%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE:
Thu Sep 5 14:17:02 PDT 2019
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.6 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
swoose
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 44
Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
Stepping: 2
CPU MHz: 2925.993
BogoMIPS: 5851.93
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 12288K
NUMA node0 CPU(s): 0-23
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp pti tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d
------------
Memory Specs
total used free shared buff/cache available
Mem: 70G 15G 41G 666M 13G 53G
Swap: 4.7G 373M 4.3G
No LSB modules are available.
%env variables are good for passing to bash cells
%env wd=/home/sam/analyses/20190905_pgen_v074.a3_repeats_counts
wd="/home/sam/analyses/20190905_pgen_v074.a3_repeats_counts"
%env rysnc_owl=owl:/volume1/web/halfshell/genomic-databank/
%env gff=Panopea-generosa-vv0.74.a3.TE.gff3
%env wget_gffs=--directory-prefix=${wd} --recursive --quiety --no-directories --no-check-certificate --no-parent --accept 'Panopea-generosa-vv0.74.a3.TE.gff3' https://owl.fish.washington.edu/halfshell/genomic-databank/
# Set genome size to 942Mbp
GENOME_SIZE = 942000000
env: wd=/home/sam/analyses/20190905_pgen_v074.a3_repeats_counts env: rysnc_owl=owl:/volume1/web/halfshell/genomic-databank/ env: gff=Panopea-generosa-vv0.74.a3.TE.gff3 env: wget_gffs=--directory-prefix=$/home/sam/analyses/20190905_pgen_v074.a3_repeats_counts --recursive --quiety --no-directories --no-check-certificate --no-parent --accept 'Panopea-generosa-vv0.74.a3.TE.gff3' https://owl.fish.washington.edu/halfshell/genomic-databank/
# Calculate percentage of genome comprised of a given feature
def ind_repeats_percent(feature_length_sum):
return round(float(feature_length_sum / GENOME_SIZE * 100), 2)
import fnmatch
import os
import pandas
%%bash
mkdir --parents ${wd}
cd {wd}
/home/sam/analyses/20190905_pgen_v074.a3_repeats_counts
Info on GFFs is here: [https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome-feature-tracks-3)
%%bash
rsync \
--archive \
--verbose \
--progress \
--include="${gff}" \
--exclude="*" \
"${rysnc_owl}" \
.
echo ""
echo ""
echo "----------------------------------------------------------"
ls -lh
receiving incremental file list
./
Panopea-generosa-vv0.74.a3.TE.gff3
160,525,914 100% 986.11kB/s 0:02:38 (xfr#1, to-chk=0/2)
sent 80 bytes received 160,545,654 bytes 564,308.38 bytes/sec
total size is 160,525,914 speedup is 1.00
----------------------------------------------------------
total 154M
-rw-rw-r-- 1 sam users 154M Sep 5 08:48 Panopea-generosa-vv0.74.a3.TE.gff3
# %%bash
# time \
# wget "${wget_gffs}"
# ls -lh ${wd}
%%bash
head ${gff}
##gff-version 3 ##Generated using GenSAS, Tuesday 9th of July 2019 09:21:16 PM ##Project Name : Pgenerosa_v074 ##Job Name : RepeatMasker ##Tool : RepeatMasker 4.0.7 PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1876 1934 12 + . ID=19534.GS22252505.PGEN_.repeat00000002;Name=19534.GS22252505.PGEN_.repeat00000002;repeat_match=%28ATTC%29n;repeat_class=Simple_repeat; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 2962 3024 249 - . ID=19534.GS22252505.PGEN_.repeat00000003;Name=19534.GS22252505.PGEN_.repeat00000003;repeat_match=HalSINE1;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 8054 8084 28 + . ID=19534.GS22252505.PGEN_.repeat00000004;Name=19534.GS22252505.PGEN_.repeat00000004;repeat_match=%28CGT%29n;repeat_class=Simple_repeat; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 8318 8614 1430 + . ID=19534.GS22252505.PGEN_.repeat00000005;Name=19534.GS22252505.PGEN_.repeat00000005;repeat_match=BivaMeta-SINE1_HyCu;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 8572 8621 279 + . ID=19534.GS22252505.PGEN_.repeat00000006;Name=19534.GS22252505.PGEN_.repeat00000006;repeat_match=BivaV-SINE1_BaAz;repeat_class=Unspecified;
%%bash
# Set array of GFF features to parse out
gff_features=(DNA LINE LTR SINE Simple_repeat Unknown)
# Loop through array and create new GFFs from each feature
for feature in ${gff_features[@]}
do
echo "Parsing ${feature} from ${gff}..."
