1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842
|
#!/bin/bash
#*****************************************************************************
# discoSnp++: discovering polymorphism from raw unassembled NGS reads
# A tool from the GATB (Genome Assembly Tool Box)
# Copyright (C) 2014 INRIA
# Authors: P.Peterlongo, E.Drezen
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#*****************************************************************************
red=`tput setaf 1`
green=`tput setaf 2`
yellow=`tput setaf 3`
cyan=`tput setaf 6`
bold=`tput bold`
reset=`tput sgr0`
die() {
printf '%s\n' "$1" >&2
exit 1
}
function myrealpath { echo $(cd $(dirname $1); pwd)/$(basename $1); }
option_cores_gatb=""
option_cores_post_analysis=""
Ttot="$(date +%s)"
#### constant #####
max_C=2147483647 #$((2**31-1))
###########################################################
#################### DEFAULT VALUES #######################
###########################################################
version="2.3.X"
read_sets="" # A file of file(s)
read_sets_kissreads=""
prefix="discoRes" # all intermediate and final files will be written will start with this prefix
k=31 # size of kmers
b=0 # smart branching approach: bubbles in which both paths are equaly branching are discarded, all others are accepted
c=3 # minimal coverage
C=$max_C # maximal coverage
d=1 # estimated number of error per read (used by kissreads only)
D=100 # maximal size of searched deletions
max_ambigous_indel=20
P=3 # number of polymorphsim per bubble
option_max_symmetrical_crossroads=""
l="-l"
extend="-t"
x=""
y=""
output_coverage_option=""
genotyping="-genotype"
remove=1
verbose=1
stop_after_kissnp=0
e=""
prefix_trash=`head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13 ; echo ''`
#EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron
if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
read_file_names_bin=$EDIR/build/bin/read_file_names
dbgh5_bin=$EDIR/build/ext/gatb-core/bin/dbgh5
kissnp2_bin=$EDIR/build/bin/kissnp2
kissreads2_bin=$EDIR/build/bin/kissreads2
create_coverage_h5_file_bin=$EDIR/build/bin/create_coverage_h5_file
else # VERSION BINARY
read_file_names_bin=$EDIR/bin/read_file_names
dbgh5_bin=$EDIR/bin/dbgh5
kissnp2_bin=$EDIR/bin/kissnp2
kissreads2_bin=$EDIR/bin/kissreads2
create_coverage_h5_file_bin=$EDIR/bin/create_coverage_h5_file
fi
chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
useref=""
wraith="false"
genome=""
bwa_path_option=""
option_phase_variants=""
bwa_distance=4
dsk_build_dir=""
#######################################################################
#################### END HEADER #######################
#######################################################################
function help {
echo " ************"
echo " *** HELP ***"
echo " ************"
echo "run_discoSnp++.sh, a pipelining kissnp2 and kissreads for calling SNPs and small indels from NGS reads without the need of a reference genome"
echo "Version "$version
echo "Usage: ./run_discoSnp++.sh -r read_file_of_files [OPTIONS]"
echo -e "MANDATORY"
echo -e "\t -r|--fof <file name of a file of file(s)>"
echo -e "\t\t The input read files indicated in a file of file(s)"
echo -e "\t\t Example: -r bank.fof with bank.fof containing the two lines \n\t\t\t data_sample/reads_sequence1.fasta\n\t\t\t data_sample/reads_sequence2.fasta.gz"
echo -e "\t -f Absolute path to compiled dsk (directory containing compiled dsk and dsk2ascii)"
echo -e "\nOPTIONS"
echo -e "\t -k | --k_size value <int value>"
echo -e "\t\t Set the length of used kmers. Must fit the compiled value."
echo -e "\t\t Default=31"
echo -e "\t -c | --min_coverage value <int value>"
echo -e "\t\t Set the minimal coverage per read set: Used by kissnp2 (don't use kmers with lower coverage) and kissreads (read coherency threshold)."
echo -e "\t\t This coverage can be automatically detected per read set (in this case use \"auto\" or specified per read set, see the documentation."
echo -e "\t\t Default=3"
echo -e "\t -C | --max_coverage value <int value in 0, 1 or 2>"
echo -e "\t\t Set the maximal coverage for each read set: Used by kissnp2 (don't use kmers with higher coverage)."
echo -e "\t\t Default=2^31-1"
echo -e "\t -b | --branching value. "
echo -e "\t\t 0: forbid variants for which any of the two paths is branching (high precision, lowers the recall in complex genomes)."
