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Updates to ICeCAP #1

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f3b0a14
fix folder name
abrown44 Jul 18, 2022
84676a2
Update shiftrev.c
abrown44 Jul 18, 2022
b841420
Update new.c
abrown44 Jul 18, 2022
4737688
Update trim_galore
abrown44 Jul 18, 2022
298fe15
Update README.md
abrown44 Jul 18, 2022
aa6cd79
Revert "Update README.md"
abrown44 Jul 18, 2022
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0 referenceC/MANUAL_v1.4.pdf → reference_C/MANUAL_v1.4.pdf
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0 referenceC/MANUAL_v1.4.tex → reference_C/MANUAL_v1.4.tex
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0 referenceC/NGS2.sh → reference_C/NGS2.sh
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0 referenceC/PEAKY.R → reference_C/PEAKY.R
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0 referenceC/bedGraphToBigWig → reference_C/bedGraphToBigWig
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0 referenceC/combineReads.c → reference_C/combineReads.c
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0 referenceC/combineReads.h → reference_C/combineReads.h
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0 referenceC/complementReverse.c → reference_C/complementReverse.c
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0 referenceC/complementReverse.h → reference_C/complementReverse.h
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0 referenceC/extend.c → reference_C/extend.c
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0 referenceC/graphics.sh → reference_C/graphics.sh
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0 referenceC/make_hg19.sh → reference_C/make_hg19.sh
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20 changes: 13 additions & 7 deletions referenceC/new.c → reference_C/new.c
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

#define PACKAGE "ICECap"
#define VERSION "0.01"
#define CHROMOSOMES 22
#define CHROMOSOMES 25
#define WIN_SHIFT1 1
#define RESOLUTION 1000

Expand Down Expand Up @@ -245,7 +245,7 @@ number_for_key(char *key)
}
sprintf(zom,"%d",SCALE);
sprintf(wind,"%d",window);
sprintf(stamp,concat(concat(concat("/NewAnalysis_Z",zom),"_W"),wind));
sprintf(stamp,concat(concat(concat("/Analysis_Z",zom),"_W"),wind));


init(lane,folder,folderN,PATHBOWTIE,chrom_start,chrom_end,stamp,stamp2,stats);
Expand Down Expand Up @@ -335,7 +335,7 @@ printf("\n %d Chromosomes will be considered \n",chrom_end);

if(strlen(folderN)==0){folderN=folder; }else{ sprintf(zom,"%d",SCALE);

sprintf(stamp,concat(concat(concat("/NewAnalysis_Z",zom),"_W"),wind));
sprintf(stamp,concat(concat(concat("/Analysis_Z",zom),"_W"),wind));
mkdir(concat(concat(folder,lane),stamp),0777); mkdir(concat(concat(concat(concat(folder,lane),stamp),"/weights"),stamp2),0777);
mkdir(concat(concat(concat(concat(concat(folder,lane),stamp),"/"),stats),stamp2),0777);
mkdir(concat(concat(concat(concat(concat(concat(folder,lane),stamp),"/"),stats),stamp2),"/fdr"),0777);
Expand Down Expand Up @@ -691,8 +691,10 @@ fclose(fout6);
FILE *tads= fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".tad"), "w+");
FILE *peakY = fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".pkY"), "w+");
FILE *peakY2 = fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".cool"), "w+");

FILE *gff;
FILE *peakC;
FILE *peakC;

FILE *wig= fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".wig"), "w+");

pchic=0;
Expand All @@ -708,7 +710,8 @@ sprintf(sbait,"%d",i);
if(strcasecmp(stringarray[i],"")!=0){sprintf(sbait,"%s",stringarray[i]);}