echo "Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.${feature}.gff3"
head -n 5 ${gff} > Panopea-generosa-vv0.74.a3.repeats.${feature}.gff3
echo "Parsing matching feature lines for ${feature} feature..."
grep ${feature} ${gff} >> Panopea-generosa-vv0.74.a3.repeats.${feature}.gff3
echo "Done with parsing ${feature}."
feature_count=$(tail --lines +6 Panopea-generosa-vv0.74.a3.repeats.${feature}.gff3 | wc -l)
echo "Identified ${feature_count} ${feature} features."
echo "Output file is: Panopea-generosa-vv0.74.a3.repeats.${feature}.gff3"
echo ""
done
echo "----------------------------------------------"
echo ""
ls -lh
Parsing DNA from Panopea-generosa-vv0.74.a3.TE.gff3... Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.DNA.gff3 Parsing matching feature lines for DNA feature... Done with parsing DNA. Identified 38612 DNA features. Output file is: Panopea-generosa-vv0.74.a3.repeats.DNA.gff3 Parsing LINE from Panopea-generosa-vv0.74.a3.TE.gff3... Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.LINE.gff3 Parsing matching feature lines for LINE feature... Done with parsing LINE. Identified 73797 LINE features. Output file is: Panopea-generosa-vv0.74.a3.repeats.LINE.gff3 Parsing LTR from Panopea-generosa-vv0.74.a3.TE.gff3... Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.LTR.gff3 Parsing matching feature lines for LTR feature... Done with parsing LTR. Identified 11752 LTR features. Output file is: Panopea-generosa-vv0.74.a3.repeats.LTR.gff3 Parsing SINE from Panopea-generosa-vv0.74.a3.TE.gff3... Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.SINE.gff3 Parsing matching feature lines for SINE feature... Done with parsing SINE. Identified 146416 SINE features. Output file is: Panopea-generosa-vv0.74.a3.repeats.SINE.gff3 Parsing Simple_repeat from Panopea-generosa-vv0.74.a3.TE.gff3... Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.Simple_repeat.gff3 Parsing matching feature lines for Simple_repeat feature... Done with parsing Simple_repeat. Identified 299997 Simple_repeat features. Output file is: Panopea-generosa-vv0.74.a3.repeats.Simple_repeat.gff3 Parsing Unknown from Panopea-generosa-vv0.74.a3.TE.gff3... Writing GFF3 header to Panopea-generosa-vv0.74.a3.repeats.Unknown.gff3 Parsing matching feature lines for Unknown feature... Done with parsing Unknown. Identified 1465471 Unknown features. Output file is: Panopea-generosa-vv0.74.a3.repeats.Unknown.gff3 ---------------------------------------------- total 1.1G -rw-rw-r-- 1 sam users 9.6M Sep 5 15:27 Panopea-generosa-vv0.74.a3.repeats.DNA.gff3 -rw-rw-r-- 1 sam users 19M Sep 5 15:27 Panopea-generosa-vv0.74.a3.repeats.LINE.gff3 -rw-rw-r-- 1 sam users 2.9M Sep 5 15:27 Panopea-generosa-vv0.74.a3.repeats.LTR.gff3 -rw-rw-r-- 1 sam users 73M Sep 5 15:27 Panopea-generosa-vv0.74.a3.repeats.Simple_repeat.gff3 -rw-rw-r-- 1 sam users 37M Sep 5 15:27 Panopea-generosa-vv0.74.a3.repeats.SINE.gff3 -rw-rw-r-- 1 sam users 356M Sep 5 15:27 Panopea-generosa-vv0.74.a3.repeats.Unknown.gff3 -rw-rw-r-- 1 sam users 550M Sep 5 15:13 Panopea-generosa-vv0.74.a3.TE.gff3
%%bash
# Check the output files
for file in Panopea-generosa-vv0.74.a3.repeats*.gff3
do
echo ""
echo ""
echo "${file}"
echo "----------------------------------------------"
head ${file}
done
