The two scripts in this repository can be used to recursively generate a pedigree, given
tab-separated data of the form individual parent1 parent2; and also to determine what
other lines in the data have a specified line in their pedigree, and any aliases and comments
regarding the specified line.
Usage: parentage.pl -parents FILE [-options]
Examples:
To generate a file of the parents throughout the pedigree for each individual:
parentage.pl -parents data/parentage.tsv -outfile data/parentage-list.tsv -format list
To report the parentage for a given query, built up from the immediate parents through successive genrations:
parentage.pl -parents data/parentage.tsv -q Hardin
To report the parentage for a given query, in a tabular format suitable for viewing with https://helium.hutton.ac.uk
parentage.pl -parents data/parentage.tsv -q Hardin -format table0 -outfile QUERY
Given a file of individuals and parents, recursively determine the pedigree
(the parentage going back as many generations as possible) for an individual.
Can be calculated for a single indicated individual or for all in the parents file.
The parents file should be structured like this.
The individual (progeny) is on the left, and the parents are on the right
indID parent1 parent2
A B C
D B C
E B F
Required:
-parents File listing the individuals and parents
Options:
-query ID of an individual for which to calculate parentage.
If not provided, report parentage for all individuals.
-outfile Print to indicated filename; otherwise to STDOUT.
If -outfile "QUERY" is indicated, the query name will be used (with spaces replaced by underscores).
-outdir If outfile is specified, write files to this directory. Default "."
-format Output format. Options: string, table0, table1, list
string: pedigree string, in parenthetical tree format. Printed at increasing depth unless -last_only
table0: query parent1 parent2 With header line but no other information
table1: query parent1 parent2 With termination information and final pedigree string
list: individual and all parents throughout the pedigree, comma-separated (no parentheses)
-last_only For string format, print only the last pedigree string; otherwise, print one for each data line.
-max_count The maximum number of individuals in the pedigree to report.
When this number is reached, the pedigree of that size will be reported,
even if other parents may be found in the input data.
-verbose Report some intermediate information.
-help This message.
Wrapper program that generates a report including synonyms, comments, and lines with the query individual in their pedigree:
Usage:
parentage_report.pl -query ID [-options]
Three data files are required, and an optional fourth ensures a much faster run.
If the data files named as follows and available in a directory "data" at
the same location as the script, the script will use these file names and locations
by default, so they don't need to be specified explicitly:
-parentage data/parentage.tsv
-synonyms data/parentage-synonyms.tsv
-comments data/parentage-comments.tsv
-plist data/parentage-list.tsv # Optional but recommended
Given the requried input data, generate a report about an individual, including the pedigree,
any aliases/synonyms for the line, the lines which have the individual in their pedigree,
and any available comments about the individual.
In the invocation without -plist, the parentage.tsv file is taken in as data for calculating
pedigrees for all lines, and then the query is checked against those pedigrees to find which lines
contain the query individual in the pedigree. This option is space-efficient (parentage.tsv is small)
but relatively time-consuming to run (it takes several seconds to recalculate all pedigrees).
In the invocation WITH -plist, the parentage-list.tsv file has, for each individual, the lines in the
pedigrees of that individual. The query is checked against each of those lists to find which lines
contain the query individual in the pedigree. This option is relatively space-inefficient
(the parentage-list.tsv file may be several megabytes) but fast to run.
The parentage-list.tsv can be generated by the script parentage.pl:
./parentage.pl -par data/parentage.tsv -f list -outfile data/parentage-list.tsv
To generate a standard report in JSON format
./parentage_report.pl -plist data/parentage-list.tsv -q Hardin
To generate just the three-column pedigree table suitable for submitting to the Helium viewer:
./parentage_report.pl -plist data/parentage-list.tsv -table -q Hardin
Some other lines to try, to check various characteristics of the data:
Hardin, Hayes, Hamlin, Gnome, Franklin, Flyer, Flambeau, Williams, "Williams 82", Lee
Required:
-query ID of an individual for which to generate a report
Required, with defaults indicated above:
-parents File with three columns: individuals and parents individuals and the parents;
-synonyms File with two columns: individual and synonym (if multiple synonyms, one line for each);
-comments File with two columns: individual and comments
Options:
-plist Tab-separated file with individual (first column) and all progenitors for that individual
-text_out Print a plain-text report to STDOUT; otherwise to JSON (default)
-pretty For JSON output, format for human viewing (with line returns, indentation)
-table_out Print pedigree table, suitable for submitting to the Helium viewer, to STDOUT.
With this option, the other output is not reported (neither JSON nor test_out)
-max_count The maximum number of individuals in the pedigree to report.
-verbose Report some intermediate information.
-help This message.
First use parentage.pl to generate (one time only) a file data/parentage-list.tsv
./parentage.pl -parents data/parentage.tsv -outfile data/parentage-list.tsv -format list
Then call parentage_report.pl, taking advantage of the data files with default names and locations.
This generates a report in JSON format (flag -pretty for human viewing, and reformatted and abbreviated somewhat here):
./parentage_report.pl -query Hardin -max 10 -pretty
{
"table" : [
[ "Genotype", "FemaleParent", "MaleParent" ],
[ "Hardin", "Corsoy 3", "Cutler 71" ],
...