echo -e "\t\t Default value"
echo -e "\t\t 1: (smart branching) forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position"
echo -e "\t\t2: No limitation on branching (lowers the precision, high recall)"
echo -e "\t -s | --symmetrical value <int value>"
echo -e "\t\t In -b 2 mode only: maximal number of symmetrical crossroads traversed while trying to close a bubble. Default: no limit"
echo -e "\t -g | --graph <file name>"
echo -e "\t\t Reuse a previously created graph (.h5 file) with same prefix and same k and c parameters."
echo -e "\t -X\t Stop discoSnp++ right after variant calling - the output is only a fasta file with no coverage information."
echo -e "\t -D | --deletion_max_size <int>"
echo -e "\t\t discoSnp++ will search for deletions of size from 1 to D included. Default=100"
echo -e "\t -a | --ambiguity_max_size <int>"
echo -e "\t\t Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output [default '20']"
echo -e "\t -P | --max_snp_per_bubble <int>"
echo -e "\t\t discoSnp++ will search up to P SNPs in a unique bubble. Default=3"
echo -e "\t --fof_mapping <file name of a file of file(s)>"
echo -e "\t\t If this option is used this fof is used when mapping back reads on the predicted variants instead of the original fof file provided by -r|--fof option"
echo -e "\t -p | --prefix <string>"
echo -e "\t\t All out files will start with this prefix. Default=\"discoRes\""
echo -e "\t -l | --no_low_complexity"
echo -e "\t\t Remove low complexity bubbles"
echo -e "\t -T | --contigs"
echo -e "\t\t Extend found polymorphisms with contigs (default: extend with unitigs)"
echo -e "\t -d | --max_substitutions <int>"
echo -e "\t\t Set the number of authorized substitutions used while mapping reads on found SNPs (kissreads). Default=1"
echo -e "\t -n | --no_genotype"
echo -e "\t\t Do not compute the genotypes"
echo -e "\t -u | --max_threads <int>"
echo -e "\t\t Max number of used threads. 0 means all threads"
echo -e "\t\t default 0"
echo -e "\nREFERENCE GENOME AND/OR VCF CREATION OPTIONS"
echo -e "\t -G | --reference_genome <file name>"
echo -e "\t\t Reference genome file (fasta, fastq, gzipped or nor). In absence of this file the VCF created by VCF_creator won't contain mapping related results."
echo -e "\t -R"
echo -e "\t\t Use the reference file also in the variant calling, not only for mapping results"
echo -e "\t -B | --bwa_path <directory name>"
echo -e "\t\t bwa path. e.g. /home/me/my_programs/bwa-0.7.12/ (note that bwa must be pre-compiled)"
echo -e "\t\t Optional unless option -G used and bwa is not in the binary path."
echo -e "\t -e\t Map variant predictions on reference genome with their unitig or contig extensions."
echo -e "\t\t Useless unless mapping on reference genome is required (option -G). "
echo
echo -e "\t -w\t Wraith mode: only show all discoSnp++ commands without running them"
echo -e "\t -v <0 or 1>"
echo -e "\t\t Verbose 0 (avoids progress output) or 1 (enables progress output) -- default=1."
echo -e "\t -h | --help"
echo -e "\t\t Prints this message and exist\n"
echo "Any further question: read the readme file or contact us via the Biostar forum: https://www.biostars.org/t/discosnp/"
}
while :; do
case $1 in
-f)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then # checks that there exists a second value and its is not the start of the next option
dsk_build_dir=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-A)
option_phase_variants="-phasing"
echo "Will phase variants during kissreads process - WARNING this option is too experimental and thus not described in the help message"
echo "You can obtain clusters using script : \"script/from_phased_alleles_to_clusters.sh file_name_of_phased_alleles\" (the filename(s) is/are given during kissreads process"
;;
-X)
stop_after_kissnp=1
;;
-w)
wraith="true"
;;
-R)
useref="true"
output_coverage_option="-dont_output_first_coverage"
;;
-a|--ambiguity_max_size)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then # checks that there exists a second value and its is not the start of the next option
max_ambigous_indel=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-v)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
verbose=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-s|--symmetrical)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
option_max_symmetrical_crossroads="-max_symmetrical_crossroads "$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-T|--contigs)
extend="-T"
;;
-g|--graph)
remove=0
;;
-n|--no_genotype)
genotyping=""
;;
-l|--no_low_complexity)
l=""
;;
-h|-\?|--help)
help
exit
;;
-r|--fof)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
read_sets=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
--fof_mapping)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
read_sets_kissreads=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-b|--branching)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
b=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-p|--prefix)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
prefix=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-k | --k_size)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
k=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-P|--max_snp_per_bubble)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
P=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-c|--min_coverage)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
c=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-C|--max_coverage)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
C=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-d|--max_substitutions)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
d=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-D|--deletion_max_size)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
D=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
B|--bwa_path)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
bwa_path_option="-B "$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-x)
x="-x" ##CHARLOTTE
;;
-y)
y="-x" ##CHARLOTTE
;;
-G|--reference_genome)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
genome=$2
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-e)
e="-e"
;;
-u|--max_threads)
if [ "$2" ] && [ ${2:0:1} != "-" ] ; then
option_cores_gatb="-nb-cores $2"
option_cores_post_analysis="-t $2"
shift
else
die 'ERROR: "'$1'" option requires a non-empty option argument.'