Panopea-generosa-vv0.74.a3.repeats.DNA.gff3 ---------------------------------------------- ##gff-version 3 ##Generated using GenSAS, Monday 15th of July 2019 06:30:16 AM ##Project Name : Pgenerosa_v074 ##Job Name : Masked Repeat Consensus ##Tool : Mask Sequence Consensus PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 60243 60322 325 - . ID=19647.GS22252505.PGEN_.repeat00000029;Name=19534.GS22252505.PGEN_.repeat00000030;repeat_match=DNA2-25_CGi;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 99944 100057 231 - . ID=19647.GS22252505.PGEN_.repeat00000070;Name=19534.GS22252505.PGEN_.repeat00000071;repeat_match=DNA-8-3_HM;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 99996 100093 243 - . ID=19647.GS22252505.PGEN_.repeat00000072;Name=19534.GS22252505.PGEN_.repeat00000073;repeat_match=DNA-8-3_HM;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 175568 175784 354 + . ID=19647.GS22252505.PGEN_.repeat00000125;Name=19534.GS22252505.PGEN_.repeat00000126;repeat_match=DNA6-7_CGi;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 176798 177015 413 - . ID=19647.GS22252505.PGEN_.repeat00000126;Name=19534.GS22252505.PGEN_.repeat00000127;repeat_match=DNA6-7_CGi;repeat_class=Unspecified; Panopea-generosa-vv0.74.a3.repeats.LINE.gff3 ---------------------------------------------- ##gff-version 3 ##Generated using GenSAS, Monday 15th of July 2019 06:30:16 AM ##Project Name : Pgenerosa_v074 ##Job Name : Masked Repeat Consensus ##Tool : Mask Sequence Consensus PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 9841029 9841128 231 - . ID=19647.GS22252505.PGEN_.repeat00006523;Name=19534.GS22252505.PGEN_.repeat00006524;repeat_match=LINE-1_AA;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 29525247 29525307 228 - . ID=19647.GS22252505.PGEN_.repeat00018917;Name=19534.GS22252505.PGEN_.repeat00018918;repeat_match=LINE-1_AA;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 53452706 53452792 230 - . ID=19647.GS22252505.PGEN_.repeat00033564;Name=19534.GS22252505.PGEN_.repeat00033565;repeat_match=LINE-1_AA;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 62496090 62496144 227 - . ID=19647.GS22252505.PGEN_.repeat00039216;Name=19534.GS22252505.PGEN_.repeat00039217;repeat_match=LINER1;repeat_class=Unspecified; PGA_scaffold5__109_contigs__length_67248332 GenSAS_5d250896def4c-repeatmasker repeat_region 9822634 9822692 241 + . ID=19647.GS22252509.PGEN_.repeat00190759;Name=19534.GS22252509.PGEN_.repeat00190760;repeat_match=LINE-1_AA;repeat_class=Unspecified; Panopea-generosa-vv0.74.a3.repeats.LTR.gff3 ---------------------------------------------- ##gff-version 3 ##Generated using GenSAS, Monday 15th of July 2019 06:30:16 AM ##Project Name : Pgenerosa_v074 ##Job Name : Masked Repeat Consensus ##Tool : Mask Sequence Consensus PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1038677 1038733 240 - . ID=19647.GS22252505.PGEN_.repeat00000714;Name=19534.GS22252505.PGEN_.repeat00000715;repeat_match=BURRO3_LTR;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1060569 1060608 255 - . ID=19647.GS22252505.PGEN_.repeat00000735;Name=19534.GS22252505.PGEN_.repeat00000736;repeat_match=Gypsy-21_PBa-LTR;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1265345 1265753 259 - . ID=19647.GS22252505.PGEN_.repeat00000872;Name=19534.GS22252505.PGEN_.repeat00000873;repeat_match=Gypsy-31_SM-LTR;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1555555 1555840 277 - . ID=19647.GS22252505.PGEN_.repeat00001054;Name=19534.GS22252505.PGEN_.repeat00001055;repeat_match=Gypsy-7B_LVa-LTR;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1655290 