FILE *peakC = fopen(concat(concat(concat(concat(concat(concat(outdir2,lane),"_BAIT_"),sbait),"_Z"),zom),".pkC"), "w+");
FILE *gff = fopen(concat(concat(concat(concat(concat(concat(outdir2,lane),"_BAIT_"),sbait),"_Z"),zom),".gff"), "w+");
FILE *gff = fopen(concat(concat(concat(concat(concat(outdir2,lane),"_BAIT_"),sbait),"_Z1"),".gff"), "w+");


if(pchic==1){
}else{
Expand Down Expand Up @@ -750,7 +753,7 @@ fprintf(tads,"%d\t",hic[i][j]);
fdist=100000000;}
if(hic[i][j]>0){
if(j>=i){fprintf(peakY2,"%d\t%d\t%d\n",i,j,hic[i][j]);}
printf("BOH: %d\t%d\t%d\t%d\n",i,j,chrombait[i],chrombait[j]);
/* printf("BOH: %d\t%d\t%d\t%d\n",i,j,chrombait[i],chrombait[j]); */
if(chrombait[i]!=chromgrid[j]){
fprintf(peakY,"%d\t%d\t%d\t%f\t%f\t%f\n",totfragments[chrombait[i]-1]+cgrid(chrombait[i],baitpoints[chrombait[i]][i-totbaits[chrombait[i]-1]]+(1-pchic)*RESOLUTION,gp,gridpoints),j,hic[i][j],fdist,1,1);
}else{
Expand All @@ -763,6 +766,9 @@ fprintf(peakY,"%d\t%d\t%d\t%f\t%f\t%f\n",totfragments[chrombait[i]-1]+cgrid(chro
}
}
}
if(pchic==1){
if(hic[i][j]!=0){fprintf(gff,"%s\tICE\t%s\t%d\t%d\t%d\t+\t0\t.\n",record[chromgrid[j]].name_chromosome,sbait,gridpoints[chromgrid[j]][j-(totfragments[chromgrid[j]-1]+1)],gridpoints[chromgrid[j]][j-(totfragments[chromgrid[j]-1])],hic[i][j]);}
}
}

fclose(peakC);
Expand Down Expand Up @@ -818,7 +824,7 @@ sprintf(command,"sed -i 's/chr//' %s",concat(concat(outdir,lane),".tsv"));
system(command);
printf("%s\n",command);

sprintf(command,"R --vanilla < %sPEAKY.R --args %s %s %s %s %d ",folderrefC,outdir,concat(concat(concat(concat(outdir,lane),"_Z"),zom),".pkY"),concat(outdir,"/bins/"),concat(concat(outdir,lane),".tsv"),window);
sprintf(command,"R --no-save < %sPEAKY.R --args %s %s %s %s %d ",folderrefC,outdir,concat(concat(concat(concat(outdir,lane),"_Z"),zom),".pkY"),concat(outdir,"/bins/"),concat(concat(outdir,lane),".tsv"),window);
printf("%s\n",command);
system(command);

Expand Down
0 referenceC/new2.c → reference_C/new2.c
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0 referenceC/new3.c → reference_C/new3.c
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0 referenceC/parallel → reference_C/parallel
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0 referenceC/plot.c → reference_C/plot.c
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0 referenceC/plot_mapping_portion.R → reference_C/plot_mapping_portion.R
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0 referenceC/plot_mapping_portion2.R → reference_C/plot_mapping_portion2.R
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0 referenceC/plot_pairing_portion.R → reference_C/plot_pairing_portion.R
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0 referenceC/plot_pairing_portion2.R → reference_C/plot_pairing_portion2.R
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9 changes: 5 additions & 4 deletions referenceC/shiftrev.c → reference_C/shiftrev.c
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@@ -1,6 +1,7 @@
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#define LINE_MAX 0x4000