fi
;;
-?*)
printf 'WARN: Unknown option (exit): %s\n' "$1" >&2
exit 1
;;
:)
echo "${red}Option $1 requires an argument.${reset}" >&2
exit 1
;;
--) # End of all options.
shift
break
;;
-?*)
printf 'WARN: Unknown option (ignored): %s\n' "$1" >&2
;;
*) # Default case: No more options, so break out of the loop.
break
esac
shift
done
if [ ! -d "$dsk_build_dir" ]; then
echo "${red}You must provide dsk bin direction (option -f)${reset}"
help
exit 1
fi
if [ -z "$read_sets" ]; then
echo "${red}You must provide at least one read set (-r|--fof)${reset}"
help
exit 1
fi
######### CHECK THE k PARITY ##########
rest=$(( $k % 2 ))
if [ $rest -eq 0 ]
then
echo "${red}k=$k is even number, to avoid palindromes, we set it to $(($k-1))${reset}"
k=$(($k-1))
fi
#######################################
c_filename=`echo ${c} | tr ',' '_'`
if [ $C -ne $max_C ]
then
h5prefix=${prefix}_k_${k}_c_${c_filename}_C_${C}
else
h5prefix=${prefix}_k_${k}_c_${c_filename}
fi
kissprefix=${h5prefix}_D_${D}_P_${P}_b_${b}
readsFilesDump=${prefix}_read_files_correspondance.txt
mapped_readsFilesDump=${prefix}_mapped_read_files_correspondance.txt
#######################################
c_dbgh5=$c
rm -f ${read_sets}_${kissprefix}_removemeplease
if [[ "$useref" == "true" ]]; then
if [ -z "$genome" ]; then
echo "${red}You can't use option -R without providing a reference genome (-G)${reset}"
help
exit 1
fi
myrealpath $genome > ${read_sets}_${kissprefix}_removemeplease
c_dbgh5="1,"$c
fi
cat $read_sets >> ${read_sets}_${kissprefix}_removemeplease
#######################################################################
#################### OPTIONS SUMMARY #######################
#######################################################################
if [[ "$wraith" == "false" ]]; then
echo -e "${yellow}Running discoSnp++ "$version", in directory "$EDIR" with following parameters:"
echo -e "\t read_sets="$read_sets
echo -e "\t prefix="$h5prefix
echo -e "\t c="$c
echo -e "\t C="$C
echo -e "\t k="$k
echo -e "\t b="$b
echo -e "\t d="$d
echo -e "\t D="$D
echo -e "\t s="$option_max_symmetrical_crossroads
echo -e "\t P="$P
if [ ! -z "${read_sets_kissreads}" ]; then
echo -e "\t fof_mapping read_file_of_files="${read_sets_kissreads}
fi
echo -e "\t p="$prefix
echo -e "\t G="$genome
echo -e "\t e="$e
echo -e -n "\t starting date="
date
echo "${reset}"
fi
#######################################################################
#################### END OPTIONS SUMMARY #######################
#######################################################################
#############################################################
#################### DUMP READ FILES #######################
#############################################################
${read_file_names_bin} -in $read_sets > $readsFilesDump
if [ ! -z "${read_sets_kissreads}" ]; then
${read_file_names_bin} -in ${read_sets_kissreads} > $mapped_readsFilesDump
fi
############################################################
#################### GRAPH CREATION #######################
############################################################
if [ $remove -eq 1 ]; then
rm -f $h5prefix.h5
fi
if [ ! -e $h5prefix.h5 ]; then
T="$(date +%s)"
echo -e "${yellow}############################################################"
echo -e "#################### GRAPH CREATION #######################"