1655412 242 - . ID=19647.GS22252505.PGEN_.repeat00001099;Name=19534.GS22252505.PGEN_.repeat00001100;repeat_match=Gypsy-30_SM-LTR;repeat_class=Unspecified; Panopea-generosa-vv0.74.a3.repeats.Simple_repeat.gff3 ---------------------------------------------- ##gff-version 3 ##Generated using GenSAS, Monday 15th of July 2019 06:30:16 AM ##Project Name : Pgenerosa_v074 ##Job Name : Masked Repeat Consensus ##Tool : Mask Sequence Consensus PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 1876 1934 12 + . ID=19647.GS22252505.PGEN_.repeat00000001;Name=19534.GS22252505.PGEN_.repeat00000002;repeat_match=%28ATTC%29n;repeat_class=Simple_repeat; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 8054 8084 28 + . ID=19647.GS22252505.PGEN_.repeat00000003;Name=19534.GS22252505.PGEN_.repeat00000004;repeat_match=%28CGT%29n;repeat_class=Simple_repeat; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 9671 9700 13 + . ID=19647.GS22252505.PGEN_.repeat00000006;Name=19534.GS22252505.PGEN_.repeat00000007;repeat_match=%28ACGG%29n;repeat_class=Simple_repeat; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 14388 14424 21 + . ID=19647.GS22252505.PGEN_.repeat00000008;Name=19534.GS22252505.PGEN_.repeat00000009;repeat_match=%28ACAGACG%29n;repeat_class=Simple_repeat; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 18639 18670 12 + . ID=19647.GS22252505.PGEN_.repeat00000009;Name=19534.GS22252505.PGEN_.repeat00000010;repeat_match=%28AGGGGG%29n;repeat_class=Simple_repeat; Panopea-generosa-vv0.74.a3.repeats.SINE.gff3 ---------------------------------------------- ##gff-version 3 ##Generated using GenSAS, Monday 15th of July 2019 06:30:16 AM ##Project Name : Pgenerosa_v074 ##Job Name : Masked Repeat Consensus ##Tool : Mask Sequence Consensus PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 2962 3024 249 - . ID=19647.GS22252505.PGEN_.repeat00000002;Name=19534.GS22252505.PGEN_.repeat00000003;repeat_match=HalSINE1;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 8318 8614 1430 + . ID=19647.GS22252505.PGEN_.repeat00000004;Name=19534.GS22252505.PGEN_.repeat00000005;repeat_match=BivaMeta-SINE1_HyCu;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 8572 8621 279 + . ID=19647.GS22252505.PGEN_.repeat00000005;Name=19534.GS22252505.PGEN_.repeat00000006;repeat_match=BivaV-SINE1_BaAz;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 20530 20623 308 - . ID=19647.GS22252505.PGEN_.repeat00000010;Name=19534.GS22252505.PGEN_.repeat00000011;repeat_match=BivaV-SINE1_BaAz;repeat_class=Unspecified; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d250896def4c-repeatmasker repeat_region 20897 21090 519 + . ID=19647.GS22252505.PGEN_.repeat00000011;Name=19534.GS22252505.PGEN_.repeat00000012;repeat_match=BivaMeta-SINE1_HyCu;repeat_class=Unspecified; Panopea-generosa-vv0.74.a3.repeats.Unknown.gff3 ---------------------------------------------- ##gff-version 3 ##Generated using GenSAS, Monday 15th of July 2019 06:30:16 AM ##Project Name : Pgenerosa_v074 ##Job Name : Masked Repeat Consensus ##Tool : Mask Sequence Consensus PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d25089d78791-repeatmodeler repeat_region 265 338 334 + . ID=19647.GS22252505.PGEN_.repeat00632680;Name=19535.GS22252505.PGEN_.repeat00000002;repeat_match=rnd-5_family-367;repeat_class=Unknown; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d25089d78791-repeatmodeler