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modified:   .gitignore
	new file:   data/cds/sp_chlorodb/parameters.sh
	deleted:    data/ir/LSC_RefDB.fasta
	deleted:    data/ir/SSC_RefDB.fasta
	modified:   detectors/cds/bin/go_cds.sh
	modified:   detectors/normalize/lib/lookforIR.lib.sh
	modified:   detectors/normalize/lib/selectIR.py
	modified:   organnot/Dockerfile
	new file:   organnot/README.md
	new file:   organnot/dorgannot
	deleted:    ports/.DS_Store
	deleted:    src/ncbiblast/binaries/.gitignore
	deleted:    src/prokov/lxpack/tests/S.fasta
	deleted:    src/prokov/lxpack/tests/St.fasta
	deleted:    src/prokov/lxpack/tests/Stt.fasta
	deleted:    src/prokov/lxpack/tests/aS.fasta
	deleted:    src/prokov/lxpack/tests/aSt.fasta
	deleted:    src/prokov/lxpack/tests/aStt.fasta
	deleted:    src/prokov/lxpack/tests/aaS.fasta
	deleted:    src/prokov/lxpack/tests/aaSt.fasta
	deleted:    src/prokov/lxpack/tests/aaStt.fasta
	new file:   src/repseek/repseek-2014.09.tgz
This commit is contained in:
Eric Coissac
2025-03-05 21:56:39 +01:00
parent 5d09615f27
commit 4b71fe8c4c
22 changed files with 94 additions and 75646 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
.gitignore vendored
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@ -1,16 +1,20 @@
**/*.fasta.gz
**/*.fasta
**/*.gbk
**/*.gbff
**/.DS_Store
**/*.log
**/*.dat
**/toto*
ports/**
/test/
/samples/
/toto.embl
/toto.fasta
/toto.log
data/cds/sp_chlorodb/genes
data/cds/sp_chlorodb/rawdata
phylonorway
src/gnuparallel/build.i386-darwin
!data/**
!data/**
data/**/*.log
data/rrna/RRNA_*/*.fasta.gz
data/rrna/RRNA_*/*/*.fasta.gz
data/ir/*.fasta.gz

28
data/cds/sp_chlorodb/parameters.sh Normal file
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@ -0,0 +1,28 @@
# sourced file
set CORE_NCDS_CUTOFF = 200
set CORE_START_ATG_CUTOFF = 50
set CORE_START_DFT_CUTOFF = 50
set CORE_START_OTH_CUTOFF = 10
set CORE_STOP_CUTOFF = 200
set CORE_SPLICE_CUTOFF = 50
set SHEL_NCDS_CUTOFF = 10
set CORE_DELTA = Inf
set CORE_COVMIN = 30
set CORE_PMAX = 1e-6
set CORE_IDMIN = 30
set CORE_SIZMIN = 50
set SHEL_DELTA = 0.5
set SHEL_COVMIN = 30
set SHEL_PMAX = 1e-6
set SHEL_IDMIN = 30
set SHEL_SIZMIN = 10
set DUST_DELTA = 0.5
set DUST_COVMIN = 30
set DUST_PMAX = 1e-6
set DUST_IDMIN = 30
set DUST_SIZMIN = 10

56213
data/ir/LSC_RefDB.fasta
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File diff suppressed because it is too large Load Diff

19075
data/ir/SSC_RefDB.fasta
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File diff suppressed because it is too large Load Diff

2
detectors/cds/bin/go_cds.sh
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@ -26,7 +26,7 @@ needarg 1
Fasta=$1; shift
needfile $Fasta
needfile "$Fasta"
# Genome names is set from the base
# name of the genome file without its extension

6
detectors/normalize/lib/lookforIR.lib.sh
View File

@ -27,9 +27,9 @@ function lookForIR {
-outfmt 6 \
-max_target_seqs 10000 | \
awk -v id_match=80 -v lmin=100 \
'($4 > lmin) && (($3+0)>id_match) {
SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10));
if ($7 < $8)
'($4+0 > lmin) && (($3+0)>id_match) {
SAME=(($7+0 < $8+0) && ($9+0 < $10+0)) || (($7+0 > $8+0) && ($9+0 > $10+0));
if ($7+0 < $8+0)
{print substr($2,1,3),$7,$8,SAME}
else
{print substr($2,1,3),$8,$7,SAME}