],
"query" : [ "Hardin" ],
"comments" : [ "PVP 8100052" ],
"synonyms" : [ "PI 548526", "A76-102009" ],
"matches" : [ "05KL119276", ... ],
"construction" : [
"( Corsoy 3 , Cutler 71 )",
"( Corsoy 3 , ( Cutler 4 , SL5 ) )",
"( Corsoy 3 , ( Cutler 4 , ( ( Kent 7 , L49-4196 ) , ( Kent 8 , Mukden ) ) ) )"
]
}
Alternatively, adding the -text flag for a plain-text output
./parentage_report.pl -query Hardin -max 10 -text
comments:
PVP 8100052
construction:
( Corsoy 3 , Cutler 71 )
( Corsoy 3 , ( Cutler 4 , SL5 ) )
( Corsoy 3 , ( Cutler 4 , ( ( Kent 7 , L49-4196 ) , ( Kent 8 , Mukden ) ) ) )
matches:
05KL119276
05KL135608
Asgrow A2242
MT002989
OW1012750
PI 669396
Syngenta S16-Y6
XP1928
query:
Hardin
synonyms:
PI 548526
A76-102009
table:
Genotype FemaleParent MaleParent
Hardin Corsoy 3 Cutler 71
Cutler 71 Cutler 4 SL5
SL5 ( Kent 7 X L49-4196 ) ( Kent 8 X Mukden )
Report the output as a table of genotype-parent-parent triples and a tree-like pedigree string
(the default output option), and limit the reported pedigree size by setting max_ped_size 10.
Note: given the example data, with 14740 individuals with corresponding parents indicated, pedigrees
are generated for each; below, only the first 10 lines of the output are shown.
./parentage.pl -parents data/parentage.tsv -max 10 | head
## 1 ##
00CY622138 == ( ( B152 , B231 ) , 11415 )
## 2 ##
02JR310007 == ( CM4035N , Pioneer P93B82 )
02JR310007 == ( CM4035N , ( Pioneer P9273 , ( ( MO304 , Asgrow A3127 ) , ( Asgrow 3733 , Resnik ) ) ) )
02JR310007 == ( CM4035N , ( ( Pioneer P2981 , Asgrow A3127 ) , ( ( MO304 , Asgrow A3127 ) , ( Asgrow 3733 , Resnik ) ) ) )
02JR310007 == ( CM4035N , ( ( ( Hark , ( Corsoy , Calland ) ) , Asgrow A3127 ) , ( ( MO304 , Asgrow A3127 ) , ( Asgrow 3733 , Resnik ) ) ) )
!! Terminating search because number of individuals is greater than max_ped_size 10
## 3 ##
02JR310007BC1 == ( 02JR310007 , ( 02JR310007 , 3607F9-AOYN ) )
Report the output as a table of genotype-parent-parent triples, with header line. This can be written to a file and used as input to the Helium pedigree viewer
./parentage.pl -p data/parentage.tsv -f table0 -q Essex
Genotype FemaleParent MaleParent
Essex Lee S5-7075
Lee S-100 C.N.S.
S5-7075 N48-1248 Perry
N48-1248 Roanoke N45-745
N45-745 Ogden C.N.S.
Ogden Tokyo PI 54610
Perry Patoka L37-1355
Here is the pedigree image generated by the Helium pedigree viewer from the input above (for -query Essex):
Here is the corresponding pedigree string, generated with
./parentage.pl -parents data/parentage.tsv -q Essex -f string
Essex == ( Lee , S5-7075 )
Essex == ( ( S-100 , C.N.S. ) , S5-7075 )
Essex == ( ( S-100 , C.N.S. ) , ( N48-1248 , Perry ) )
Essex == ( ( S-100 , C.N.S. ) , ( ( Roanoke , N45-745 ) , Perry ) )
Essex == ( ( S-100 , C.N.S. ) , ( ( Roanoke , ( Ogden , C.N.S. ) ) , Perry ) )
Essex == ( ( S-100 , C.N.S. ) , ( ( Roanoke , ( ( Tokyo , PI 54610 ) , C.N.S. ) ) , Perry ) )
Essex == ( ( S-100 , C.N.S. ) , ( ( Roanoke , ( ( Tokyo , PI 54610 ) , C.N.S. ) ) , ( Patoka , L37-1355 ) ) )
The api.pl script uses the Mojolicious library to provide a simple REST API for parentage_report.pl:
An HTTP GET /genotypes request will return a JSON array of all genotypes that can be used as a query:
perl api.pl get /genotypes
An HTTP GET /?q=<query> request will return a JSON response for the query:
perl api.pl get '/?q=Essex'
Appending '/pedigree.helium.zip' will produce a zip file in a format compatible with the Helium pedigree viewer:
perl api.pl get '/pedigree.helium.zip?q=Essex' > pedigree.helium.zip
If this API is served from a public web server, the zip file can be imported directly by the Helium public web server (entering the URL in the Helium "Import > "Load Pedigree > Germinate Link" menu).
To start a Mojo::Server::Daemon listening on default port 3000:
perl api.pl daemon # development mode; for production: daemon -m production
Then queries can be tested, e.g., with curl:
curl -f 'http://localhost:3000/?q=Essex'