echo -e "############################################################${reset}"
i=0
# cleaning
rmCmd="rm -f *trashme_[0-9]*.fa.gz"
echo "${green}"${rmCmd}"${cyan}"
${rmCmd}
echo ${reset}
#
input_h5s=""
IFS=',' read -r -a array <<< "${c_dbgh5}" # split the cmin entry (comma separated)
ab_index_size="${#array[@]}"
for line in `cat ${read_sets}_${kissprefix}_removemeplease`; do
min_abundance="${array[$i]}"
if [ $i -ge ${ab_index_size} ]
then
min_abundance="${array[${ab_index_size}-1]}";
fi
i=`expr $i + 1`
dskCmd="${dsk_build_dir}/dsk -file ${line} -abundance-min ${min_abundance} -abundance-max 2147483647 -solidity-kind sum -kmer-size $k -out ${prefix_trash}_trashme_${i}.h5"
toaskiiCmd="${dsk_build_dir}/dsk2ascii -file ${prefix_trash}_trashme_${i}.h5 -out /dev/null/dummy -fasta -c"
dump_cov_cmd="${create_coverage_h5_file_bin} -in ${prefix_trash}_trashme_${i}.h5 -coverage_file ${prefix_trash}_trashme_${i}_cov_only.h5"
rm_dsk_h5_file_cmd="rm -f ${prefix_trash}_trashme_${i}.h5"
echo "${green}"${dskCmd} ${cyan}" && "${green} ${toaskiiCmd} " | gzip -1 > ${prefix_trash}_trashme_${i}.fa.gz && "${dump_cov_cmd}" && "${rm_dsk_h5_file_cmd}"&${cyan} "
if [[ "$wraith" == "false" ]]; then
${dskCmd} && ${toaskiiCmd} | gzip -1> ${prefix_trash}_trashme_${i}.fa.gz && ${dump_cov_cmd} && ${rm_dsk_h5_file_cmd} &
fi
# echo ${reset}
if [ $? -ne 0 ]
then
echo "${red}there was a problem with dsk${reset}"
exit 1
fi
input_h5s=${input_h5s}${prefix_trash}_trashme_${i}_cov_only.h5,
# enables to run up to 10 jobs in parallel
while [ 1 ]
do
a=`jobs -r|wc -l` # number of previous jobs stilil running
if [ $a -lt 10 ]
then
break
fi
sleep 10
done
done
# wait for the last jobs to finish
for job in `jobs -p`
do
wait $job || let "FAIL+=1"
done
rmCmd="rm -f ${prefix_trash}_trashme_allsolid.fa.gz"
for file in `ls ${prefix_trash}_trashme_[0-9]*.fa.gz`;
do
cat_cmd="cat $file >> ${prefix_trash}_trashme_allsolid.fa.gz && rm -f $file"
echo "${green}"${cat_cmd}"${cyan}"
if [[ "$wraith" == "false" ]]; then
cat $file >> ${prefix_trash}_trashme_allsolid.fa.gz && rm -f $file
fi
if [ $? -ne 0 ]
then
echo "${red}there was a problem concatenation of single kmer fasta files${reset}"
exit 1
fi
done
# echo "${green}"${rmCmd}"${cyan}"
# ${rmCmd}
# catCmd="cat ${prefix_trash}_trashme_[0-9]*.fa.gz" #> allsolid.fa.gz
# echo "${green}"${catCmd} "> ${prefix_trash}_trashme_allsolid.fa.gz${cyan}"
# if [[ "$wraith" == "false" ]]; then
# ${catCmd} > ${prefix_trash}_trashme_allsolid.fa.gz
# fi
# if [ $? -ne 0 ]
# then
# echo "${red}there was a problem concatenation of single kmer fasta files${reset}"
# exit 1
# fi
echo "${green}ls ${prefix_trash}_trashme_allsolid.fa.gz > ${prefix_trash}_trashme_allsolid.txt${cyan}"
ls ${prefix_trash}_trashme_allsolid.fa.gz > ${prefix_trash}_trashme_allsolid.txt
graphCmd="${dbgh5_bin} -in ${prefix_trash}_trashme_allsolid.txt -out $h5prefix -kmer-size $k -abundance-min 1 -abundance-max $C -solidity-kind sum ${option_cores_gatb} -verbose $verbose -skip-bcalm -skip-bglue -no-mphf"
echo "${green}"${graphCmd}"${cyan}"
if [[ "$wraith" == "false" ]]; then
${graphCmd}
fi
echo "${reset}"
if [ $? -ne 0 ]
then
echo "there was a problem with graph construction"
exit 1
fi
#####################################################################
