Release/1.3.2

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Change Log
 
+## [1.3.2] - 2017-02-07
+### Added
+- Alignment command can now directly take a protein multi-FASTA and skip ORF detection (-p option)
+- Prepare and alignment commands can now make use of a proxy server (HTTP/SOCKS) for contacting UniProt (-P option)
+
 ## [1.3.1] - 2017-01-01
 ### Added
 - UniProt report now includes max mapping quality for each protein

align.c

@@ -107,15 +107,17 @@ int command_align(int argc, char *argv[]) {
 	FILE * reportPriStream = 0, * reportSecStream = 0;
 	char * readsProName = 0, * indexProName = 0, * prefixName = 0;
 	char * samName = 0, * reportPriName = 0, * reportSecName = 0;
+    const char * proxyAddress;
 
 	memset(&aux, 0, sizeof(ktp_aux_t));
 	memset(pes, 0, VALUE_DOMAIN * sizeof(mem_pestat_t));
 	for (i = 0; i < VALUE_DOMAIN; ++i) pes[i].failed = 1;
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
+    proxyAddress = NULL;
 
-	while ((c = getopt(argc, argv, "1epabgnMCSPVYJjf:F:u:k:o:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "1epabgnMCSVYJjf:F:u:k:o:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:P:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == 'u') opt->outputType = atoi(optarg);
 		else if (c == 'f') opt->min_orf_len = atoi(optarg);
@@ -129,9 +131,9 @@ int command_align(int argc, char *argv[]) {
 		else if (c == 'T') opt->T = atoi(optarg), opt0.T = 1;
 		else if (c == 'U') opt->pen_unpaired = atoi(optarg), opt0.pen_unpaired = 1;
 		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
-		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
+		//else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
 		else if (c == 'a') opt->flag |= MEM_F_ALL;
-		else if (c == 'p') opt->flag |= MEM_F_PE | MEM_F_SMARTPE;
+		//else if (c == 'p') opt->flag |= MEM_F_PE | MEM_F_SMARTPE;
 		else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
 		else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
 		else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP;
@@ -142,6 +144,7 @@ int command_align(int argc, char *argv[]) {
 		else if (c == 'g') opt->proteinFlag |= ALIGN_FLAG_GEN_NT;
 		else if (c == 'n') opt->proteinFlag |= ALIGN_FLAG_KEEP_PRO;
 		else if (c == 'J') opt->proteinFlag &= ~ALIGN_FLAG_ADJUST_ORF;
+        else if (c == 'p') opt->proteinFlag |= ALIGN_FLAG_MANUAL_PRO;
 		else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
 		else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
 		else if (c == 'v') bwa_verbose = atoi(optarg);
@@ -157,6 +160,7 @@ int command_align(int argc, char *argv[]) {
 		else if (c == 'C') aux.copy_comment = 1;
 		else if (c == 'K') fixed_chunk_size = atoi(optarg);
 		else if (c == 'X') opt->mask_level = atof(optarg);
+        else if (c == 'P') proxyAddress = optarg;
 		else if (c == 'h') {
 			opt0.max_XA_hits = opt0.max_XA_hits_alt = 1;
 			opt->max_XA_hits = opt->max_XA_hits_alt = strtol(optarg, &p, 10);
@@ -344,8 +348,14 @@ int command_align(int argc, char *argv[]) {
 
 	}
 
-	// Detect ORFs and write protein file
-	writeReadsProtein(argv[optind + 1], readsProName, opt);
+    if (opt->proteinFlag & ALIGN_FLAG_MANUAL_PRO) {
+        // Protein input given, skip ORF detection
+        sprintf(readsProName, argv[optind + 1]);
+    }
+    else {
+        // Detect ORFs and write protein file
+        writeReadsProtein(argv[optind + 1], readsProName, opt);
+    }
 
 	// Open ORFs sequence
 	ko = kopen(readsProName, &fd);
@@ -385,14 +395,14 @@ int command_align(int argc, char *argv[]) {
 
