r 0a6c1cfe4dc8 rapsodyn/extractseq.xml
--- a/rapsodyn/extractseq.xml Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/extractseq.xml Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,4 @@
-