repeat_region 855 1050 451 + . ID=19647.GS22252505.PGEN_.repeat00632681;Name=19535.GS22252505.PGEN_.repeat00000003;repeat_match=rnd-5_family-1818;repeat_class=Unknown; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d25089d78791-repeatmodeler repeat_region 1040 1183 651 - . ID=19647.GS22252505.PGEN_.repeat00632682;Name=19535.GS22252505.PGEN_.repeat00000004;repeat_match=rnd-3_family-335;repeat_class=Unknown; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d25089d78791-repeatmodeler repeat_region 1618 1752 282 - . ID=19647.GS22252505.PGEN_.repeat00632684;Name=19535.GS22252505.PGEN_.repeat00000006;repeat_match=rnd-6_family-1300;repeat_class=Unknown; PGA_scaffold1__77_contigs__length_89643857 GenSAS_5d25089d78791-repeatmodeler repeat_region 1764 1846 508 + . ID=19647.GS22252505.PGEN_.repeat00632685;Name=19535.GS22252505.PGEN_.repeat00000007;repeat_match=rnd-1_family-872;repeat_class=Unknown;
# Set list of column header names
gff_header = ['seqid','source','type','start','end','score','strand','phase','attributes']
total_repeats_percent = 0
for file in os.listdir('.'):
if fnmatch.fnmatch(file, 'Panopea-generosa-vv0.74.a3.repeats*.gff3'):
print('\n' * 2)
print(file)
print("-------------------------")
# Import GFF.
# Skip first row and file is tab-separated
gff=pandas.read_csv(file, header=None, skiprows=5, sep="\t")
# Rename columns
gff.columns = gff_header
# Subtract start value from end value.
# Have to add 1 so that sequence length can't equal zero
gff['seqlength'] = gff.apply(lambda position: position['end'] - position['start'] + 1, axis=1)
gff_sum = gff['seqlength'].sum()
total_repeats_percent += ind_repeats_percent(gff_sum)
print ("percent" , ind_repeats_percent(gff_sum))
# Apply functions in list to seqlength column
gff_stats = gff['seqlength'].agg(['sum', 'mean', 'min', 'median', 'max'])
print (gff_stats.round(2))
print('\n' * 2)
print("-------------------------")
print ("Repeats composition of genome (percent):" , total_repeats_percent)
Panopea-generosa-vv0.74.a3.repeats.DNA.gff3 ------------------------- percent 1.2 sum 11316890.00 mean 293.09 min 1.00 median 154.00 max 7012.00 Name: seqlength, dtype: float64 Panopea-generosa-vv0.74.a3.repeats.Simple_repeat.gff3 -------------------------
/home/sam/programs/minicocnda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3049: DtypeWarning: Columns (5) have mixed types. Specify dtype option on import or set low_memory=False. interactivity=interactivity, compiler=compiler, result=result)
percent 2.03 sum 19132744.00 mean 63.78 min 1.00 median 41.00 max 12422.00 Name: seqlength, dtype: float64 Panopea-generosa-vv0.74.a3.repeats.LINE.gff3 ------------------------- percent 3.11 sum 29258694.00 mean 396.48 min 11.00 median 227.00 max 6604.00 Name: seqlength, dtype: float64 Panopea-generosa-vv0.74.a3.repeats.LTR.gff3 ------------------------- percent 0.46 sum 4355629.00 mean 370.63 min 1.00 median 276.00 max 6541.00 Name: seqlength, dtype: float64 Panopea-generosa-vv0.74.a3.repeats.SINE.gff3 ------------------------- percent 2.3 sum 21645991.00 mean 147.84 min 1.00 median 142.00 max 934.00 Name: seqlength, dtype: float64 Panopea-generosa-vv0.74.a3.repeats.Unknown.gff3 ------------------------- percent 31.14 sum 2.933161e+08 mean 2.001500e+02 min 1.100000e+01 median 1.450000e+02 max 1.098100e+04 Name: seqlength, dtype: float64 ------------------------- Repeats composition of genome (percent): 40.24