 	// Generate UniProt report if requested
 	if (prefixName != NULL) {
-		renderUniprotReport(opt->outputType, 1, reportPriStream);
+		renderUniprotReport(opt->outputType, 1, reportPriStream, proxyAddress);
 		if (opt->flag & MEM_F_ALL) {
-			renderUniprotReport(opt->outputType, 0, reportSecStream);
+			renderUniprotReport(opt->outputType, 0, reportSecStream, proxyAddress);
 		}
 	}
 
-	// Delete protein file unless requested otherwise
-	if (!(opt->proteinFlag & ALIGN_FLAG_KEEP_PRO)) {
+	// Delete generated protein file unless requested otherwise
+	if (!(opt->proteinFlag & ALIGN_FLAG_KEEP_PRO) && !(opt->proteinFlag & ALIGN_FLAG_MANUAL_PRO)) {
 		remove(readsProName);
 	}
 
@@ -425,6 +435,7 @@ int renderAlignUsage(const mem_opt_t * passOptions) {
 	fprintf(stderr, "Usage: paladin align [options] <idxbase> <in.fq>\n\n");
 
 	fprintf(stderr, "Gene detection options:\n\n");
+    fprintf(stderr, "       -p            disable ORF detection and treat input as protein sequence\n");
 	fprintf(stderr, "       -b            disable brute force ORF detection\n");
 	fprintf(stderr, "       -J            do not adjust minimum ORF length (constant value) for shorter read lengths\n");
 	fprintf(stderr, "       -f INT        minimum ORF length accepted (as constant value) [%d]\n", passOptions->min_orf_len);
@@ -467,6 +478,7 @@ int renderAlignUsage(const mem_opt_t * passOptions) {
 	fprintf(stderr, "       -u INT        report type generated when using reporting and a UniProt reference [%d]\n", passOptions->outputType);
 	fprintf(stderr, "                        0: Simple ID summary report\n");
 	fprintf(stderr, "                        1: Detailed report (Contacts uniprot.org)\n\n");
+    fprintf(stderr, "       -P STR        HTTP or SOCKS proxy address\n");
 	fprintf(stderr, "       -g            generate detected ORF nucleotide sequence FASTA\n");
 	fprintf(stderr, "       -n            keep protein sequence after alignment\n");
 	//fprintf(stderr, "       -p            smart pairing (ignoring in2.fq)\n");

bntseq.c

@@ -1,30 +1,3 @@
-/* The MIT License
-
-   Copyright (c) 2008 Genome Research Ltd (GRL).
-
-   Permission is hereby granted, free of charge, to any person obtaining
-   a copy of this software and associated documentation files (the
-   "Software"), to deal in the Software without restriction, including
-   without limitation the rights to use, copy, modify, merge, publish,
-   distribute, sublicense, and/or sell copies of the Software, and to
-   permit persons to whom the Software is furnished to do so, subject to
-   the following conditions:
-
-   The above copyright notice and this permission notice shall be
-   included in all copies or substantial portions of the Software.
-
-   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-   SOFTWARE.
-*/
-
-/* Contact: Toni Westbrook <anthonyw@wildcats.unh.edu> */
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

bwamem.c

@@ -90,7 +90,7 @@ mem_opt_t *mem_opt_init()
 	return o;
 }
 
-void filterCompetingAln(worker_t * passWorker, int passCount) {
+void filterCompetingAln(worker_t * passWorker, int passCount, int passDisable) {
 	int seqIdx, alnIdx, bestIdx;
 	int currentSeq, readSeq;
 	int seqTotal, bestTotal;
@@ -101,6 +101,12 @@ void filterCompetingAln(worker_t * passWorker, int passCount) {
 
 	// Iterate through each sequence and alignment
 	for (seqIdx = 0 ; seqIdx < passCount - 1 ; seqIdx++) {
+        // If filtering disabled, simply mark sequence as best
+        if (passDisable) {
+            passWorker->regs[seqIdx].active = 1;
+            continue;
+        }
+
 		// Check if we're in a new sequence or in an alternate frame
 		sscanf(passWorker->seqs[seqIdx].name, "%d:", &readSeq);
 		if (readSeq != currentSeq) {
@@ -113,12 +119,11 @@ void filterCompetingAln(worker_t * passWorker, int passCount) {
 			bestIdx = seqIdx;
 		}
 
