├── .gitignore ├── README.md ├── sam2consensus.py └── LICENSE /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # sam2consensus 2 | Get the consensus sequences for short sequencing reads mapped to a reference. Version 2.0 3 | 4 | ## _Brief description_ 5 | The program takes as input a SAM file (.sam or .sam.gz) resulting from mapping short reads to a reference (the reference 6 | sequences can correspond to separate genes for example), then it calculates the consensus sequence from the aligned 7 | reads alone. If you have BAM files you will need to convert them first with `samtools`. A single or multiple consensus thresholds can be specified, the program also adds insertions, if many long 8 | long insertions are expected, we recommend to perform indel ralignment before for optimal results. The consensus method 9 | is the one used by Geneious and described in detail in http://assets.geneious.com/manual/8.1/GeneiousManualse41.html 10 | 11 | Regions with no coverage are filled with -s (or a different character if specified). Input SAM files don't need to be 12 | sorted. Original reference FASTAs are not necessary since the consensus is reference-free. 13 | 14 | It will produce a FASTA file per reference containing as many sequences as thresholds were specified. 15 | 16 | ## _Usage_ 17 | Just type `python sam2consensus.py -h` to show the help of the program: 18 | ``` 19 | usage: sam2consensus.py [-h] -i FILENAME [-c THRESHOLDS] [-n N] [-o OUTFOLDER] 20 | [-p PREFIX] [-m MIN_DEPTH] [-f FILL] [-d MAXDEL] 21 | 22 | +------------------------------------------------------------------+ 23 | | sam2consensus.py: extract the consensus sequence from a SAM file | 24 | +------------------------------------------------------------------+ 25 | 26 | The program takes as input a SAM file (.sam or .sam.gz) resulting from mapping 27 | short reads to a reference (the reference sequences can correspond to separate 28 | genes for example), then it calculates the consensus sequence from the aligned 29 | reads alone. A single or multiple consensus thresholds can be specified, the 30 | program also adds insertions, if many long insertions are expected, we recommend 31 | to perform indel ralignment before for optimal results. The consensus method is 32 | the one used by Geneious and described in detail in 33 | http://assets.geneious.com/manual/8.1/GeneiousManualse41.html 34 | 35 | Regions with no coverage are filled with -s (or a different character if 36 | specified). Input SAM files don't need to be sorted. Original reference FASTAs 37 | are not necessary since the consensus is reference-free. 38 | 39 | It will produce a FASTA file per reference containing as many sequences as 40 | thresholds were specified. 41 | 42 | optional arguments: 43 | -h, --help show this help message and exit 44 | -i FILENAME, --input FILENAME 45 | Name of the SAM file, SAM does not need to be sorted 46 | and can be compressed with gzip 47 | -c THRESHOLDS, --consensus-thresholds THRESHOLDS 48 | List of consensus thresold(s) separated by commas, no 49 | spaces, example: -c 0.25,0.75,0.50, default=0.25 50 | -n N Split FASTA output sequences every n nucleotides, 51 | default=do not split sequence 52 | -o OUTFOLDER, --outfolder OUTFOLDER 53 | Name of output folder, default=same folder as input 54 | -p PREFIX, --prefix PREFIX 55 | Prefix for output file name, default=input filename 56 | without .sam extension 57 | -m MIN_DEPTH, --min-depth MIN_DEPTH 58 | Minimum read depth at each site to report the 59 | nucleotide in the consensus, default=1 60 | -f FILL, --fill FILL Character for padding regions not covered in the 61 | reference, default= - (gap) 62 | -d MAXDEL, --maxdel MAXDEL 63 | Ignore deletions longer than this value, default=150 64 | ``` 65 | 66 | ## _Examples_ 67 | In the following examples, if you added the script to the `PATH` you can omit `python` from the commands. 