30
detectors/normalize/lib/selectIR.py
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@ -50,13 +50,15 @@ for line in data:
# <Zafacs> 07/13/2023
# Hack for avoiding crash when LSC and SSC have no blast similarity
# Need to be reworked
if (len(chloro['SSC']) > 0) :
maxSSC = float(max(abs(n) for n in chloro['SSC']))
chloro['SSC']=[n / maxSSC for n in chloro['SSC']]
if (len(chloro['SSC']) > 0) :
sSSC = sum(abs(x) for x in chloro['SSC'])
# maxSSC = float(max(abs(n) for n in chloro['SSC']))
chloro['SSC']=[n / sSSC for n in chloro['SSC']]
if (len(chloro['LSC']) > 0) :
maxLSC = float(max(abs(n) for n in chloro['LSC']))
chloro['LSC']=[n / maxLSC for n in chloro['LSC']]
sLSC = sum(abs(x) for x in chloro['LSC'])
# maxLSC = float(max(abs(n) for n in chloro['LSC']))
chloro['LSC']=[n / sLSC for n in chloro['LSC']]
scoreMax=0
len1Max=0
@ -105,17 +107,19 @@ for line in repeats:
c = float(c_lsc + c_ssc)
o = float(o_lsc + o_ssc)
if c > 0:
c_lsc /= c
c_ssc /= c
# if c > 0:
# c_lsc /= c
# c_ssc /= c
if o > 0:
o_lsc /= o
o_ssc /= o
# if o > 0:
# o_lsc /= o
# o_ssc /= o
score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
#score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
score = abs(abs(c_lsc) + abs(o_ssc) - abs(o_lsc) - abs(c_ssc))
# pvalue=
# print >>sys.stderr,"c.lsc = %f c.ssc = %f o.lsc = %f o.ssc = %f score = %6.4f (len=%d)" % (c_lsc,c_ssc,o_lsc,o_ssc,score,len1)
# print("c.lsc = %f c.ssc = %f o.lsc = %f o.ssc = %f score = %6.4f (len=%d)" % (c_lsc,c_ssc,o_lsc,o_ssc,score,len1),
# file=sys.stderr)
if (score >= scoreMax) and ((len1 > len1Max) or (len2 > len2Max)):
scoreMax = score

34
organnot/Dockerfile
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@ -1,4 +1,4 @@
FROM ubuntu:lunar as builder
FROM ubuntu:jammy AS builder
LABEL dockerfile.version="1"
LABEL software="phyloskims"
@ -9,10 +9,10 @@ LABEL software="phyloskims"
##
WORKDIR /
RUN apt update --fix-missing && apt upgrade -y
RUN apt install -y build-essential
RUN apt install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
RUN git clone https://git.metabarcoding.org/org-asm/org-annotate.git
RUN apt-get update --fix-missing && apt upgrade -y
RUN apt-get install -y build-essential
RUN apt-get install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
RUN git clone https://github.com/PhyloSkims/annotate.git org-annotate
#
# Compile tools
@ -28,14 +28,14 @@ RUN make
#
##
WORKDIR "/"
RUN apt install -y python3-pip python3-dev python3-venv
RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
RUN python3 -m venv org-assembler
WORKDIR "/org-asm"
RUN bash -c '../org-assembler/bin/pip3 install -r requirements.txt'
RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity'
WORKDIR "/"
# WORKDIR "/"
# RUN apt install -y python3-pip python3-dev python3-venv
# RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
# RUN python3 -m venv org-assembler
# WORKDIR "/org-asm"
# RUN bash -c '../org-assembler/bin/pip3 install -r requirements.txt'
# RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity'
# WORKDIR "/"
##
#
@ -43,14 +43,14 @@ WORKDIR "/"
#
##
FROM ubuntu:lunar as phyloskims
FROM ubuntu:jammy AS phyloskims
WORKDIR /
RUN apt update --fix-missing && apt upgrade -y
RUN apt install -y tcsh bash gawk parallel zlib1g libglib2.0-0 clustalo muscle cd-hit hmmer
RUN apt-get install -y tcsh bash gawk parallel zlib1g libglib2.0-0 clustalo muscle cd-hit hmmer
COPY --from=builder /org-annotate /org-annotate
RUN rm -rf /org-annotate/src
COPY --from=builder /org-assembler /org-assembler
COPY --from=builder /org-assembler/bin/oa /bin
# COPY --from=builder /org-assembler /org-assembler
# COPY --from=builder /org-assembler/bin/oa /bin
COPY organnot /bin
RUN chmod +x /bin/organnot
#