-                // Aggregate all score totals for this sequence
-                seqTotal = 0;
-                for (alnIdx = 0 ; alnIdx < passWorker->regs[seqIdx].n ; alnIdx++) {
-                        seqTotal += passWorker->regs[seqIdx].a[alnIdx].score;
-                }
-
+        // Aggregate all score totals for this sequence
+        seqTotal = 0;
+        for (alnIdx = 0 ; alnIdx < passWorker->regs[seqIdx].n ; alnIdx++) {
+            seqTotal += passWorker->regs[seqIdx].a[alnIdx].score;
+        }
 
 		// Check if current alignment is best so far
 		if (seqTotal > bestTotal) {
@@ -128,7 +133,7 @@ void filterCompetingAln(worker_t * passWorker, int passCount) {
 	}
 
 	// Filter final sequence
-	passWorker->regs[bestIdx].active = 1;
+    if (!passDisable) passWorker->regs[bestIdx].active = 1;
 }
 
 int getAlignmentType(worker_t * passWorker, int passEntry, int passAlignment) {
@@ -1300,7 +1305,7 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
 	}
 
 	// Filter competing alignments from multi-frame encoding during ORF detection process
-	filterCompetingAln(&w, n);
+    filterCompetingAln(&w, n, opt->proteinFlag & ALIGN_FLAG_MANUAL_PRO);
 
 	kt_for(opt->n_threads, worker2, &w, (opt->flag&MEM_F_PE)? n>>1 : n);
 

bwamem.h

@@ -130,7 +130,7 @@ typedef struct {
 extern "C" {
 #endif
 
-	void filterCompetingAln(worker_t * passWorker, int passCount);
+	void filterCompetingAln(worker_t * passWorker, int passCount, int passDisable);
 	int getAlignmentType(worker_t * passWorker, int passEntry, int passAlignment);
 
 	smem_i *smem_itr_init(const bwt_t *bwt);

bwt.c

@@ -1,5 +1,3 @@
-/* Contact: Toni Westbrook <anthonyw@wildcats.unh.edu> */
-
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>

bwt.h

@@ -1,5 +1,3 @@
-/* Contact: Toni Westbrook <anthonyw@wildcats.unh.edu> */
-
 #ifndef BWA_BWT_H
 #define BWA_BWT_H
 

bwtindex.c

@@ -1,5 +1,3 @@
-/* Contact: Toni Westbrook <anthonyw@wildcats.unh.edu> */
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -393,7 +391,7 @@ int command_index(int argc, char *argv[]) {
 int command_prepare(int argc, char *argv[]) {
 	char c;
 	char refArg[] = "-p0";
-	const char * refName;
+	const char * refName, * proxyAddress;
 	int refType, valid;
 
 	// Fixed passthrough arguments
@@ -404,10 +402,12 @@ int command_prepare(int argc, char *argv[]) {
 	valid = 1;
 	refType = -1;
 	refName = NULL;
+    proxyAddress = NULL;
 
-	while ((c = getopt(argc, argv, "r:f:")) >= 0) {
+	while ((c = getopt(argc, argv, "r:f:P:")) >= 0) {
 		if (c == 'r') refType = atoi(optarg);
 		if (c == 'f') refName = optarg;
+        if (c == 'P') proxyAddress = optarg;
 		if (c == '?') valid = 0;
 	}
 
@@ -420,7 +420,8 @@ int command_prepare(int argc, char *argv[]) {
 			fprintf(stderr, "    -r <#>         Reference Database:\n");
 			fprintf(stderr, "                     1: UniProtKB Reviewed (Swiss-Prot)\n");
 			fprintf(stderr, "                     2: UniProtKB Clustered 90%% (UniRef90)\n\n");
-			fprintf(stderr, "    -f <ref.fasta> Skip download, use local copy of reference database (may be indexed)\n\n");
+			fprintf(stderr, "    -f <ref.fasta> Skip download, use local copy of reference database (may be indexed)\n");
+            fprintf(stderr, "    -P <address>   HTTP or SOCKS proxy address\n\n");
 			fprintf(stderr, "Examples:\n\n");
 			fprintf(stderr, "   paladin prepare -r2\n");
 			fprintf(stderr, "   paladin prepare -r1 -f uniprot_sprot.fasta.gz\n");
@@ -432,7 +433,7 @@ int command_prepare(int argc, char *argv[]) {
 