#################### COVERAGE FILE CREATION #######################
#####################################################################
## create the string trashme_1.h5,trashme_2.h5,...,trashme_n.h5 string
create_cov_file_cmd="${create_coverage_h5_file_bin} -in ${input_h5s} -coverage_file ${h5prefix}_cov.h5"
echo "${green}"${create_cov_file_cmd}"${cyan}"
if [[ "$wraith" == "false" ]]; then
${create_cov_file_cmd}
fi
echo ${reset}
if [ $? -ne 0 ]
then
echo "${red}there was a problem with graph construction${reset}"
exit 1
fi
cleanCmd="rm -rf ${prefix_trash}_trashme_*"
echo ${green}${cleanCmd}${reset}
if [[ "$wraith" == "false" ]]; then
${cleanCmd}
fi
T="$(($(date +%s)-T))"
if [[ "$wraith" == "false" ]]; then
echo "${yellow}Graph creation time in seconds: ${T}${reset}"
fi
else
if [[ "$wraith" == "false" ]]; then
echo -e "${yellow}File $h5prefix.h5 exists. We use it as input graph${reset}"
fi
fi
######################################################
#################### KISSNP2 #######################
######################################################
T="$(date +%s)"
echo -e "${yellow}############################################################"
echo -e "#################### KISSNP2 MODULE #######################"
echo -e "############################################################${reset}"
kissnp2Cmd="${kissnp2_bin} -in $h5prefix.h5 -out $kissprefix -b $b $l $x -P $P -D $D $extend $option_cores_gatb $output_coverage_option -coverage_file ${prefix_trash}_trashme_fake_cov.h5 -max_ambigous_indel ${max_ambigous_indel} ${option_max_symmetrical_crossroads} -verbose $verbose"
echo ${green}${kissnp2Cmd}${cyan}
if [[ "$wraith" == "false" ]]; then
${kissnp2Cmd}
fi
echo ${reset}
if [ $? -ne 0 ]
then
echo "${red}there was a problem with kissnp2${reset}"
exit 1
fi
rm -f ${prefix_trash}_trashme_allsolid.txt
T="$(($(date +%s)-T))"
if [[ "$wraith" == "false" ]]; then
echo "${yellow}Bubble detection time in seconds: ${T}${reset}"
fi
if [ ! -f $kissprefix.fa ]
then
if [[ "$wraith" == "false" ]]; then
echo "${yellow}No polymorphism predicted by discoSnp++"
echo -e -n "\t ending date="
date
echo -e " Thanks for using discoSnp++ - http://colibread.inria.fr/discoSnp/${reset}"
exit
fi
fi
if [ $stop_after_kissnp -eq 1 ]; then
if [[ "$wraith" == "false" ]]; then
echo "${yellow}-X option detected, computation stopped after variant detection."
echo "Results (with no read coverage) are located here: "$kissprefix.fa
echo -e -n "\t ending date="
date
echo -e " Thanks for using discoSnp++ - http://colibread.inria.fr/discoSnp/${reset}"
exit
fi
fi
#######################################################################
#################### KISSREADS #######################
#######################################################################
T="$(date +%s)"
if [[ "$wraith" == "false" ]]; then
echo -e "${yellow}#############################################################"
echo -e "#################### KISSREADS MODULE #######################"
echo -e "#############################################################${reset}"
fi
smallk=$k
if (( $smallk>31 )) ; then
smallk=31
fi
i=5 #avoid modidy this (or increase this if memory needed by kissread is too high. Min 1. Large i (7-10) decreases memory and increases time).
index_stride=$(($i+1)); size_seed=$(($smallk-$i)) # DON'T modify this.