5
organnot/README.md Normal file
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@ -0,0 +1,5 @@
To build the docker image:
```bash
docker build --load --platform linux/amd64 -t phyloskims/annotate .
```

15
organnot/dorgannot Executable file
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@ -0,0 +1,15 @@
#!/bin/bash
#IMAGE=gricad-registry.univ-grenoble-alpes.fr/leca/projets/malbio/phyloskims
IMAGE=phyloskims/annotate
TAG=latest
singularity -h >/dev/null 2>&1 && DOCKER="singularity --silent exec --bind .:/data docker://"
docker -h >/dev/null 2>&1 && DOCKER="docker run --volume .:/data "
if [[ -z "$DOCKER" ]] ; then
echo "Cannot found neither singularity or docker on your system"
exit 1
fi
eval "${DOCKER}${IMAGE}:${TAG} organnot $*"

BIN
ports/.DS_Store vendored
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Binary file not shown.

2
src/ncbiblast/binaries/.gitignore vendored
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@ -1,2 +0,0 @@
bin.*
.DS_Store

34
src/prokov/lxpack/tests/S.fasta
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@ -1,34 +0,0 @@
>test
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

35
src/prokov/lxpack/tests/St.fasta
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@ -1,35 +0,0 @@
>test
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
T

35
src/prokov/lxpack/tests/Stt.fasta
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@ -1,35 +0,0 @@
>test
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TT

35
src/prokov/lxpack/tests/aS.fasta
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@ -1,35 +0,0 @@
>test
A
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

36
src/prokov/lxpack/tests/aSt.fasta
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@ -1,36 +0,0 @@
>test
A
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
T

36
src/prokov/lxpack/tests/aStt.fasta
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@ -1,36 +0,0 @@
>test
A
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TT

35
src/prokov/lxpack/tests/aaS.fasta
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@ -1,35 +0,0 @@
>test
AA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

36
src/prokov/lxpack/tests/aaSt.fasta
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@ -1,36 +0,0 @@
>test
AA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
T

36
src/prokov/lxpack/tests/aaStt.fasta
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@ -1,36 +0,0 @@
>test
AA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATGAAAACTGAAAACGCAAAAACAAATCAAACATTAGTTGAGAATTCACT
GAACACACAATTATCAAACTGGTTTCTTTTATACTCTAAGCTCCACCGTT
TCCATTGGTATGTGAAAGGGCCTCATTTCTTTACATTGCACGAGAAATTT
GAAGAACTTTATGACCATGCGGCTGAAACAGTGGATACCATCGCTGAGCG
CCTGCTGGCGATTGGCGGACAGCCTGTTGCCACAGTGAAAGAATACACTG
AGCATGCATCTATCACAGACGGCGGAAACGAAACATCAGCATCAGAAATG
GTACAAGCATTGGTAAACGACTACAAACAAATCAGCAGCGAATCTAAATT
CGTGATCGGCCTGGCTGAAGAAAATCAAGACAATGCGACAGCGGACTTGT
TTGTCGGATTAATTGAAGAAGTTGAAAAACAAGTGTGGATGCTTTCCTCT
TATTTAGGGTAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTACCCTA
AATAAGAGGAAAGCATCCACACTTGTTTTTCAACTTCTTCAATTAATCCG
ACAAACAAGTCCGCTGTCGCATTGTCTTGATTTTCTTCAGCCAGGCCGAT
CACGAATTTAGATTCGCTGCTGATTTGTTTGTAGTCGTTTACCAATGCTT
GTACCATTTCTGATGCTGATGTTTCGTTTCCGCCGTCTGTGATAGATGCA
TGCTCAGTGTATTCTTTCACTGTGGCAACAGGCTGTCCGCCAATCGCCAG
CAGGCGCTCAGCGATGGTATCCACTGTTTCAGCCGCATGGTCATAAAGTT
CTTCAAATTTCTCGTGCAATGTAAAGAAATGAGGCCCTTTCACATACCAA
TGGAAACGGTGGAGCTTAGAGTATAAAAGAAACCAGTTTGATAATTGTGT
GTTCAGTGAATTCTCAACTAATGTTTGATTTGTTTTTGCGTTTTCAGTTT
TCAT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TT

BIN
src/repseek/repseek-2014.09.tgz Normal file
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