 	// We can generalize this in the future to include other reference types
 	if (!refName) {
-		if ((refName = downloadUniprotReference(refType))[0] == 0) {
+		if ((refName = downloadUniprotReference(refType, proxyAddress))[0] == 0) {
 			return 1;
 		}
 	}

bwtindex.h

@@ -1,4 +1,3 @@
-
 #ifndef BWTINDEX_H_
 #define BWTINDEX_H_
 

main.c

@@ -1,7 +1,7 @@
 /*
    The MIT License
 
-   Copyright (c) 2015 by Anthony Westbrook, University of New Hampshire <anthonyw@wildcats.unh.edu>
+   Copyright (c) 2015 by Anthony Westbrook, University of New Hampshire <anthony.westbrook@unh.edu>
    Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
 
    Permission is hereby granted, free of charge, to any person obtaining
@@ -51,7 +51,7 @@
    UniProt-generated functional profile. This text file may be used for all
    downstream characterizations.
 
-   Contact: Toni Westbrook <anthonyw@wildcats.unh.edu>
+   Contact: Toni Westbrook <anthony.westbrook@unh.edu>
    For information regarding BWA, contact Heng Li <lh3@sanger.ac.uk>
 */
 
@@ -135,7 +135,7 @@ int renderVersion() {
 	fprintf(stderr, "Program: PALADIN (Protein Alignment and Detection Interface)\n");
 
 	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
-	fprintf(stderr, "Contact: Toni Westbrook (UNH) <anthonyw@wildcats.unh.edu>\n");
+	fprintf(stderr, "Contact: Toni Westbrook (UNH) <anthony.westbrook@unh.edu>\n");
 	fprintf(stderr, "Based on: BWA by Heng Li <lh3@sanger.ac.uk>\n\n");
 
 	return 1;

main.h

@@ -1,7 +1,7 @@
 /*
    The MIT License
 
-   Copyright (c) 2015 by Anthony Westbrook, University of New Hampshire <anthonyw@wildcats.unh.edu>
+   Copyright (c) 2015 by Anthony Westbrook, University of New Hampshire <anthony.westbrook@unh.edu>
    Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
 
    Permission is hereby granted, free of charge, to any person obtaining
@@ -51,7 +51,7 @@
    UniProt-generated functional profile. This text file may be used for all
    downstream characterizations.
 
-   Contact: Toni Westbrook <anthonyw@wildcats.unh.edu>
+   Contact: Toni Westbrook <anthony.westbrook@unh.edu>
    For information regarding BWA, contact Heng Li <lh3@sanger.ac.uk>
 */
 
@@ -66,7 +66,7 @@
 #define PACKAGE_VERSION STR(PACKAGE_VERSION_MAJOR) "." STR(PACKAGE_VERSION_MINOR) "." STR(PACKAGE_VERSION_REV)
 #define PACKAGE_VERSION_MAJOR 1
 #define PACKAGE_VERSION_MINOR 3
-#define PACKAGE_VERSION_REV 1
+#define PACKAGE_VERSION_REV 2
 #endif
 
 // Render usage and version details

protein.c

@@ -1,5 +1,3 @@
-/* Contact: Toni Westbrook <anthonyw@wildcats.unh.edu> */
-
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>

protein.h

@@ -1,5 +1,3 @@
-/* Contact: Toni Westbrook <anthonyw@wildcats.unh.edu> */
-
 #ifndef PROTEIN_H_
 #define PROTEIN_H_
 
@@ -11,10 +9,11 @@
 #define OUTPUT_TYPE_UNIPROT_SIMPLE 0
 #define OUTPUT_TYPE_UNIPROT_FULL   1
 
-#define ALIGN_FLAG_BRUTE_ORF   0x0001
+#define ALIGN_FLAG_BRUTE_ORF  0x0001
 #define ALIGN_FLAG_GEN_NT     0x0002
 #define ALIGN_FLAG_KEEP_PRO   0x0004
 #define ALIGN_FLAG_ADJUST_ORF 0x0008
+#define ALIGN_FLAG_MANUAL_PRO 0x0010
 
 extern unsigned char codon_aa_hash[64];