if [ ! -z "${read_sets_kissreads}" ]; then
read_sets=${read_sets_kissreads}
fi
kissreadsCmd="${kissreads2_bin} -predictions $kissprefix.fa -reads $read_sets -co ${kissprefix}_coherent -unco ${kissprefix}_uncoherent -k $k -size_seeds ${size_seed} -index_stride ${index_stride} -hamming $d $genotyping -coverage_file ${h5prefix}_cov.h5 $option_cores_gatb -verbose $verbose $y ${option_phase_variants}"
echo ${green}$kissreadsCmd${cyan}
if [[ "$wraith" == "false" ]]; then
$kissreadsCmd
fi
if [ $? -ne 0 ]
then
echo "${red}there was a problem with kissreads2${reset}":
exit 1
fi
T="$(($(date +%s)-T))"
echo "${yellow}Kissreads (mapping reads on bubbles) time in seconds: ${T}${reset}"
#######################################################################
#################### SORT AND FORMAT RESULTS #########################
#######################################################################
echo -e "${yellow}###############################################################"
echo -e "#################### SORT AND FORMAT RESULTS #################"
echo -e "###############################################################${reset}"
if [[ "$wraith" == "false" ]]; then
sort -rg ${kissprefix}_coherent | cut -d " " -f 2 | tr ';' '\n' > ${kissprefix}_coherent.fa
fi
if [ $? -ne 0 ]
then
echo "${red}there was a problem with the result sorting.${reset}"
exit 1
fi
if [[ "$wraith" == "false" ]]; then
sort -rg ${kissprefix}_uncoherent | cut -d " " -f 2 | tr ';' '\n' > ${kissprefix}_uncoherent.fa
fi
if [ $? -ne 0 ]
then
echo "${red}there was a problem with the result sorting.${reset}"
exit 1
fi
rm -f $kissprefix.fa ${kissprefix}_coherent ${kissprefix}_uncoherent
rm -rf ${read_sets}_${kissprefix}_removemeplease
rm -rf ${prefix_trash}_trashme
#######################################################################
#################### DISCOSNP FINISHED ###############################
#######################################################################
#######################################################################
#################### Deal with VCF ###############################
#######################################################################
T="$(date +%s)"
echo -e "${yellow}###############################################################"
echo -e "#################### CREATE VCF #######################"
echo -e "###############################################################${reset}"
if [ -z "$genome" ]; then # NO reference genome use, vcf creator mode 1
vcfCreatorCmd="$EDIR/scripts/run_VCF_creator.sh -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf"
echo ${green}$vcfCreatorCmd${cyan}
if [[ "$wraith" == "false" ]]; then
$vcfCreatorCmd
fi
echo ${reset}
if [ $? -ne 0 ]
then
echo "${red}there was a problem with VCF creation. See how to use the \"run_VCF_creator.sh\" alone.${reset}"
exit 1
fi
else # A Reference genome is provided, vcf creator mode 2
vcfCreatorCmd="$EDIR/scripts/run_VCF_creator.sh $bwa_path_option -G $genome $bwa_path_option -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf -I $option_cores_post_analysis $e"
echo ${green}$vcfCreatorCmd${cyan}
if [[ "$wraith" == "false" ]]; then
$vcfCreatorCmd
fi
if [ $? -ne 0 ]
then
echo "${red}there was a problem with VCF creation. See how to use the \"run_VCF_creator.sh\" alone.${reset}"
exit 1
fi
fi
T="$(($(date +%s)-T))"
if [[ "$wraith" == "false" ]]; then
echo "${yellow}Vcf creation time in seconds: ${T}"
echo -e "###############################################################"
echo -e "#################### DISCOSNP++ FINISHED ######################"
echo -e "###############################################################"
Ttot="$(($(date +%s)-Ttot))"
echo "DiscoSnp++ total time in seconds: ${Ttot}"
echo -e "################################################################################################################"
echo -e " fasta of predicted variant is \""${kissprefix}_coherent.fa"\""
if [ -z "$genome" ]; then
echo -e " Ghost VCF file (1-based) is \""${kissprefix}_coherent.vcf"\""
else
echo -e " VCF file (1-based) is \""${kissprefix}_coherent.vcf"\""
echo -e " An IGV ready VCF file (sorted by position, only mapped variants, 0-based) is \""${kissprefix}_coherent_for_IGV.vcf"\""
fi
echo -e " Thanks for using discoSnp++ - http://colibread.inria.fr/discoSnp/ - Forum: http://www.biostars.org/t/discoSnp/"
echo -e "################################################################################################################${reset}"
fi
|