Expand Down Expand Up @@ -76,9 +77,9 @@ if(strncmp(vflag[i],"16",2)==0){
while(*c!=0)
{
char* p2;
if(!isdigit(*c)) { fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
if(!isdigit(*c)) { fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
int n=strtol(c,&p2,10);
if(n<1){ fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
if(n<1){ fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
switch(*p2)
{
case 'M':{ while(n>0) { icount++; --n; } break; }
Expand All @@ -97,9 +98,9 @@ if(strncmp(vflag[j],"16",2)==0){
while(*c!=0)
{
char* p2;
if(!isdigit(*c)) { fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
if(!isdigit(*c)) { fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
int n=strtol(c,&p2,10);
if(n<1){ fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
if(n<1){ fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
switch(*p2)
{
case 'M':{ while(n>0) { jcount++; --n; } break; }
Expand Down
0 referenceC/t.c → reference_C/t.c
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0 referenceC/test → reference_C/test
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18 changes: 9 additions & 9 deletions referenceC/trim_galore → reference_C/trim_galore
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Expand Up @@ -44,7 +44,7 @@ file_sanity_check($filenames[0]);

########################################################################

my $path_to_fastqc = '/usr/bin/fastqc';
my $path_to_fastqc = '/well/jknight/software/rescomp/bin/fastqc';

# Before we start let's have quick look if Cutadapt seems to be working with the path information provided
# To change the path to Cutadapt use --path_to_cutadapt /full/path/to/the/Cutadapt/executable
Expand All @@ -54,7 +54,7 @@ if(defined $path_to_cutadapt){
# we'll simply use this
}
else{
$path_to_cutadapt = '/usr/people/whgu0738/.local/bin/cutadapt'; # default, assuming it is in the PATH
$path_to_cutadapt = '/apps/well/python/2.7.11/bin/cutadapt'; # default, assuming it is in the PATH
warn "Path to Cutadapt set as: '$path_to_cutadapt' (default)\n";
}
my $cutadapt_version;
Expand Down Expand Up @@ -338,7 +338,7 @@ sub trim{
warn " >>> Now performing adaptive quality trimming with a Phred-score cutoff of: $cutoff <<<\n\n";
sleep (1);

open (QUAL,"$path_to_cutadapt -e $error_rate -q $cutoff -a X $filename |") or die "Can't open pipe to Cutadapt: $!";
open (QUAL,"$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -a X $filename |") or die "Can't open pipe to Cutadapt: $!";

my $qual_count = 0;

Expand Down Expand Up @@ -417,19 +417,19 @@ sub trim{
if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
warn "\n >>> Now performing adapter trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}
else{ # this is read 2 of a pair
warn "\n >>> Now performing adapter trimming for the adapter sequence: '$a2' from file $temp <<< \n";
sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -e $error_rate -O $stringency -a $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -f fastq -e $error_rate -O $stringency -a $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}
}
### Using the same adapter for both read 1 and read 2
else{
warn "\n >>> Now performing adapter trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
sleep (3);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}

close WRITER or die $!; # not needed
Expand Down Expand Up @@ -587,19 +587,19 @@ sub trim{
if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
warn "\n >>> Now performing quality (cutoff $cutoff) and adapter trimming in a single pass for the adapter sequence: '$adapter' from file $filename <<< \n";
sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
}
else{ # this is read 2 of a pair
warn "\n >>> Now performing quality (cutoff $cutoff) and adapter trimming in a single pass for the adapter sequence: '$a2' from file $filename <<< \n";
sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -e $error_rate -q $cutoff -O $stringency $trim_n -a $a2 $filename") or die "Failed to launch Cutadapt: $!";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency $trim_n -a $a2 $filename") or die "Failed to launch Cutadapt: $!";
}
}
### Using the same adapter for both read 1 and read 2
else{
warn "\n >>> Now performing quality (cutoff $cutoff) and adapter trimming in a single pass for the adapter sequence: '$adapter' from file $filename <<< \n";
sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
}

close WRITER or die $!; # not needed
Expand Down
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0 referenceC/utilities.h → reference_C/utilities.h
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0 referenceC/utilities2.c → reference_C/utilities2.c
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