68 | 69 | _Example 1:_ Using the default consensus threshold of 0.25: 70 | ```bash 71 | python sam2consensus.py -i myfile.sam 72 | ``` 73 | 74 | _Example 2:_ Using multiple consensus thresholds of 0.25, 0.50, and 0.75 and specifying an output folder: 75 | ```bash 76 | python sam2consensus.py -i myfile.sam -c 0.25,0.50,0.75 -o results 77 | ``` 78 | 79 | _Example 3:_ Using a custom consensus threshold of 0.75 and changing padding character for uncovered regions to "N": 80 | ```bash 81 | python sam2consensus.py -i myfile.sam -c 0.75 -f N 82 | ``` 83 | 84 | _Example 4:_ Specifying a prefix "sample1" and increasing minimum mapping depth to 10: 85 | ```bash 86 | python sam2consensus.py -i myfile.sam -pre sample1 -m 10 87 | ``` 88 | 89 | ## _Credits_ 90 | - Code: [Edgardo M. Ortiz](mailto:e.ortiz.v@gmail.com) 91 | - Data and testing: [Deise J. P. Gonçalves](mailto:deisejpg@gmail.com) 92 | -------------------------------------------------------------------------------- /sam2consensus.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | # -*- coding: utf-8 -*- 3 | 4 | 5 | ''' 6 | +------------------------------------------------------------------+ 7 | | sam2consensus.py: extract the consensus sequence from a SAM file | 8 | +------------------------------------------------------------------+ 9 | 10 | The program takes as input a SAM file (.sam or .sam.gz) resulting from mapping 11 | short reads to a reference (the reference sequences can correspond to separate 12 | genes for example), then it calculates the consensus sequence from the aligned 13 | reads alone. A single or multiple consensus thresholds can be specified, the 14 | program also adds insertions, if many long insertions are expected, we recommend 15 | to perform indel ralignment before for optimal results. The consensus method is 16 | the one used by Geneious and described in detail in 17 | http://assets.geneious.com/manual/8.1/GeneiousManualse41.html 18 | 19 | Regions with no coverage are filled with -s (or a different character if 20 | specified). Input SAM files don't need to be sorted. Original reference FASTAs 21 | are not necessary since the consensus is reference-free. 22 | 23 | It will produce a FASTA file per reference containing as many sequences as 24 | thresholds were specified. 25 | ''' 26 | 27 | 28 | __author__ = "Edgardo M. Ortiz" 29 | __credits__ = "Deise J.P. Gonçalves" 30 | __version__ = "2.1" 31 | __email__ = "e.ortiz.v@gmail.com" 32 | __date__ = "2019-01-11" 33 | 34 | 35 | 36 | import sys 37 | import os 38 | import re 39 | import operator 40 | import argparse 41 | import gzip 42 | import math 43 | 44 | 45 | 46 | def parsecigar(cigarstring, seq, pos_ref): 47 | ''' 48 | Modifies a sequence according to its CIGAR string, modified for speed according to frequency of CIGAR tags 49 | 50 | :param cigarstring: cigar string, v3 or v4 are allowed 51 | :param seq: raw sequence 52 | :param pos_ref: position in the reference of the leftmost aligned nucleotide (0-based) 53 | :return: edited sequence according to cigar string, list of tuples for 54 | insertions indicating coordinate in the reference and the 55 | sequence inserted 56 | ''' 57 | 58 | matches = re.findall(r"(\d+)([MIDNSHPX=]{1})", cigarstring) 59 | cigar = [{"type": m[1], "length": int(m[0])} for m in matches] 60 | start = 0 61 | start_ref = pos_ref 62 | seqout = "" 63 | insert = [] 64 | for c in range(0, len(cigar)): 65 | l = cigar[c]["length"] 66 | if cigar[c]["type"] in ["=","X","M"]: 67 | seqout += seq[start:start + l] 68 | start += l 69 | start_ref += l 70 | elif cigar[c]["type"] in ["D","N","P"]: 71 | seqout += "-" * l 72 | start_ref += l 73 | elif cigar[c]["type"] == "I": 74 | insert.append((start_ref, seq[start:start+l])) 75 | start += l 76 | elif cigar[c]["type"] == "S": 77 | start += l 78 | elif cigar[c]["type"] == "H": 79 | continue 80 | else: 81 | print("SAM file probably contains unmapped reads") 82 | return seqout, insert 83 | 84 | 85 | 86 | def main(): 87 | parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) 88 | parser.add_argument("-i", "--input", action="store", dest="filename", required=True, 89 | help="Name of the SAM file, SAM does not need to be sorted and can be compressed with gzip") 90 | parser.add_argument("-c", "--consensus-thresholds", action="store", dest="thresholds", type=str, default="0.25", 91 | help="List of consensus thresold(s) separated by commas, no spaces, example: -c 0.25,0.75,0.50, default=0.25") 92 | parser.add_argument("-n", action="store", dest="n", type=int, default=0, 93 | help="Split FASTA output sequences every n nucleotides, default=do not split sequence") 94 | parser.add_argument("-o", "--outfolder", action="store", dest="outfolder", default="./", 95 | help="Name of output folder, default=same folder as input") 96 | parser.add_argument("-p", "--prefix", action="store", dest="prefix", default="", 97 | help="Prefix for output file name, default=input filename without .sam extension") 98 | parser.add_argument("-m", "--min-depth", action="store", dest="min_depth", type=int, default=1, 99 | help="Minimum read depth at each site to report the nucleotide in the consensus, default=1") 100 | parser.add_argument("-f", "--fill", action="store", dest="fill", default="-", 101 | help="Character for padding regions not covered in the reference, default= - (gap)") 102 | parser.add_argument("-d", "--maxdel", action="store", dest="maxdel", default=150, 103 | help="Ignore deletions longer than this value, default=150") 104 | args = parser.parse_args() 105 | 106 | 107 | 108 | filename = args.filename 109 | 110 | # Prepare the opener if the SAM file is compressed 111 | if filename.endswith(".gz"): 112 | opener = gzip.open 113 | else: 114 | opener = open 115 | 116 | # Parse list of consensus thresholds 117 | thresholds = args.thresholds.split(",") 118 | thresholds = [float(i) for i in thresholds] 119 | 120 | # Prefix will be input filename without extension 121 | if args.prefix == "": 122 | prefix = "".join(args.filename.split("/")[-1]).split(".")[0] 123 | else: 124 | prefix = args.prefix 125 | 126 | # Create output folder if it doesn't exist 127 | outfolder = args.outfolder.rstrip("/") 128 | if not os.path.exists(outfolder): 129 | os.makedirs(outfolder) 130 | outfolder += "/" 131 | 132 | min_depth = args.min_depth 133 | 134 | nchar = args.n 135 | 136 | fill = args.fill 137 | 138 | maxdel = args.maxdel 139 | 140 | 141 | 142 | # Start processing SAM file 143 | print("\nProcessing file "+filename+":\n") 144 | 145 | # First process header of file to extract reference information 146 | 147 | header_length = 0 148 | 149 | with opener(filename) as mapfile: 150 | 151 | sequences = {} # Container of sequences per reference for consensus calculation 152 | coverages = {} # Container for coverage per site for each reference 153 | insertions = {} # Container for insertions with coordinates per reference 154 | 155 | for line in mapfile: 156 | 157 | if line.startswith("@"): 158 | header_length += 1 159 | 160 | if line.startswith("@SQ"): 161 | 162 | # Obtain reference name and length, skipping description if present 163 | refname = line.split("\t")[1].replace("SN:","").split()[0] 164 | reflength = int(line.split("\t")[2].replace("LN:","")) 165 | 166 | # Prepare empty dictionaries to parse aligned reads and populate them later 167 | sequences[refname] = [{"-":0,"A":0,"C":0,"G":0,"N":0,"T":0} for nuc in range(reflength)] 168 | coverages[refname] = [0]*reflength 169 | insertions[refname] = [] 170 | 171 | else: 172 | break 173 | 174 | print("SAM header processed, "+str(len(sequences))+" references found.\n") 175 | mapfile.close() 176 | 177 | 178 | 179 | # Process the reads that were aligned to the references 180 | with opener(filename) as mapfile: 181 | # Set read counter to show progress 182 | reads_total = 0 - header_length 183 | reads_mapped = 0 184 | 185 | while 1: 186 | # Load large SAM file by chunks 187 | mapfile_chunk = mapfile.readlines(50000) 188 | if not mapfile_chunk: 189 | break 190 | 191 | for line in mapfile_chunk: 192 | 193 | # Skip header and unmapped reads 194 | reads_total += 1 195 | if line[0] != "@" and line.split("\t")[5] != "*": 196 | 197 | reads_mapped += 1 198 | sam_record = line.split("\t") 199 | 200 | refname = sam_record[2].split()[0] ## Reference name, skip description if mapper kept it 201 | pos_ref = int(sam_record[3])-1 ## Starting position in the reference, 0-based 202 | # cigar = sam_record[5] ## CIGAR string fo the aligned read 203 | # seqraw = sam_record[9] ## Unaligned raw sequence of the read 204 | 205 | # Parse the CIGAR and obtain edited sequence and list of insertions 206 | seqout, insert = parsecigar(sam_record[5], sam_record[9], pos_ref) 207 | 208 | # Fill the nucleotides in their respective reference according to the alignment described by the 209 | # CIGAR string 210 | if seqout.count("-") <= maxdel: 211 | for nuc in seqout: 212 | sequences[refname][pos_ref][nuc] += 1 213 | pos_ref += 1 214 | else: 215 | for nuc in seqout: 216 | if nuc != "-": 217 | sequences[refname][pos_ref][nuc] += 1 218 | pos_ref += 1 219 | 220 | # Add insertions with coordinates to the dictionary of insertions per reference 221 | insertions[refname] += insert 222 | 223 | # Show progress 224 | if reads_total % 500000 == 0: 225 | print(str(reads_total)+" reads processed.") 226 | 227 | print("A total of "+str(reads_total)+" reads were processed, out of which, "+str(reads_mapped)+" reads were mapped.\n") 228 | mapfile.close() 229 | 230 | 231 | 232 | # Reformat dictionaries and get them ready for consensus calculation 233 | for refname in sequences: 234 | 235 | # Populate dictionary of coverage per site 236 | for pos in range(len(coverages[refname])): 237 | coverages[refname][pos] = sum(sequences[refname][pos].values()) 238 | 239 | # Invert the dictionary at each position {"-":0,"A":0,"C":0,"G":0,"N":0,"T":0} to have counts as keys and a 240 | # list of nucleotides with the same counts as values, skip nucs with count==0 241 | count_nucs = {} 242 | for key, value in sequences[refname][pos].iteritems(): 243 | if value != 0: 244 | count_nucs.setdefault(value,[]).append(key) 245 | 246 | # Transform to a list of sorted tuples in reverse order 247 | count_nucs = list(count_nucs.iteritems()) 248 | count_nucs.sort(reverse=True) 249 | 250 | # Multiply coverage by number of nucleotides in each count to restore the correct coverage 251 | count_nucs = [[i[0]*len(i[1]), i[1]] for i in count_nucs] 252 | sequences[refname][pos] = count_nucs 253 | 254 | 255 | 256 | # We will treat each insertion as a short alignment of motifs, for that we have to modify the raw counts of 257 | # motifs per coordinate and get them into the same shape as the dictionary that contains the nucleotide counts 258 | # for the rest of the sequence. Every column of each insertion will have a dictionary of the form: 259 | # {"-":0,"A":0,"C":0,"G":0,"N":0,"T":0} and will be parsed as the 'sequences' dictionary. 260 | 261 | # First step is to make a dictionary where the key is the inserted motif and the value is the count of the motif 262 | ins_tmp1 = {} 263 | if insertions[refname] != []: 264 | for ins in insertions[refname]: 265 | if ins[0] not in ins_tmp1: 266 | ins_tmp1[ins[0]] = {ins[1]:1} 267 | else: 268 | if ins[1] not in ins_tmp1[ins[0]]: 269 | ins_tmp1[ins[0]][ins[1]] = 1 270 | else: 271 | ins_tmp1[ins[0]][ins[1]] += 1 272 | 273 | # Now we create a new dictionary as long as the longest motif inserted for every coordinate where an 274 | # insertion was detected. Each position will contain a dictionary for counts as in the 'sequences' 275 | # dictionary: {"-":0,"A":0,"C":0,"G":0,"N":0,"T":0} 276 | ins_tmp2 = {} 277 | for pos in sorted(ins_tmp1): 278 | motif_max_len = 0 279 | for motif in ins_tmp1[pos]: 280 | motif_max_len = max(len(motif), motif_max_len) 281 | ins_tmp2[pos] = [{"-":0,"A":0,"C":0,"G":0,"N":0,"T":0} for i in range(motif_max_len)] 282 | 283 | # Now we track each nucleotide in each inserted motif and populate that new dictionary 'ins_tmp2' 284 | for pos in sorted(ins_tmp1): 285 | for motif in ins_tmp1[pos]: 286 | for col in range(len(motif)): 287 | ins_tmp2[pos][col][motif[col]] += ins_tmp1[pos][motif] 288 | 289 | # We are finally ready to reformat the nucleotide counts exactly as in the 'sequences' dictionary 290 | for pos in sorted(ins_tmp2): 291 | for col in range(len(ins_tmp2[pos])): 292 | 293 | # We need to add the count for "-" based on the coverage at the insertion position 294 | ins_tmp2[pos][col]["-"] = coverages[refname][pos] - sum(ins_tmp2[pos][col].values()) 295 | 296 | # Invert the dictionary at each position {"A":0,"C":0,"T":0,"G":0,"-":0,"N":0} to have counts as 297 | # keys and a list of nucleotides with the same counts as values, skip nucs with count==0 298 | count_nucs = {} 299 | for key, value in ins_tmp2[pos][col].iteritems(): 300 | if value != 0: 301 | count_nucs.setdefault(value,[]).append(key) 302 | 303 | # Transform to a list of sorted tuples in reverse order 304 | count_nucs = list(count_nucs.iteritems()) 305 | count_nucs.sort(reverse=True) 306 | 307 | # Multiply coverage by number of nucleotides in each count to restore the correct coverage 308 | count_nucs = [[i[0]*len(i[1]), i[1]] for i in count_nucs] 309 | ins_tmp2[pos][col] = count_nucs 310 | 311 | insertions[refname] = ins_tmp2 312 | 313 | 314 | 315 | # Dictionary to translate IUPAC ambiguities, lowercase letters are used when "-" or "N" were present for a position, 316 | # however, software like Genious for example are case insensitive and will imply ignore capitalization 317 | amb = {"-":"-", "A":"A", "C":"C", "G":"G", "N":"N", "T":"T", 318 | "-A":"a", "-C":"c", "-G":"g", "-N":"n", "-T":"t", 319 | "AC":"M", "AG":"R", "AN":"a", "AT":"W", "CG":"S", 320 | "CN":"c", "CT":"Y", "GN":"g", "GT":"K", "NT":"t", 321 | "-AC":"m", "-AG":"r", "-AN":"a", "-AT":"w", "-CG":"s", 322 | "-CN":"c", "-CT":"y", "-GN":"g", "-GT":"k", "-NT":"t", 323 | "ACG":"V", "ACN":"m", "ACT":"H", "AGN":"r", "AGT":"D", 324 | "ANT":"w", "CGN":"s", "CGT":"B", "CNT":"y", "GNT":"k", 325 | "-ACG":"v", "-ACN":"m", "-ACT":"h", "-AGN":"r", "-AGT":"d", 326 | "-ANT":"w", "-CGN":"s", "-CGT":"b", "-CNT":"y", "-GNT":"k", 327 | "ACGN":"v", "ACGT":"N", "ACNT":"h", "AGNT":"d", "CGNT":"b", 328 | "-ACGN":"v", "-ACGT":"N", "-ACNT":"h", "-AGNT":"d", "-CGNT":"b", 329 | "-ACGNT":"N"} 330 | 331 | 332 | 333 | # If a reference had zero reads mapped we need to erase it from the dictionaries 334 | sequences2erase = [] 335 | for refname in coverages: 336 | if sum(coverages[refname]) == 0: 337 | sequences2erase.append(refname) 338 | for refname in sequences2erase: 339 | del sequences[refname] 340 | del insertions[refname] 341 | 342 | 343 | 344 | # Obtain consensus sequence(s) from the 'sequences' and 'insertions' dictionary 345 | fastas = {} 346 | for refname in sequences: 347 | 348 | for t in thresholds: 349 | 350 | fasta_seqout = "" 351 | fasta_header = "" 352 | sumcov = 0 353 | 354 | # Obtain sequence from the 'sequences' dictionary 355 | for pos in range(len(sequences[refname])): 356 | if sequences[refname][pos] != []: 357 | sumcov += coverages[refname][pos] 358 | if coverages[refname][pos] >= min_depth: 359 | nucs = [] 360 | cov_nucs = 0 361 | for count in sequences[refname][pos]: 362 | if cov_nucs < t*coverages[refname][pos]: 363 | nucs += count[1] 364 | cov_nucs += count[0] 365 | else: 366 | break 367 | fasta_seqout += amb["".join(sorted(nucs))] 368 | 369 | # Add insertions when applicable 370 | if refname in insertions: 371 | if pos in insertions[refname]: 372 | for col in range(len(insertions[refname][pos])): 373 | nucs = [] 374 | cov_nucs = 0 375 | for count in insertions[refname][pos][col]: 376 | if cov_nucs < t*coverages[refname][pos]: 377 | nucs += count[1] 378 | cov_nucs += count[0] 379 | else: 380 | break 381 | if amb["".join(sorted(nucs))] == "-": 382 | continue 383 | else: 384 | fasta_seqout += amb["".join(sorted(nucs))] 385 | sumcov += coverages[refname][pos] 386 | else: 387 | fasta_seqout += fill 388 | else: 389 | fasta_seqout += fill 390 | 391 | # Prepare headers for FASTA file 392 | # sequence name is: sammplename|consensus_threshold 393 | # sequence description is reference:refname coverage:XXX.XX length:XXXX consensus_threshold:XX% 394 | fasta_header = (">"+prefix+"|c"+str(int(t*100))+" reference:"+refname+ 395 | " coverage:"+str(round(float(sumcov)/float(len(fasta_seqout)), 2))+ 396 | " length:"+str(len(fasta_seqout.replace("-","")))+ 397 | " consensus_threshold:"+str(int(t*100))+"%") 398 | 399 | # Add only if sequence is not empty 400 | if len(fasta_seqout.replace("-","")) > 0: 401 | if refname not in fastas: 402 | fastas[refname] = [[fasta_header,fasta_seqout]] 403 | else: 404 | fastas[refname].append([fasta_header,fasta_seqout]) 405 | else: 406 | continue 407 | 408 | 409 | 410 | # Write output files, one FASTA file per reference, containing as many sequences as consensus thresholds were asked 411 | for reference in fastas: 412 | outnameprefix = reference+"__"+prefix 413 | outfile = open(outfolder+outnameprefix+".fasta", "w") 414 | if nchar == 0: 415 | outfile.write("\n".join([i[0]+"\n"+i[1] for i in fastas[reference]])+"\n") 416 | else: 417 | outfile.write("\n".join([i[0]+"\n"+"\n".join([i[1][s:s+nchar] for s in range(0, len(i[1]), nchar)]) for i in fastas[reference]])+"\n") 418 | outfile.close() 419 | if len(thresholds) == 1: 420 | print("Consensus sequence at "+str(int(thresholds[0]*100))+"% saved for "+ 421 | reference+" in: "+outfolder+outnameprefix+".fasta") 422 | else: 423 | print("Consensus sequences at "+",".join([str(int(i*100))+"%" for i in thresholds])+" saved for "+ 424 | reference+" in: "+outfolder+outnameprefix+".fasta") 425 | 426 | print("Done.\n") 427 | 428 | 429 | if __name__ == "__main__": 430 | main() 431 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | --------------------------------------------------------------------------------